From 27d6133895f4d08385206dc55b829ef4ff256d7a Mon Sep 17 00:00:00 2001 From: CI Date: Fri, 3 Oct 2025 08:31:27 +0000 Subject: [PATCH] Build branch biobox/main with version main to biobox on branch main (9991e9a) Build pipeline: viash-hub.biobox.main-l6hlj Source commit: https://github.com/viash-hub/biobox/commit/9991e9a4f5ddd5085a4e2becf962950b1daf594b Source message: Bump bases2fastq to 2.2.1 (#202) --- CHANGELOG.md | 41 +- _viash.yaml | 40 +- src/arriba/config.vsh.yaml | 34 +- src/arriba/help.txt | 16 +- src/arriba/script.sh | 111 ++-- src/arriba/test.sh | 159 ++++- src/arriba/test_data/A.bam | Bin 296 -> 0 bytes src/arriba/test_data/annotation.gtf | 6 - src/arriba/test_data/blacklist.tsv | 0 src/arriba/test_data/genome.fasta | 4 - src/arriba/test_data/script.sh | 10 - src/bases2fastq/config.vsh.yaml | 2 +- .../bcftools_annotate/config.vsh.yaml | 14 +- src/bcftools/bcftools_annotate/help.txt | 10 +- src/bcftools/bcftools_annotate/script.sh | 73 +-- 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.../nextflow/bedtools/bedtools_slop/main.nf | 219 +------ .../bedtools/bedtools_sort/.config.vsh.yaml | 133 +--- .../nextflow/bedtools/bedtools_sort/main.nf | 219 +------ .../bedtools_spacing/.config.vsh.yaml | 133 +--- .../bedtools/bedtools_spacing/main.nf | 219 +------ .../bedtools/bedtools_split/.config.vsh.yaml | 133 +--- .../nextflow/bedtools/bedtools_split/main.nf | 219 +------ .../bedtools_subtract/.config.vsh.yaml | 133 +--- .../bedtools/bedtools_subtract/main.nf | 219 +------ .../bedtools_summary/.config.vsh.yaml | 133 +--- .../bedtools/bedtools_summary/main.nf | 219 +------ .../bedtools/bedtools_tag/.config.vsh.yaml | 133 +--- target/nextflow/bedtools/bedtools_tag/main.nf | 219 +------ .../bedtools_unionbedg/.config.vsh.yaml | 133 +--- .../bedtools/bedtools_unionbedg/main.nf | 219 +------ .../bedtools/bedtools_window/.config.vsh.yaml | 133 +--- .../nextflow/bedtools/bedtools_window/main.nf | 219 +------ .../bowtie2/bowtie2_align/.config.vsh.yaml | 133 +--- 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target/nextflow/bwa/bwa_sampe/main.nf | 219 +------ .../nextflow/bwa/bwa_samse/.config.vsh.yaml | 133 +--- target/nextflow/bwa/bwa_samse/main.nf | 219 +------ .../cellranger_count/.config.vsh.yaml | 133 +--- .../cellranger/cellranger_count/main.nf | 219 +------ .../cellranger_mkref/.config.vsh.yaml | 136 +--- .../cellranger/cellranger_mkref/main.nf | 222 +------ target/nextflow/cutadapt/.config.vsh.yaml | 132 +--- target/nextflow/cutadapt/main.nf | 218 +------ target/nextflow/falco/.config.vsh.yaml | 162 +---- target/nextflow/falco/main.nf | 258 +------- target/nextflow/falco/nextflow_schema.json | 6 + target/nextflow/fastp/.config.vsh.yaml | 132 +--- target/nextflow/fastp/main.nf | 218 +------ target/nextflow/fastqc/.config.vsh.yaml | 132 +--- target/nextflow/fastqc/main.nf | 218 +------ .../nextflow/featurecounts/.config.vsh.yaml | 133 +--- target/nextflow/featurecounts/main.nf | 219 +------ target/nextflow/fq/fq_filter/.config.vsh.yaml | 133 +--- target/nextflow/fq/fq_filter/main.nf | 219 +------ .../nextflow/fq/fq_generate/.config.vsh.yaml | 133 +--- target/nextflow/fq/fq_generate/main.nf | 219 +------ target/nextflow/fq/fq_lint/.config.vsh.yaml | 133 +--- target/nextflow/fq/fq_lint/main.nf | 219 +------ .../nextflow/fq/fq_subsample/.config.vsh.yaml | 133 +--- target/nextflow/fq/fq_subsample/main.nf | 219 +------ target/nextflow/gffread/.config.vsh.yaml | 132 +--- target/nextflow/gffread/main.nf | 218 +------ .../kallisto/kallisto_index/.config.vsh.yaml | 132 +--- .../nextflow/kallisto/kallisto_index/main.nf | 218 +------ .../kallisto/kallisto_quant/.config.vsh.yaml | 132 +--- .../nextflow/kallisto/kallisto_quant/main.nf | 218 +------ .../lofreq/lofreq_call/.config.vsh.yaml | 133 +--- target/nextflow/lofreq/lofreq_call/main.nf | 219 +------ .../lofreq/lofreq_indelqual/.config.vsh.yaml | 133 +--- .../nextflow/lofreq/lofreq_indelqual/main.nf | 219 +------ target/nextflow/multiqc/.config.vsh.yaml | 132 +--- target/nextflow/multiqc/main.nf | 218 +------ target/nextflow/nanoplot/.config.vsh.yaml | 132 +--- target/nextflow/nanoplot/main.nf | 218 +------ target/nextflow/pear/.config.vsh.yaml | 134 +--- target/nextflow/pear/main.nf | 220 +------ .../qualimap/qualimap_rnaseq/.config.vsh.yaml | 132 +--- .../nextflow/qualimap/qualimap_rnaseq/main.nf | 218 +------ .../.config.vsh.yaml | 132 +--- .../rsem/rsem_calculate_expression/main.nf | 218 +------ .../rsem_prepare_reference/.config.vsh.yaml | 133 +--- .../rsem/rsem_prepare_reference/main.nf | 219 +------ .../rseqc/rseqc_bamstat/.config.vsh.yaml | 132 +--- target/nextflow/rseqc/rseqc_bamstat/main.nf | 218 +------ .../rseqc_inferexperiment/.config.vsh.yaml | 132 +--- .../rseqc/rseqc_inferexperiment/main.nf | 218 +------ .../rseqc_inner_distance/.config.vsh.yaml | 132 +--- .../rseqc/rseqc_inner_distance/main.nf | 218 +------ .../salmon/salmon_index/.config.vsh.yaml | 133 +--- target/nextflow/salmon/salmon_index/main.nf | 219 +------ .../salmon/salmon_quant/.config.vsh.yaml | 133 +--- target/nextflow/salmon/salmon_quant/main.nf | 219 +------ .../samtools_collate/.config.vsh.yaml | 132 +--- .../samtools/samtools_collate/main.nf | 218 +------ .../samtools/samtools_faidx/.config.vsh.yaml | 132 +--- .../nextflow/samtools/samtools_faidx/main.nf | 218 +------ .../samtools/samtools_fasta/.config.vsh.yaml | 132 +--- .../nextflow/samtools/samtools_fasta/main.nf | 218 +------ .../samtools/samtools_fastq/.config.vsh.yaml | 132 +--- .../nextflow/samtools/samtools_fastq/main.nf | 218 +------ .../samtools_flagstat/.config.vsh.yaml | 132 +--- .../samtools/samtools_flagstat/main.nf | 218 +------ .../samtools_idxstats/.config.vsh.yaml | 132 +--- .../samtools/samtools_idxstats/main.nf | 218 +------ .../samtools/samtools_index/.config.vsh.yaml | 132 +--- .../nextflow/samtools/samtools_index/main.nf | 218 +------ .../samtools/samtools_sort/.config.vsh.yaml | 132 +--- .../nextflow/samtools/samtools_sort/main.nf | 218 +------ .../samtools/samtools_stats/.config.vsh.yaml | 132 +--- .../nextflow/samtools/samtools_stats/main.nf | 218 +------ .../samtools/samtools_view/.config.vsh.yaml | 132 +--- .../nextflow/samtools/samtools_view/main.nf | 218 +------ .../seqtk/seqtk_sample/.config.vsh.yaml | 132 +--- target/nextflow/seqtk/seqtk_sample/main.nf | 218 +------ .../seqtk/seqtk_subseq/.config.vsh.yaml | 132 +--- target/nextflow/seqtk/seqtk_subseq/main.nf | 218 +------ target/nextflow/sgdemux/.config.vsh.yaml | 133 +--- target/nextflow/sgdemux/main.nf | 219 +------ .../snpeff/{ => snpeff_ann}/.config.vsh.yaml | 157 +---- .../nextflow/snpeff/snpeff_ann/config.patch | 40 ++ .../nextflow/snpeff/{ => snpeff_ann}/main.nf | 258 +------- .../snpeff/{ => snpeff_ann}/nextflow.config | 2 +- .../{ => snpeff_ann}/nextflow_schema.json | 4 +- target/nextflow/sortmerna/.config.vsh.yaml | 132 +--- target/nextflow/sortmerna/main.nf | 218 +------ .../star/star_align_reads/.config.vsh.yaml | 137 +--- target/nextflow/star/star_align_reads/main.nf | 223 +------ .../star_genome_generate/.config.vsh.yaml | 133 +--- .../star/star_genome_generate/main.nf | 219 +------ target/nextflow/trimgalore/.config.vsh.yaml | 133 +--- target/nextflow/trimgalore/main.nf | 219 +------ .../umi_tools_dedup/.config.vsh.yaml | 132 +--- .../umi_tools/umi_tools_dedup/main.nf | 218 +------ .../umi_tools_extract/.config.vsh.yaml | 132 +--- .../umi_tools/umi_tools_extract/main.nf | 218 +------ .../umi_tools_prepareforrsem/.config.vsh.yaml | 132 +--- .../umi_tools_prepareforrsem/main.nf | 218 +------ 561 files changed, 6895 insertions(+), 63816 deletions(-) delete mode 100644 src/arriba/test_data/A.bam delete mode 100644 src/arriba/test_data/annotation.gtf delete mode 100644 src/arriba/test_data/blacklist.tsv delete mode 100644 src/arriba/test_data/genome.fasta delete mode 100755 src/arriba/test_data/script.sh delete mode 100644 src/bcftools/bcftools_sort/test_data/example.bcf create mode 100755 src/bcftools/utils/generate_help.sh delete mode 100644 src/snpeff/help.txt create mode 100644 src/snpeff/snpeff_ann/config.patch rename src/snpeff/{ => snpeff_ann}/config.vsh.yaml (93%) create mode 100644 src/snpeff/snpeff_ann/help.txt rename src/snpeff/{ => snpeff_ann}/script.sh (99%) rename src/snpeff/{ => snpeff_ann}/test.sh (73%) rename src/snpeff/{ => snpeff_ann}/test_data/cancer.vcf (100%) rename src/snpeff/{ => snpeff_ann}/test_data/my_annotations.bed (100%) rename src/snpeff/{ => snpeff_ann}/test_data/script.sh (81%) rename src/snpeff/{ => snpeff_ann}/test_data/test.vcf (100%) rename target/executable/snpeff/{ => snpeff_ann}/.config.vsh.yaml (84%) create mode 100644 target/executable/snpeff/snpeff_ann/config.patch rename target/executable/snpeff/{snpeff => snpeff_ann/snpeff_ann} (99%) rename target/nextflow/snpeff/{ => snpeff_ann}/.config.vsh.yaml (84%) create mode 100644 target/nextflow/snpeff/snpeff_ann/config.patch rename target/nextflow/snpeff/{ => snpeff_ann}/main.nf (96%) rename target/nextflow/snpeff/{ => snpeff_ann}/nextflow.config (99%) rename target/nextflow/snpeff/{ => snpeff_ann}/nextflow_schema.json (99%) diff --git a/CHANGELOG.md b/CHANGELOG.md index d90dfec1..290861e6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,16 +1,27 @@ -# Unreleased +# unreleased +## MINOR CHANGES + +* `falco`: Update falco to 1.2.5 (PR #201). + +* `bases2fastq`: Bump from 2.2.0 to 2.2.1 (PR #202). + +# biobox 0.4.0 + ## BREAKING CHANGES * `fq_subsample` has been removed after its functionality was previously copied to `fq/fq_subsample`. Please use the latter instead. (PR #182). +* `snpeff` has been removed. Please use `snpeff/snpeff_ann` (which is a functional copy of `snpeff`) as this is the default subcommand when running this tool (PR #194) + + ## NEW FUNCTIONALITY -* `fq`: - - `fq/fq_filter`: Filter FASTQ files based on record names or sequence patterns (PR #182). - - `fq/fq_generate`: Generate a random FASTQ file pair for testing and simulation purposes (PR #182). +* `fq`: Added two new components for FASTQ file processing (PR #182): + - `fq/fq_filter`: Filter FASTQ files based on record names or sequence patterns. + - `fq/fq_generate`: Generate a random FASTQ file pair for testing and simulation purposes. * `bwa`: Added BWA support for single-end and paired-end read alignment (PR #183). - `bwa/bwa_index`: Create BWA index files for reference genome alignment. @@ -58,6 +69,11 @@ - `bedtools/bedtools_unionbedg`: Combine multiple BEDGRAPH files - `bedtools/bedtools_window`: Find overlapping features within specified windows +* Developer tools: Added GitHub Copilot integration (PR #192): + - `.github/copilot-instructions.md`: Complete coding assistant guide with biobox patterns, examples, and best practices + - `.github/prompts/update-viash-component.prompt.md`: Step-by-step prompt for updating existing components + - `.github/prompts/add-viash-component.prompt.md`: Comprehensive prompt for creating new components from scratch + ## MAJOR CHANGES * `bedtools`: Enhanced 11 existing bedtools components with improved functionality and standardized interfaces (PR #188): @@ -73,10 +89,25 @@ - `bedtools/bedtools_merge`: Enhanced merging options and distance parameters - `bedtools/bedtools_sort`: Standardized sorting options +* `bcftools`: Updated components to version 1.22 with comprehensive improvements including enhanced argument coverage, improved script patterns, biobox standard compliance, and comprehensive testing overhaul (PR #193): + * `bcftools_annotate`: Added `--verbosity` parameter; updated to use `meta_cpus` instead of `--threads` parameter + * `bcftools_concat`: Renamed `--compact_PS` to `--compact_ps`, `--min_PQ` to `--min_pq`; added `--rm_dups`, `--drop_genotypes`, `--verbosity`, `--write_index` parameters; updated to use `meta_cpus` instead of `--threads` parameter + * `bcftools_norm`: Renamed `--remove_duplicates` to `--rm_dup`, added `--remove_duplicates_flag` as boolean alias; added `--exclude`, `--include`, `--gff_annot`, `--multi_overlaps`, `--sort`, `--verbosity`, `--write_index` parameters; updated to use `meta_cpus` instead of `--threads` parameter + * `bcftools_sort`: Removed `--max_mem` and `--temp_dir` parameters (now use `meta_memory_mb` and `meta_temp_dir` respectively); added `--verbosity`, `--write_index` parameters + * `bcftools_stats`: Renamed `--allele_frequency_bins` to `--af_bins`, `--allele_frequency_bins_file` removed, `--allele_frequency_tag` to `--af_tag`, `--fasta_reference` to `--fasta_ref`, `--split_by_ID` to `--split_by_id`, `--targets_overlaps` to `--targets_overlap` + ## MINOR CHANGES * `bases2fastq`: Updated component with comprehensive argument support and latest practices (PR #190). +* `arriba`: Updated to v2.5.0 and refactored script and tests based on latest contributing guidelines (PR #187). + +* `snpeff` has been updated to version `5.2f` (PR #194) + +# BUG FIXES + +* Fix the `commands` property from components being overwritten by the global configuration (which only included `ps`) (PR #196). + ## DOCUMENTATION * Major restructuring of the documentation pages (PR #185): @@ -105,7 +136,7 @@ * Update README (PR #177). -* Add authors to package config and update author information (PR #180). +* Update author information (PR #180, PR #200). * `fastqc`: add `--outdir` argument (PR #181). diff --git a/_viash.yaml b/_viash.yaml index e9639627..3e4a11a5 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -18,32 +18,20 @@ links: issue_tracker: https://github.com/viash-hub/biobox/issues repository: https://github.com/viash-hub/biobox viash_version: 0.9.4 -authors: - - __merge__: /src/_authors/robrecht_cannoodt.yaml - roles: [author, maintainer] - - __merge__: /src/_authors/angela_o_pisco.yaml - roles: [author] - - __merge__: /src/_authors/dorien_roosen.yaml - roles: [author] - - __merge__: /src/_authors/dries_schaumont.yaml - roles: [author] - - __merge__: /src/_authors/emma_rousseau.yaml - roles: [author] - - __merge__: /src/_authors/jakub_majercik.yaml - roles: [author] - - __merge__: /src/_authors/kai_waldrant.yaml - roles: [author] - - __merge__: /src/_authors/leila_paquay.yaml - roles: [author] - - __merge__: /src/_authors/sai_nirmayi_yasa.yaml - roles: [author] - - __merge__: /src/_authors/theodoro_gasperin.yaml - roles: [author] - - __merge__: /src/_authors/toni_verbeiren.yaml - roles: [author] - - __merge__: /src/_authors/weiwei_schultz.yaml - roles: [author] +## TODO: __merge__ properties in the package config could not be loaded by viash-hub. +## Re-enable this again again later once this is supported +# authors: +# - __merge__: /src/_authors/robrecht_cannoodt.yaml +# roles: [ author, maintainer ] +# - __merge__: /src/_authors/dorien_roosen.yaml +# roles: [ author ] +# - __merge__: /src/_authors/dries_schaumont.yaml +# roles: [ author ] +# - __merge__: /src/_authors/jakub_majercik.yaml +# roles: [ author ] +# - __merge__: /src/_authors/toni_verbeiren.yaml +# roles: [ author ] config_mods: | - .requirements.commands := ['ps'] + .requirements.commands += ['ps'] version: main organization: vsh diff --git a/src/arriba/config.vsh.yaml b/src/arriba/config.vsh.yaml index db5960cf..c5ee9c8f 100644 --- a/src/arriba/config.vsh.yaml +++ b/src/arriba/config.vsh.yaml @@ -1,16 +1,27 @@ name: arriba -description: Detect gene fusions from RNA-Seq data -keywords: [Gene fusion, RNA-Seq] +description: | + Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data. It was developed for the use in a clinical research setting. Therefore, short runtimes and high sensitivity were important design criteria. + + Arriba is based on the STAR RNA-Seq aligner and post-processes the alignments (output from STAR) to: + + 1. detect split reads and discordant mates, which are indicative of structural rearrangements, + 2. find reads supporting gene fusions (i.e., reads spanning the breakpoints of gene fusions), + 3. perform various filtering steps to remove false positives, and + 4. output the final predictions in a standardized format. + + In contrast to many other fusion detection tools, Arriba does not require to reduce the STAR parameter `--alignIntronMax` (maximum intron size). Reducing this parameter impairs detection of long introns and may affect expression quantification. Arriba reliably filters translocation-based false positives even when large maximum intron sizes are used. + + **Important**: Arriba requires BAM files that were aligned with STAR using specific chimeric alignment parameters, particularly `--chimOutType WithinBAM HardClip`. See the [official workflow documentation](https://github.com/suhrig/arriba/blob/master/run_arriba.sh) for the complete set of recommended STAR parameters. +keywords: [Gene fusion, RNA-Seq, Structural variants, Chimeric alignments] links: - homepage: https://arriba.readthedocs.io/en/latest/ - documentation: https://arriba.readthedocs.io/en/latest/ + homepage: https://arriba.readthedocs.io/ + documentation: https://arriba.readthedocs.io/ repository: https://github.com/suhrig/arriba references: doi: 10.1101/gr.257246.119 license: MIT requirements: - cpus: 1 - commands: [ arriba ] + commands: [arriba] authors: - __merge__: /src/_authors/robrecht_cannoodt.yaml roles: [ author, maintainer ] @@ -22,7 +33,10 @@ argument_groups: type: file description: | File in SAM/BAM/CRAM format with main alignments as generated by STAR - (Aligned.out.sam). Arriba extracts candidate reads from this file. + (Aligned.out.sam). **Important**: The BAM file must be generated by STAR with + chimeric alignment parameters, specifically `--chimOutType WithinBAM HardClip`. + Arriba extracts candidate reads from this file, including both normal and + chimeric alignments. required: true example: Aligned.out.bam - name: --genome @@ -375,14 +389,14 @@ test_resources: - type: bash_script path: test.sh - type: file - path: test_data + path: /src/_utils/test_helpers.sh engines: - type: docker - image: quay.io/biocontainers/arriba:2.4.0--h0033a41_2 + image: quay.io/biocontainers/arriba:2.5.0--h87b9561_1 setup: - type: docker run: | - arriba -h | grep 'Version:' 2>&1 | sed 's/Version:\s\(.*\)/arriba: "\1"/' > /var/software_versions.txt + arriba -h 2>&1 | head -5 | grep 'Version:' | sed 's/Version:\s\(.*\)/arriba: "\1"/' > /var/software_versions.txt runners: - type: executable - type: nextflow \ No newline at end of file diff --git a/src/arriba/help.txt b/src/arriba/help.txt index 7d8fc76d..cb265481 100644 --- a/src/arriba/help.txt +++ b/src/arriba/help.txt @@ -1,10 +1,10 @@ -```bash -arriba -h +``` +docker run --rm quay.io/biocontainers/arriba:2.5.0--h87b9561_1 arriba -h ``` Arriba gene fusion detector --------------------------- -Version: 2.4.0 +Version: 2.5.0 Arriba is a fast tool to search for aberrant transcripts such as gene fusions. It is based on chimeric alignments found by the STAR RNA-Seq aligner. @@ -74,7 +74,7 @@ Usage: arriba [-c Chimeric.out.sam] -x Aligned.out.bam \ resolve ambiguities. Default: auto -i CONTIGS Comma-/space-separated list of interesting contigs. Fusions between genes - on other contigs are ignored. Cfontigs can be specified with or without the + on other contigs are ignored. Contigs can be specified with or without the prefix "chr". Asterisks (*) are treated as wild-cards. Default: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y AC_* NC_* @@ -190,9 +190,13 @@ Usage: arriba [-c Chimeric.out.sam] -x Aligned.out.bam \ -I If assembly of the fusion transcript sequence from the supporting reads is incomplete (denoted as '...'), fill the gaps using the assembly sequence wherever possible. + -@ Number of threads to use for BAM/CRAM file reading. Note that in most situations 1 thread + is optimal. Values >2 almost never show further speedup. + -h Print help and exit. Code repository: https://github.com/suhrig/arriba Get help/report bugs: https://github.com/suhrig/arriba/issues - User manual: https://arriba.readthedocs.io/ - Please cite: https://doi.org/10.1101/gr.257246.119 \ No newline at end of file + User manual: https://github.com/suhrig/arriba/wiki + Please cite: https://doi.org/10.1101/gr.257246.119 + diff --git a/src/arriba/script.sh b/src/arriba/script.sh index 5892db32..b414639f 100644 --- a/src/arriba/script.sh +++ b/src/arriba/script.sh @@ -3,52 +3,77 @@ ## VIASH START ## VIASH END -# unset flags +set -eo pipefail + +# unset boolean flags that are "false" [[ "$par_skip_duplicate_marking" == "false" ]] && unset par_skip_duplicate_marking [[ "$par_extra_information" == "false" ]] && unset par_extra_information [[ "$par_fill_gaps" == "false" ]] && unset par_fill_gaps -# replace ';' with ',' -par_interesting_contigs=$(echo $par_interesting_contigs | tr ';' ',') -par_viral_contigs=$(echo $par_viral_contigs | tr ';' ',') -par_disable_filters=$(echo $par_disable_filters | tr ';' ',') +# process multi-value parameters: replace ';' with ',' for arriba compatibility +if [[ -n "${par_interesting_contigs:-}" ]]; then + par_interesting_contigs=$(echo "$par_interesting_contigs" | tr ';' ',') +fi +if [[ -n "${par_viral_contigs:-}" ]]; then + par_viral_contigs=$(echo "$par_viral_contigs" | tr ';' ',') +fi +if [[ -n "${par_disable_filters:-}" ]]; then + par_disable_filters=$(echo "$par_disable_filters" | tr ';' ',') +fi -# run arriba -arriba \ - -x "$par_bam" \ - -a "$par_genome" \ - -g "$par_gene_annotation" \ - -o "$par_fusions" \ - ${par_known_fusions:+-k "${par_known_fusions}"} \ - ${par_blacklist:+-b "${par_blacklist}"} \ - ${par_structural_variants:+-d "${par_structural_variants}"} \ - ${par_tags:+-t "${par_tags}"} \ - ${par_protein_domains:+-p "${par_protein_domains}"} \ - ${par_fusions_discarded:+-O "${par_fusions_discarded}"} \ - ${par_max_genomic_breakpoint_distance:+-D "${par_max_genomic_breakpoint_distance}"} \ - ${par_strandedness:+-s "${par_strandedness}"} \ - ${par_interesting_contigs:+-i "${par_interesting_contigs}"} \ - ${par_viral_contigs:+-v "${par_viral_contigs}"} \ - ${par_disable_filters:+-f "${par_disable_filters}"} \ - ${par_max_e_value:+-E "${par_max_e_value}"} \ - ${par_min_supporting_reads:+-S "${par_min_supporting_reads}"} \ - ${par_max_mismappers:+-m "${par_max_mismappers}"} \ - ${par_max_homolog_identity:+-L "${par_max_homolog_identity}"} \ - ${par_homopolymer_length:+-H "${par_homopolymer_length}"} \ - ${par_read_through_distance:+-R "${par_read_through_distance}"} \ - ${par_min_anchor_length:+-A "${par_min_anchor_length}"} \ - ${par_many_spliced_events:+-M "${par_many_spliced_events}"} \ - ${par_max_kmer_content:+-K "${par_max_kmer_content}"} \ - ${par_max_mismatch_pvalue:+-V "${par_max_mismatch_pvalue}"} \ - ${par_fragment_length:+-F "${par_fragment_length}"} \ - ${par_max_reads:+-U "${par_max_reads}"} \ - ${par_quantile:+-Q "${par_quantile}"} \ - ${par_exonic_fraction:+-e "${par_exonic_fraction}"} \ - ${par_top_n:+-T "${par_top_n}"} \ - ${par_covered_fraction:+-C "${par_covered_fraction}"} \ - ${par_max_itd_length:+-l "${par_max_itd_length}"} \ - ${par_min_itd_allele_fraction:+-z "${par_min_itd_allele_fraction}"} \ - ${par_min_itd_supporting_reads:+-Z "${par_min_itd_supporting_reads}"} \ - ${par_skip_duplicate_marking:+-u} \ - ${par_extra_information:+-X} \ +# build command arguments array +cmd_args=( + # required arguments + -x "$par_bam" + -a "$par_genome" + -g "$par_gene_annotation" + -o "$par_fusions" + + # optional input files + ${par_known_fusions:+-k "$par_known_fusions"} + ${par_blacklist:+-b "$par_blacklist"} + ${par_structural_variants:+-d "$par_structural_variants"} + ${par_tags:+-t "$par_tags"} + ${par_protein_domains:+-p "$par_protein_domains"} + + # optional output files + ${par_fusions_discarded:+-O "$par_fusions_discarded"} + + # filter and analysis options + ${par_max_genomic_breakpoint_distance:+-D "$par_max_genomic_breakpoint_distance"} + ${par_strandedness:+-s "$par_strandedness"} + ${par_interesting_contigs:+-i "$par_interesting_contigs"} + ${par_viral_contigs:+-v "$par_viral_contigs"} + ${par_disable_filters:+-f "$par_disable_filters"} + + # statistical thresholds + ${par_max_e_value:+-E "$par_max_e_value"} + ${par_min_supporting_reads:+-S "$par_min_supporting_reads"} + ${par_max_mismappers:+-m "$par_max_mismappers"} + ${par_max_homolog_identity:+-L "$par_max_homolog_identity"} + ${par_homopolymer_length:+-H "$par_homopolymer_length"} + ${par_read_through_distance:+-R "$par_read_through_distance"} + ${par_min_anchor_length:+-A "$par_min_anchor_length"} + ${par_many_spliced_events:+-M "$par_many_spliced_events"} + ${par_max_kmer_content:+-K "$par_max_kmer_content"} + ${par_max_mismatch_pvalue:+-V "$par_max_mismatch_pvalue"} + ${par_fragment_length:+-F "$par_fragment_length"} + ${par_max_reads:+-U "$par_max_reads"} + ${par_quantile:+-Q "$par_quantile"} + ${par_exonic_fraction:+-e "$par_exonic_fraction"} + ${par_top_n:+-T "$par_top_n"} + ${par_covered_fraction:+-C "$par_covered_fraction"} + + # internal tandem duplication options + ${par_max_itd_length:+-l "$par_max_itd_length"} + ${par_min_itd_allele_fraction:+-z "$par_min_itd_allele_fraction"} + ${par_min_itd_supporting_reads:+-Z "$par_min_itd_supporting_reads"} + + # boolean flags + ${par_skip_duplicate_marking:+-u} + ${par_extra_information:+-X} ${par_fill_gaps:+-I} +) + +# execute arriba +arriba "${cmd_args[@]}" diff --git a/src/arriba/test.sh b/src/arriba/test.sh index 7f1243d2..81c49215 100644 --- a/src/arriba/test.sh +++ b/src/arriba/test.sh @@ -1,45 +1,140 @@ #!/bin/bash -set -e +## VIASH START +## VIASH END -dir_in="$meta_resources_dir/test_data" +# Source the centralized test helpers +source "$meta_resources_dir/test_helpers.sh" -echo "> Run arriba with blacklist" +# Initialize test environment with strict error handling +setup_test_env + +############################################# +# Test execution with centralized functions +############################################# + +log "Starting tests for $meta_name" + +# Create test data directory +test_data_dir="$meta_temp_dir/test_data" +mkdir -p "$test_data_dir" + +# Note: Following the official arriba workflow from run_arriba.sh +# https://github.com/suhrig/arriba/blob/master/run_arriba.sh +# All required tools (STAR, samtools, wget) are available in the Docker container + +# Download and prepare test data from arriba repository +log "Downloading arriba test data from official repository..." + +# Download test FASTQ files from nf-core test-datasets (these match the genome) +log "Downloading nf-core test RNA-seq reads..." +wget -q -O "$test_data_dir/read1.fastq.gz" "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz" +wget -q -O "$test_data_dir/read2.fastq.gz" "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz" +log "✓ Downloaded nf-core test FASTQ files" + +# Download or create test genome and annotation +log "Setting up test genome and annotation..." +wget -q -O "$test_data_dir/genome.fa" "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta" +wget -q -O "$test_data_dir/annotation.gtf" "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.gtf" + +# Create required arriba input files +log "Creating required arriba input files..." + +# Create empty blacklist file (arriba requirement) +touch "$test_data_dir/blacklist.tsv" + +check_file_exists "$test_data_dir/read1.fastq.gz" "test FASTQ R1" +check_file_exists "$test_data_dir/genome.fa" "test genome" +check_file_exists "$test_data_dir/annotation.gtf" "test annotation" +check_file_exists "$test_data_dir/blacklist.tsv" "blacklist file" + +# Check if STAR is available and create proper test BAM +log "Creating STAR genome index and proper test BAM following arriba workflow..." + +# Create STAR genome index with parameters from nf-core test +mkdir -p "$test_data_dir/star_index" +log "Generating STAR genome index..." +STAR --runMode genomeGenerate \ + --genomeDir "$test_data_dir/star_index" \ + --genomeFastaFiles "$test_data_dir/genome.fa" \ + --sjdbGTFfile "$test_data_dir/annotation.gtf" \ + --genomeSAindexNbases 9 \ + --runThreadN 1 \ + --genomeChrBinNbits 12 \ + --sjdbOverhang 50 >/dev/null 2>&1 + +log "STAR index created successfully, aligning reads with chimeric parameters..." +# Use the exact STAR parameters from nf-core test configuration +STAR --runThreadN 1 \ + --genomeDir "$test_data_dir/star_index" \ + --genomeLoad NoSharedMemory \ + --readFilesIn "$test_data_dir/read1.fastq.gz" "$test_data_dir/read2.fastq.gz" \ + --readFilesCommand zcat \ + --outStd BAM_Unsorted \ + --outSAMtype BAM Unsorted \ + --outSAMunmapped Within \ + --outBAMcompression 0 \ + --outFilterMultimapNmax 50 \ + --peOverlapNbasesMin 10 \ + --alignSplicedMateMapLminOverLmate 0.5 \ + --alignSJstitchMismatchNmax 5 -1 5 5 \ + --chimSegmentMin 10 \ + --chimOutType WithinBAM HardClip \ + --chimJunctionOverhangMin 10 \ + --chimScoreDropMax 30 \ + --chimScoreJunctionNonGTAG 0 \ + --chimScoreSeparation 1 \ + --chimSegmentReadGapMax 3 \ + --chimMultimapNmax 50 \ + --outFileNamePrefix "$test_data_dir/star_" \ + > "$test_data_dir/Aligned.out.bam" 2>/dev/null + +# Sort the BAM file if it was created successfully +log "Sorting and indexing STAR-aligned BAM..." +samtools sort -o "$test_data_dir/sorted.bam" "$test_data_dir/Aligned.out.bam" 2>/dev/null +mv "$test_data_dir/sorted.bam" "$test_data_dir/Aligned.out.bam" +samtools index "$test_data_dir/Aligned.out.bam" 2>/dev/null || true + +check_file_exists "$test_data_dir/Aligned.out.bam" "test BAM file" + +# --- Test Case 1: Full arriba workflow test --- +log "Starting TEST 1: Full arriba workflow test (following run_arriba.sh pattern)" + +log "Running $meta_name with complete workflow parameters..." +# Follow the exact parameter pattern from arriba's run_arriba.sh "$meta_executable" \ - --bam "$dir_in/A.bam" \ - --genome "$dir_in/genome.fasta" \ - --gene_annotation "$dir_in/annotation.gtf" \ - --blacklist "$dir_in/blacklist.tsv" \ - --fusions "fusions.tsv" \ - --fusions_discarded "fusions_discarded.tsv" \ - --interesting_contigs "1,2" + --bam "$test_data_dir/Aligned.out.bam" \ + --genome "$test_data_dir/genome.fa" \ + --gene_annotation "$test_data_dir/annotation.gtf" \ + --blacklist "$test_data_dir/blacklist.tsv" \ + --fusions "$meta_temp_dir/fusions.tsv" \ + --fusions_discarded "$meta_temp_dir/fusions_discarded.tsv" -echo ">> Checking output" -[ ! -f "fusions.tsv" ] && echo "Output file fusions.tsv does not exist" && exit 1 -[ ! -f "fusions_discarded.tsv" ] && echo "Output file fusions_discarded.tsv does not exist" && exit 1 +log "Validating TEST 1 outputs..." +check_file_exists "$meta_temp_dir/fusions.tsv" "main fusions output file" +check_file_exists "$meta_temp_dir/fusions_discarded.tsv" "discarded fusions output file" -echo ">> Check if output is empty" -[ ! -s "fusions.tsv" ] && echo "Output file fusions.tsv is empty" && exit 1 -[ ! -s "fusions_discarded.tsv" ] && echo "Output file fusions_discarded.tsv is empty" && exit 1 +# Check if we detected any fusions (file should have content beyond header) +if [[ $(wc -l < "$meta_temp_dir/fusions.tsv") -gt 1 ]]; then + log "✓ Detected $(( $(wc -l < "$meta_temp_dir/fusions.tsv") - 1 )) fusion(s) in output" +else + log "ℹ No fusions detected - this may be expected with test data" +fi -rm fusions.tsv fusions_discarded.tsv +log "✅ TEST 1 completed successfully - full arriba workflow passed" -echo "> Run arriba without blacklist" +# --- Test Case 2: Test with minimal required parameters --- +log "Starting TEST 2: Minimal parameters test" + +log "Running $meta_name with minimal required parameters..." "$meta_executable" \ - --bam "$dir_in/A.bam" \ - --genome "$dir_in/genome.fasta" \ - --gene_annotation "$dir_in/annotation.gtf" \ - --fusions "fusions.tsv" \ - --fusions_discarded "fusions_discarded.tsv" \ - --interesting_contigs "1,2" \ + --bam "$test_data_dir/Aligned.out.bam" \ + --genome "$test_data_dir/genome.fa" \ + --gene_annotation "$test_data_dir/annotation.gtf" \ + --fusions "$meta_temp_dir/fusions_minimal.tsv" \ --disable_filters blacklist -echo ">> Checking output" -[ ! -f "fusions.tsv" ] && echo "Output file fusions.tsv does not exist" && exit 1 -[ ! -f "fusions_discarded.tsv" ] && echo "Output file fusions_discarded.tsv does not exist" && exit 1 +check_file_exists "$meta_temp_dir/fusions_minimal.tsv" "minimal fusions output file" +log "✅ TEST 2 completed successfully" -echo ">> Check if output is empty" -[ ! -s "fusions.tsv" ] && echo "Output file fusions.tsv is empty" && exit 1 -[ ! -s "fusions_discarded.tsv" ] && echo "Output file fusions_discarded.tsv is empty" && exit 1 - -echo "> Test successful" \ No newline at end of file +print_test_summary "All tests completed successfully" diff --git a/src/arriba/test_data/A.bam b/src/arriba/test_data/A.bam deleted file mode 100644 index 57511ab3537e519b0b82cc84d30637c43db5801e..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 296 zcmb2|=3rp}f&Xj_PR>jW4GhIaUsBJcB_tGlD0s;8d9%?KKQQ<5<)c~_M+`fR5AZuNn@YW$`C3w~$m(~4>kgSYe=WVcgS$m0eJ(B*{v0Gy zWb`>`t;m5QABWctHzp`DoHAnC%-}Jhqp=%kuRNLqx)@fcG%)xnq;3Bwl9ZzHWI{{V zO6SacW@csY;x^769v(f91CGMtA3hhPefdz5R>D&zcH(ns+6U%G3CA^*WtEv_b7hr- z<7JJRWtp?vycRrkaF%R&I8EKy!|CXmh9BJaT~C`l92z7}mn%f(tw`?3vSeueGBM~E N7N1 -GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG ->2 -AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA diff --git a/src/arriba/test_data/script.sh b/src/arriba/test_data/script.sh deleted file mode 100755 index e5bbcf2c..00000000 --- a/src/arriba/test_data/script.sh +++ /dev/null @@ -1,10 +0,0 @@ -# arriba test data - -# Test data was obtained from https://github.com/snakemake/snakemake-wrappers/tree/master/bio/arriba/test - -if [ ! -d /tmp/snakemake-wrappers ]; then - git clone --depth 1 --single-branch --branch master https://github.com/snakemake/snakemake-wrappers /tmp/snakemake-wrappers -fi - -cp -r /tmp/snakemake-wrappers/bio/arriba/test/* src/arriba/test_data - diff --git a/src/bases2fastq/config.vsh.yaml b/src/bases2fastq/config.vsh.yaml index ade10199..995252c8 100644 --- a/src/bases2fastq/config.vsh.yaml +++ b/src/bases2fastq/config.vsh.yaml @@ -218,7 +218,7 @@ test_resources: engines: - type: docker - image: elembio/bases2fastq:2.2 + image: elembio/bases2fastq:2.2.1 setup: - type: docker run: | diff --git a/src/bcftools/bcftools_annotate/config.vsh.yaml b/src/bcftools/bcftools_annotate/config.vsh.yaml index 67e8f46e..ce818bf0 100644 --- a/src/bcftools/bcftools_annotate/config.vsh.yaml +++ b/src/bcftools/bcftools_annotate/config.vsh.yaml @@ -223,6 +223,12 @@ argument_groups: To remove all INFO tags except "FOO" and "BAR", use "^INFO/FOO,INFO/BAR" (and similarly for FORMAT and FILTER). "INFO" can be abbreviated to "INF" and "FORMAT" to "FMT". + - name: --verbosity + alternatives: -v + type: integer + description: | + Verbosity level. + resources: - type: bash_script path: script.sh @@ -230,19 +236,15 @@ resources: test_resources: - type: bash_script path: test.sh + - path: /src/_utils/test_helpers.sh engines: - type: docker - image: debian:stable-slim + image: quay.io/biocontainers/bcftools:1.22--h3a4d415_1 setup: - - type: apt - packages: [bcftools, procps] - type: docker run: | echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftools //p')\"" > /var/software_versions.txt - test_setup: - - type: apt - packages: [tabix] runners: - type: executable diff --git a/src/bcftools/bcftools_annotate/help.txt b/src/bcftools/bcftools_annotate/help.txt index 2d1c7807..1385359c 100644 --- a/src/bcftools/bcftools_annotate/help.txt +++ b/src/bcftools/bcftools_annotate/help.txt @@ -1,8 +1,6 @@ +```bash +docker run --rm quay.io/biocontainers/bcftools:1.22--h3a4d415_1 bcftools annotate --help 2>&1 | grep -v unrecognized ``` -bcftools annotate -h -``` - -annotate: option requires an argument -- 'h' About: Annotate and edit VCF/BCF files. Usage: bcftools annotate [options] VCF @@ -24,7 +22,7 @@ Options: --no-version Do not append version and command line to the header -o, --output FILE Write output to a file [standard output] -O, --output-type u|b|v|z[0-9] u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v] - --pair-logic STR Matching records by , see man page for details [some] + --pair-logic STR Matching records by , see man page for details [some] -r, --regions REGION Restrict to comma-separated list of regions -R, --regions-file FILE Restrict to regions listed in FILE --regions-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1] @@ -35,6 +33,8 @@ Options: --single-overlaps Keep memory low by avoiding complexities arising from handling multiple overlapping intervals -x, --remove LIST List of annotations (e.g. ID,INFO/DP,FORMAT/DP,FILTER) to remove (or keep with "^" prefix). See man page for details --threads INT Number of extra output compression threads [0] + -v, --verbosity INT Verbosity level + -W, --write-index[=FMT] Automatically index the output files [off] Examples: http://samtools.github.io/bcftools/howtos/annotate.html diff --git a/src/bcftools/bcftools_annotate/script.sh b/src/bcftools/bcftools_annotate/script.sh index 18137bbf..ca3c5244 100644 --- a/src/bcftools/bcftools_annotate/script.sh +++ b/src/bcftools/bcftools_annotate/script.sh @@ -8,47 +8,48 @@ set -eo pipefail # Unset parameters unset_if_false=( - par_force - par_keep_sites - par_no_version - par_single_overlaps + par_force + par_keep_sites + par_no_version + par_single_overlaps ) for par in ${unset_if_false[@]}; do - test_val="${!par}" - [[ "$test_val" == "false" ]] && unset $par + test_val="${!par}" + [[ "$test_val" == "false" ]] && unset $par done # Execute bcftools annotate with the provided arguments bcftools annotate \ - ${par_annotations:+-a "$par_annotations"} \ - ${par_columns:+-c "$par_columns"} \ - ${par_columns_file:+-C "$par_columns_file"} \ - ${par_exclude:+-e "$par_exclude"} \ - ${par_force:+--force} \ - ${par_header_line:+-H "$par_header_line"} \ - ${par_header_lines:+-h "$par_header_lines"} \ - ${par_set_id:+-I "$par_set_id"} \ - ${par_include:+-i "$par_include"} \ - ${par_keep_sites:+-k} \ - ${par_merge_logic:+-l "$par_merge_logic"} \ - ${par_mark_sites:+-m "$par_mark_sites"} \ - ${par_min_overlap:+--min-overlap "$par_min_overlap"} \ - ${par_no_version:+--no-version} \ - ${par_samples_file:+-S "$par_samples_file"} \ - ${par_output_type:+-O "$par_output_type"} \ - ${par_pair_logic:+--pair-logic "$par_pair_logic"} \ - ${par_regions:+-r "$par_regions"} \ - ${par_regions_file:+-R "$par_regions_file"} \ - ${par_regions_overlap:+--regions-overlap "$par_regions_overlap"} \ - ${par_rename_annotations:+--rename-annots "$par_rename_annotations"} \ - ${par_rename_chromosomes:+--rename-chrs "$par_rename_chromosomes"} \ - ${par_samples:+-s "$par_samples"} \ - ${par_single_overlaps:+--single-overlaps} \ - ${par_threads:+--threads "$par_threads"} \ - ${par_remove:+-x "$par_remove"} \ - -o $par_output \ - $par_input - + ${par_annotations:+-a "$par_annotations"} \ + ${par_columns:+-c "$par_columns"} \ + ${par_columns_file:+-C "$par_columns_file"} \ + ${par_exclude:+-e "$par_exclude"} \ + ${par_force:+--force} \ + ${par_header_line:+-H "$par_header_line"} \ + ${par_header_lines:+-h "$par_header_lines"} \ + ${par_set_id:+-I "$par_set_id"} \ + ${par_include:+-i "$par_include"} \ + ${par_keep_sites:+-k} \ + ${par_merge_logic:+-l "$par_merge_logic"} \ + ${par_mark_sites:+-m "$par_mark_sites"} \ + ${par_min_overlap:+--min-overlap "$par_min_overlap"} \ + ${par_no_version:+--no-version} \ + ${par_samples_file:+-S "$par_samples_file"} \ + ${par_output_type:+-O "$par_output_type"} \ + ${par_pair_logic:+--pair-logic "$par_pair_logic"} \ + ${par_regions:+-r "$par_regions"} \ + ${par_regions_file:+-R "$par_regions_file"} \ + ${par_regions_overlap:+--regions-overlap "$par_regions_overlap"} \ + ${par_rename_annotations:+--rename-annots "$par_rename_annotations"} \ + ${par_rename_chromosomes:+--rename-chrs "$par_rename_chromosomes"} \ + ${par_samples:+-s "$par_samples"} \ + ${par_single_overlaps:+--single-overlaps} \ + ${par_remove:+-x "$par_remove"} \ + ${par_verbosity:+-v "$par_verbosity"} \ + ${meta_cpus:+--threads "$meta_cpus"} \ + -o $par_output \ + $par_input + - \ No newline at end of file + \ No newline at end of file diff --git a/src/bcftools/bcftools_annotate/test.sh b/src/bcftools/bcftools_annotate/test.sh index 39835c82..184daeac 100644 --- a/src/bcftools/bcftools_annotate/test.sh +++ b/src/bcftools/bcftools_annotate/test.sh @@ -6,27 +6,11 @@ # Exit on error set -eo pipefail -#test_data="$meta_resources_dir/test_data" - -############################################# -# helper functions -assert_file_exists() { - [ -f "$1" ] || { echo "File '$1' does not exist" && exit 1; } -} -assert_file_not_empty() { - [ -s "$1" ] || { echo "File '$1' is empty but shouldn't be" && exit 1; } -} -assert_file_contains() { - grep -q "$2" "$1" || { echo "File '$1' does not contain '$2'" && exit 1; } -} -assert_identical_content() { - diff -a "$2" "$1" \ - || (echo "Files are not identical!" && exit 1) -} -############################################# +# Source test helpers +source "$meta_resources_dir/test_helpers.sh" # Create directories for tests -echo "Creating Test Data..." +log "Creating Test Data..." TMPDIR=$(mktemp -d "$meta_temp_dir/XXXXXX") function clean_up { [[ -d "$TMPDIR" ]] && rm -r "$TMPDIR" @@ -70,24 +54,24 @@ EOF # Test 1: Remove ID annotations mkdir "$TMPDIR/test1" && pushd "$TMPDIR/test1" > /dev/null -echo "> Run bcftools_annotate remove annotations" +log "Test 1: Remove ID annotations" "$meta_executable" \ --input "../example.vcf" \ --output "annotated.vcf" \ --remove "ID" \ # checks -assert_file_exists "annotated.vcf" -assert_file_not_empty "annotated.vcf" -assert_file_contains "annotated.vcf" "1 752567 . A C" -echo "- test1 succeeded -" +check_file_exists "annotated.vcf" "output VCF file" +check_file_not_empty "annotated.vcf" "output VCF file" +check_file_contains "annotated.vcf" "1 752567 . A C" "VCF with removed ID" +log "✓ Test 1 passed" popd > /dev/null # Test 2: Annotate with -a, -c and -h options mkdir "$TMPDIR/test2" && pushd "$TMPDIR/test2" > /dev/null -echo "> Run bcftools_annotate with -a, -c and -h options" +log "Test 2: Annotate with -a, -c and -h options" "$meta_executable" \ --input "../example.vcf" \ --output "annotated.vcf" \ @@ -97,85 +81,85 @@ echo "> Run bcftools_annotate with -a, -c and -h options" --mark_sites "BAR" \ # checks -assert_file_exists "annotated.vcf" -assert_file_not_empty "annotated.vcf" -assert_file_contains "annotated.vcf" $(echo -e "1\t752567\tllama\tA\tC\t.\t.\tBAR=12345\tFOO\tFooValue1") -echo "- test2 succeeded -" +check_file_exists "annotated.vcf" "output VCF file" +check_file_not_empty "annotated.vcf" "output VCF file" +check_file_contains "annotated.vcf" $(echo -e "1\t752567\tllama\tA\tC\t.\t.\tBAR=12345\tFOO\tFooValue1") "annotated VCF content" +log "✓ Test 2 passed" popd > /dev/null -# Test 3: +# Test 3: Set ID option mkdir "$TMPDIR/test3" && pushd "$TMPDIR/test3" > /dev/null -echo "> Run bcftools_annotate with --set_id option" +log "Test 3: Set ID option" "$meta_executable" \ --input "../example.vcf" \ --output "annotated.vcf" \ --set_id "+'%CHROM\_%POS\_%REF\_%FIRST_ALT'" \ # checks -assert_file_exists "annotated.vcf" -assert_file_not_empty "annotated.vcf" -assert_file_contains "annotated.vcf" "'1_752722_G_A'" -echo "- test3 succeeded -" +check_file_exists "annotated.vcf" "output VCF file" +check_file_not_empty "annotated.vcf" "output VCF file" +check_file_contains "annotated.vcf" "'1_752722_G_A'" "VCF with set ID" +log "✓ Test 3 passed" popd > /dev/null -# Test 4: +# Test 4: Rename annotations mkdir "$TMPDIR/test4" && pushd "$TMPDIR/test4" > /dev/null -echo "> Run bcftools_annotate with --rename-annotations option" +log "Test 4: Rename annotations" "$meta_executable" \ --input "../example.vcf" \ --output "annotated.vcf" \ --rename_annotations "../rename.tsv" # checks -assert_file_exists "annotated.vcf" -assert_file_not_empty "annotated.vcf" -assert_file_contains "annotated.vcf" "##bcftools_annotateCommand=annotate --rename-annots ../rename.tsv -o annotated.vcf" -echo "- test4 succeeded -" +check_file_exists "annotated.vcf" "output VCF file" +check_file_not_empty "annotated.vcf" "output VCF file" +check_file_contains "annotated.vcf" "##bcftools_annotateCommand=annotate --rename-annots ../rename.tsv -o annotated.vcf" "VCF with command line" +log "✓ Test 4 passed" popd > /dev/null # Test 5: Rename chromosomes mkdir "$TMPDIR/test5" && pushd "$TMPDIR/test5" > /dev/null -echo "> Run bcftools_annotate with --rename-chromosomes option" +log "Test 5: Rename chromosomes" "$meta_executable" \ --input "../example.vcf" \ --output "annotated.vcf" \ --rename_chromosomes "../rename_chrm.tsv" # checks -assert_file_exists "annotated.vcf" -assert_file_not_empty "annotated.vcf" -assert_file_contains "annotated.vcf" "chr1" -echo "- test5 succeeded -" +check_file_exists "annotated.vcf" "output VCF file" +check_file_not_empty "annotated.vcf" "output VCF file" +check_file_contains "annotated.vcf" "chr1" "VCF with renamed chromosomes" +log "✓ Test 5 passed" popd > /dev/null # Test 6: Sample option mkdir "$TMPDIR/test6" && pushd "$TMPDIR/test6" > /dev/null -echo "> Run bcftools_annotate with -s option" +log "Test 6: Sample selection" "$meta_executable" \ --input "../example.vcf" \ --output "annotated.vcf" \ --samples "SAMPLE1" # checks -assert_file_exists "annotated.vcf" -assert_file_not_empty "annotated.vcf" -assert_file_contains "annotated.vcf" "##bcftools_annotateCommand=annotate -s SAMPLE1 -o annotated.vcf ../example.vcf" -echo "- test6 succeeded -" +check_file_exists "annotated.vcf" "output VCF file" +check_file_not_empty "annotated.vcf" "output VCF file" +check_file_contains "annotated.vcf" "##bcftools_annotateCommand=annotate -s SAMPLE1 -o annotated.vcf ../example.vcf" "VCF with sample selection" +log "✓ Test 6 passed" popd > /dev/null # Test 7: Single overlaps mkdir "$TMPDIR/test7" && pushd "$TMPDIR/test7" > /dev/null -echo "> Run bcftools_annotate with --single-overlaps option" +log "Test 7: Single overlaps and keep sites" "$meta_executable" \ --input "../example.vcf" \ --output "annotated.vcf" \ @@ -183,17 +167,17 @@ echo "> Run bcftools_annotate with --single-overlaps option" --keep_sites \ # checks -assert_file_exists "annotated.vcf" -assert_file_not_empty "annotated.vcf" -assert_file_contains "annotated.vcf" "annotate -k --single-overlaps -o annotated.vcf ../example.vcf" -echo "- test7 succeeded -" +check_file_exists "annotated.vcf" "output VCF file" +check_file_not_empty "annotated.vcf" "output VCF file" +check_file_contains "annotated.vcf" "annotate -k --single-overlaps -o annotated.vcf ../example.vcf" "VCF with single overlaps option" +log "✓ Test 7 passed" popd > /dev/null # Test 8: Min overlap mkdir "$TMPDIR/test8" && pushd "$TMPDIR/test8" > /dev/null -echo "> Run bcftools_annotate with --min-overlap option" +log "Test 8: Minimum overlap option" "$meta_executable" \ --input "../example.vcf" \ --output "annotated.vcf" \ @@ -203,85 +187,85 @@ echo "> Run bcftools_annotate with --min-overlap option" --min_overlap "1" # checks -assert_file_exists "annotated.vcf" -assert_file_not_empty "annotated.vcf" -assert_file_contains "annotated.vcf" "annotate -a ../annots.tsv.gz -c CHROM,FROM,TO,FMT/FOO,BAR -h ../header.hdr --min-overlap 1 -o annotated.vcf ../example.vcf" -echo "- test8 succeeded -" +check_file_exists "annotated.vcf" "output VCF file" +check_file_not_empty "annotated.vcf" "output VCF file" +check_file_contains "annotated.vcf" "annotate -a ../annots.tsv.gz -c CHROM,FROM,TO,FMT/FOO,BAR -h ../header.hdr --min-overlap 1 -o annotated.vcf ../example.vcf" "VCF with min overlap" +log "✓ Test 8 passed" popd > /dev/null # Test 9: Regions mkdir "$TMPDIR/test9" && pushd "$TMPDIR/test9" > /dev/null -echo "> Run bcftools_annotate with -r option" +log "Test 9: Region filtering" "$meta_executable" \ --input "../example.vcf.gz" \ --output "annotated.vcf" \ --regions "1:752567-752722" # checks -assert_file_exists "annotated.vcf" -assert_file_not_empty "annotated.vcf" -assert_file_contains "annotated.vcf" "annotate -r 1:752567-752722 -o annotated.vcf ../example.vcf.gz" -echo "- test9 succeeded -" +check_file_exists "annotated.vcf" "output VCF file" +check_file_not_empty "annotated.vcf" "output VCF file" +check_file_contains "annotated.vcf" "annotate -r 1:752567-752722 -o annotated.vcf ../example.vcf.gz" "VCF with region filtering" +log "✓ Test 9 passed" popd > /dev/null -# Test 10: pair-logic +# Test 10: Pair logic mkdir "$TMPDIR/test10" && pushd "$TMPDIR/test10" > /dev/null -echo "> Run bcftools_annotate with --pair-logic option" +log "Test 10: Pair logic option" "$meta_executable" \ --input "../example.vcf" \ --output "annotated.vcf" \ --pair_logic "all" # checks -assert_file_exists "annotated.vcf" -assert_file_not_empty "annotated.vcf" -assert_file_contains "annotated.vcf" "annotate --pair-logic all -o annotated.vcf ../example.vcf" -echo "- test10 succeeded -" +check_file_exists "annotated.vcf" "output VCF file" +check_file_not_empty "annotated.vcf" "output VCF file" +check_file_contains "annotated.vcf" "annotate --pair-logic all -o annotated.vcf ../example.vcf" "VCF with pair logic" +log "✓ Test 10 passed" popd > /dev/null -# Test 11: regions-overlap +# Test 11: Regions overlap mkdir "$TMPDIR/test11" && pushd "$TMPDIR/test11" > /dev/null -echo "> Run bcftools_annotate with --regions-overlap option" +log "Test 11: Regions overlap option" "$meta_executable" \ --input "../example.vcf" \ --output "annotated.vcf" \ --regions_overlap "1" # checks -assert_file_exists "annotated.vcf" -assert_file_not_empty "annotated.vcf" -assert_file_contains "annotated.vcf" "annotate --regions-overlap 1 -o annotated.vcf ../example.vcf" -echo "- test11 succeeded -" +check_file_exists "annotated.vcf" "output VCF file" +check_file_not_empty "annotated.vcf" "output VCF file" +check_file_contains "annotated.vcf" "annotate --regions-overlap 1 -o annotated.vcf ../example.vcf" "VCF with regions overlap" +log "✓ Test 11 passed" popd > /dev/null -# Test 12: include +# Test 12: Include filter mkdir "$TMPDIR/test12" && pushd "$TMPDIR/test12" > /dev/null -echo "> Run bcftools_annotate with -i option" +log "Test 12: Include filter expression" "$meta_executable" \ --input "../example.vcf" \ --output "annotated.vcf" \ --include "FILTER='PASS'" \ # checks -assert_file_exists "annotated.vcf" -assert_file_not_empty "annotated.vcf" -assert_file_contains "annotated.vcf" "annotate -i FILTER='PASS' -o annotated.vcf ../example.vcf" -echo "- test12 succeeded -" +check_file_exists "annotated.vcf" "output VCF file" +check_file_not_empty "annotated.vcf" "output VCF file" +check_file_contains "annotated.vcf" "annotate -i FILTER='PASS' -o annotated.vcf ../example.vcf" "VCF with include filter" +log "✓ Test 12 passed" popd > /dev/null -# Test 13: exclude +# Test 13: Exclude filter with merge logic mkdir "$TMPDIR/test13" && pushd "$TMPDIR/test13" > /dev/null -echo "> Run bcftools_annotate with -e option" +log "Test 13: Exclude filter with merge logic" "$meta_executable" \ --annotations "../annots.tsv.gz" \ --input "../example.vcf" \ @@ -292,14 +276,13 @@ echo "> Run bcftools_annotate with -e option" --merge_logic "FOO:first" \ # checks -assert_file_exists "annotated.vcf" -assert_file_not_empty "annotated.vcf" -assert_file_contains "annotated.vcf" "annotate -a ../annots.tsv.gz -c CHROM,FROM,TO,FMT/FOO,BAR -e FILTER='PASS' -h ../header.hdr -l FOO:first -o annotated.vcf ../example.vcf" -echo "- test13 succeeded -" +check_file_exists "annotated.vcf" "output VCF file" +check_file_not_empty "annotated.vcf" "output VCF file" +check_file_contains "annotated.vcf" "annotate -a ../annots.tsv.gz -c CHROM,FROM,TO,FMT/FOO,BAR -e FILTER='PASS' -h ../header.hdr -l FOO:first -o annotated.vcf ../example.vcf" "VCF with exclude filter and merge logic" +log "✓ Test 13 passed" popd > /dev/null - -echo "---- All tests succeeded! ----" +log "All tests completed successfully!" exit 0 diff --git a/src/bcftools/bcftools_concat/config.vsh.yaml b/src/bcftools/bcftools_concat/config.vsh.yaml index 2bb32f1c..11a2dc6b 100644 --- a/src/bcftools/bcftools_concat/config.vsh.yaml +++ b/src/bcftools/bcftools_concat/config.vsh.yaml @@ -27,124 +27,201 @@ argument_groups: - name: Inputs arguments: - name: --input - alternatives: -i + alternatives: [-i] type: file multiple: true - description: Input VCF/BCF files to concatenate. + description: | + Input VCF/BCF files to concatenate. + + All source files must have the same sample columns appearing in + the same order. Files must be sorted by chr and position. + example: "input1.vcf.gz input2.vcf.gz" - name: --file_list - alternatives: -f + alternatives: [-f] type: file - description: Read the list of VCF/BCF files from a file, one file name per line. + description: | + Read the list of VCF/BCF files from a file, one file name per line. + + Alternative to providing multiple --input files. + example: "files_list.txt" - name: Outputs arguments: - name: --output - alternatives: -o + alternatives: [-o] direction: output type: file - description: Output concatenated VCF/BCF file. + description: | + Write output to a file. + + If not specified, output goes to standard output. required: true + example: "concatenated.vcf.gz" - name: Options arguments: - - name: --allow_overlaps - alternatives: -a + alternatives: [-a] type: boolean_true - description: | - First coordinate of the next file can precede last record of the current file. - - - name: --compact_PS - alternatives: -c - type: boolean_true - description: | - Do not output PS tag at each site, only at the start of a new phase set block. - - - name: --remove_duplicates - alternatives: -d - type: string - choices: ['snps', 'indels', 'both', 'all', 'exact', 'none'] description: | - Output duplicate records present in multiple files only once: . - - - name: --ligate - alternatives: -l + First coordinate of the next file can precede last record of the current file. + + Allows overlapping records between files during concatenation. + + - name: --compact_ps + alternatives: [-c] type: boolean_true - description: Ligate phased VCFs by matching phase at overlapping haplotypes. + description: | + Do not output PS tag at each site, only at the start of a new phase set block. + + Reduces output size for phased data. + + - name: --rm_dups + alternatives: [-d] + type: string + choices: ['snps', 'indels', 'both', 'all', 'exact'] + description: | + Output duplicate records present in multiple files only once. + + **Options:** + - `snps`: Remove duplicate SNPs + - `indels`: Remove duplicate indels + - `both`: Remove duplicate SNPs and indels + - `all`: Remove all duplicates + - `exact`: Remove exact duplicates only + example: "exact" + + - name: --remove_duplicates + alternatives: [-D] + type: boolean_true + description: | + Alias for --rm_dups exact. + + Remove exact duplicate records present in multiple files. + + - name: --drop_genotypes + alternatives: [-G] + type: boolean_true + description: | + Drop individual genotype information. + + Removes all sample-specific data from output. + + - name: --ligate + alternatives: [-l] + type: boolean_true + description: | + Ligate phased VCFs by matching phase at overlapping haplotypes. + + Connects phase information across files. - name: --ligate_force type: boolean_true - description: Ligate even non-overlapping chunks, keep all sites. + description: | + Ligate even non-overlapping chunks, keep all sites. + + Forces ligation without requiring overlap validation. - name: --ligate_warn type: boolean_true - description: Drop sites in imperfect overlaps. + description: | + Drop sites in imperfect overlaps. + + Conservative ligation that removes problematic sites. - name: --no_version type: boolean_true - description: Do not append version and command line information to the header. + description: | + Do not append version and command line to the header. + + Produces cleaner output headers. - name: --naive - alternatives: -n + alternatives: [-n] type: boolean_true - description: Concatenate files without recompression, a header check compatibility is performed. + description: | + Concatenate files without recompression. + + Very fast operation with header compatibility check. - name: --naive_force type: boolean_true - description: | - Same as --naive, but header compatibility is not checked. - Dangerous, use with caution. + description: | + Same as --naive, but header compatibility is not checked. + + **Warning:** Dangerous option, use with caution. - name: --output_type - alternatives: -O + alternatives: [-O] type: string choices: ['u', 'z', 'b', 'v'] - description: | - Output type: - u: uncompressed BCF - z: compressed VCF - b: compressed BCF - v: uncompressed VCF + description: | + Output type and compression level. + + **Options:** + - `u`: uncompressed BCF + - `b`: compressed BCF + - `v`: uncompressed VCF + - `z`: compressed VCF (with optional compression level 0-9) + example: "z" - - name: --min_PQ - alternatives: -q + - name: --min_pq + alternatives: [-q] type: integer - description: Break phase set if phasing quality is lower than . + description: | + Break phase set if phasing quality is lower than specified value. + + Only relevant when working with phased data. example: 30 - name: --regions - alternatives: -r + alternatives: [-r] type: string - description: | - Restrict to comma-separated list of regions. - Following formats are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​]. - example: '20:1000000-2000000' + description: | + Restrict to comma-separated list of regions. + + **Formats supported:** chr|chr:pos|chr:beg-end|chr:beg-[,…​] + example: "chr20:1000000-2000000" - name: --regions_file - alternatives: -R + alternatives: [-R] type: file - description: | - Restrict to regions listed in a file. - Regions can be specified either on a VCF, BED, or tab-delimited file (the default). - For more information check manual. + description: | + Restrict to regions listed in a file. + + Regions can be specified in VCF, BED, or tab-delimited format. + example: "regions.bed" - name: --regions_overlap type: string - choices: ['pos', 'record', 'variant', '0', '1', '2'] - description: | - This option controls how overlapping records are determined: - set to 'pos' or '0' if the VCF record has to have POS inside a region (this corresponds to the default behavior of -t/-T); - set to 'record' or '1' if also overlapping records with POS outside a region should be included (this is the default behavior of -r/-R, - and includes indels with POS at the end of a region, which are technically outside the region); - or set to 'variant' or '2' to include only true overlapping variation (compare the full VCF representation "TA>T-" vs the true sequence variation "A>-"). + choices: ['0', '1', '2'] + description: | + Include if POS in the region (0), record overlaps (1), variant overlaps (2). + + **Options:** + - `0`: POS inside region (default for -t/-T) + - `1`: overlapping records included (default for -r/-R) + - `2`: true overlapping variation only + example: "1" - #PS: Verbose seems to be broken in this version of bcftools - # - name: --verbose - # alternatives: -v - # type: integer - # choices: [0, 1] - # description: Set verbosity level. + - name: --verbosity + alternatives: [-v] + type: integer + description: | + Set verbosity level. + + Controls amount of diagnostic output. + example: 1 + + - name: --write_index + alternatives: [-W] + type: string + description: | + Automatically index the output files. + + **Format:** Specify index format or use default. + example: "tbi" resources: - type: bash_script @@ -153,19 +230,15 @@ resources: test_resources: - type: bash_script path: test.sh + - path: /src/_utils/test_helpers.sh engines: - type: docker - image: debian:stable-slim + image: quay.io/biocontainers/bcftools:1.22--h3a4d415_1 setup: - - type: apt - packages: [bcftools, procps] - type: docker run: | - echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftools //p')\"" > /var/software_versions.txt - test_setup: - - type: apt - packages: [tabix] + bcftools --version 2>&1 | head -1 | sed 's/bcftools /bcftools: /' > /var/software_versions.txt runners: - type: executable diff --git a/src/bcftools/bcftools_concat/help.txt b/src/bcftools/bcftools_concat/help.txt index fc0f1914..57a7ba21 100644 --- a/src/bcftools/bcftools_concat/help.txt +++ b/src/bcftools/bcftools_concat/help.txt @@ -1,8 +1,6 @@ +```bash +docker run --rm quay.io/biocontainers/bcftools:1.22--h3a4d415_1 bcftools concat --help 2>&1 | grep -v unrecognized ``` -bcftools concat -h -``` - -concat: option requires an argument -- 'h' About: Concatenate or combine VCF/BCF files. All source files must have the same sample columns appearing in the same order. The program can be used, for example, to @@ -19,6 +17,7 @@ Options: -d, --rm-dups STRING Output duplicate records present in multiple files only once: -D, --remove-duplicates Alias for -d exact -f, --file-list FILE Read the list of files from a file. + -G, --drop-genotypes Drop individual genotype information. -l, --ligate Ligate phased VCFs by matching phase at overlapping haplotypes --ligate-force Ligate even non-overlapping chunks, keep all sites --ligate-warn Drop sites in imperfect overlaps @@ -32,5 +31,6 @@ Options: -R, --regions-file FILE Restrict to regions listed in a file --regions-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1] --threads INT Use multithreading with worker threads [0] - -v, --verbose 0|1 Set verbosity level [1] + -v, --verbosity INT Set verbosity level + -W, --write-index[=FMT] Automatically index the output files [off] diff --git a/src/bcftools/bcftools_concat/script.sh b/src/bcftools/bcftools_concat/script.sh index 5614cd1b..7a3ad24b 100644 --- a/src/bcftools/bcftools_concat/script.sh +++ b/src/bcftools/bcftools_concat/script.sh @@ -3,52 +3,68 @@ ## VIASH START ## VIASH END -# Exit on error set -eo pipefail -# Unset parameters +# Unset false boolean parameters unset_if_false=( - par_allow_overlaps - par_compact_PS - par_ligate - par_ligate_force - par_ligate_warn - par_no_version - par_naive - par_naive_force + par_allow_overlaps + par_compact_ps + par_remove_duplicates + par_drop_genotypes + par_ligate + par_ligate_force + par_ligate_warn + par_no_version + par_naive + par_naive_force ) for par in ${unset_if_false[@]}; do - test_val="${!par}" - [[ "$test_val" == "false" ]] && unset $par + test_val="${!par}" + [[ "$test_val" == "false" ]] && unset $par done -# Check to see whether the par_input or the par_file_list is set +# Check that either input files or file_list is provided if [[ -z "${par_input}" && -z "${par_file_list}" ]]; then - echo "Error: One of the parameters '--input' or '--file_list' must be used." - exit 1 + echo "Error: One of the parameters '--input' or '--file_list' must be used." + exit 1 fi -# Create input array -IFS=";" read -ra input <<< $par_input +# Handle multiple input files (semicolon-separated from Viash) +if [[ -n "$par_input" ]]; then + IFS=';' read -ra input_files <<< "$par_input" +fi -# Execute bcftools concat with the provided arguments -bcftools concat \ - ${par_allow_overlaps:+-a} \ - ${par_compact_PS:+-c} \ - ${par_remove_duplicates:+-d "$par_remove_duplicates"} \ - ${par_ligate:+-l} \ - ${par_ligate_force:+--ligate-force} \ - ${par_ligate_warn:+--ligate-warn} \ - ${par_no_version:+--no-version} \ - ${par_naive:+-n} \ - ${par_naive_force:+--naive-force} \ - ${par_output_type:+--O "$par_output_type"} \ - ${par_min_PQ:+-q "$par_min_PQ"} \ - ${par_regions:+-r "$par_regions"} \ - ${par_regions_file:+-R "$par_regions_file"} \ - ${par_regions_overlap:+--regions-overlap "$par_regions_overlap"} \ - ${meta_cpus:+--threads "$meta_cpus"} \ - -o $par_output \ - ${par_file_list:+-f "$par_file_list"} \ - ${input[@]} \ \ No newline at end of file +# Build command array +cmd_args=( + bcftools concat + ${par_allow_overlaps:+--allow-overlaps} + ${par_compact_ps:+--compact-PS} + ${par_rm_dups:+--rm-dups "$par_rm_dups"} + ${par_remove_duplicates:+--remove-duplicates} + ${par_drop_genotypes:+--drop-genotypes} + ${par_ligate:+--ligate} + ${par_ligate_force:+--ligate-force} + ${par_ligate_warn:+--ligate-warn} + ${par_no_version:+--no-version} + ${par_naive:+--naive} + ${par_naive_force:+--naive-force} + ${par_output_type:+--output-type "$par_output_type"} + ${par_min_pq:+--min-PQ "$par_min_pq"} + ${par_regions:+--regions "$par_regions"} + ${par_regions_file:+--regions-file "$par_regions_file"} + ${par_regions_overlap:+--regions-overlap "$par_regions_overlap"} + ${meta_cpus:+--threads "$meta_cpus"} + ${par_verbosity:+--verbosity "$par_verbosity"} + ${par_write_index:+--write-index="$par_write_index"} + ${par_output:+--output "$par_output"} + ${par_file_list:+--file-list "$par_file_list"} +) + +# Add input files to command array +if [[ -n "$par_input" ]]; then + cmd_args+=("${input_files[@]}") +fi + +# Execute command +"${cmd_args[@]}" \ No newline at end of file diff --git a/src/bcftools/bcftools_concat/test.sh b/src/bcftools/bcftools_concat/test.sh index 3c1c7bb6..166bf4fb 100644 --- a/src/bcftools/bcftools_concat/test.sh +++ b/src/bcftools/bcftools_concat/test.sh @@ -3,225 +3,136 @@ ## VIASH START ## VIASH END -# Exit on error set -eo pipefail -#test_data="$meta_resources_dir/test_data" +# Always source centralized helpers +source "$meta_resources_dir/test_helpers.sh" -############################################# -# helper functions -assert_file_exists() { - [ -f "$1" ] || { echo "File '$1' does not exist" && exit 1; } -} -assert_file_not_empty() { - [ -s "$1" ] || { echo "File '$1' is empty but shouldn't be" && exit 1; } -} -assert_file_contains() { - grep -q "$2" "$1" || { echo "File '$1' does not contain '$2'" && exit 1; } -} -assert_identical_content() { - diff -a "$2" "$1" \ - || (echo "Files are not identical!" && exit 1) -} -############################################# +# Initialize test environment +setup_test_env -# Create directories for tests -echo "Creating Test Data..." -TMPDIR=$(mktemp -d "$meta_temp_dir/XXXXXX") -function clean_up { - [[ -d "$TMPDIR" ]] && rm -r "$TMPDIR" +log "Starting tests for $meta_name" + +# Create test VCF files using helpers +create_test_vcf() { + local output_file="$1" + local chrom="$2" + local start_pos="$3" + local end_pos="$4" + + cat > "$output_file" < +##contig= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE1 +$chrom $start_pos . G C 15 PASS . GT 0/1 +$chrom $end_pos . A T 20 PASS . GT 1/1 +EOF } -trap clean_up EXIT # Create test data -cat < "$TMPDIR/example.vcf" -##fileformat=VCFv4.1 -##contig= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE1 -1 752567 llama G C,A 15 . . . 1/2 -1 752752 . G A,AAA 20 . . . ./. -EOF +log "Creating test VCF files" +create_test_vcf "$meta_temp_dir/input1.vcf" "chr1" 1000 2000 +create_test_vcf "$meta_temp_dir/input2.vcf" "chr1" 3000 4000 -bgzip -c $TMPDIR/example.vcf > $TMPDIR/example.vcf.gz -tabix -p vcf $TMPDIR/example.vcf.gz +# Compress and index VCF files for bcftools +bgzip -c "$meta_temp_dir/input1.vcf" > "$meta_temp_dir/input1.vcf.gz" +bgzip -c "$meta_temp_dir/input2.vcf" > "$meta_temp_dir/input2.vcf.gz" +tabix -p vcf "$meta_temp_dir/input1.vcf.gz" +tabix -p vcf "$meta_temp_dir/input2.vcf.gz" -cat < "$TMPDIR/example_2.vcf" -##fileformat=VCFv4.1 -##contig= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE1 -1 752569 cat G C,A 15 . . . 1/2 -1 752739 . G A,AAA 20 . . . ./. -EOF +# Create file list +echo "$meta_temp_dir/input1.vcf.gz" > "$meta_temp_dir/file_list.txt" +echo "$meta_temp_dir/input2.vcf.gz" >> "$meta_temp_dir/file_list.txt" -bgzip -c $TMPDIR/example_2.vcf > $TMPDIR/example_2.vcf.gz -tabix -p vcf $TMPDIR/example_2.vcf.gz - -cat < "$TMPDIR/file_list.txt" -$TMPDIR/example.vcf.gz -$TMPDIR/example_2.vcf.gz -EOF - -# Test 1: Default test -mkdir "$TMPDIR/test1" && pushd "$TMPDIR/test1" > /dev/null - -echo "> Run bcftools_concat default test" +# Test 1: Basic concatenation +log "Starting TEST 1: Basic concatenation" "$meta_executable" \ - --input "../example.vcf" \ - --input "../example_2.vcf" \ - --output "concatenated.vcf" \ - &> /dev/null + --input "$meta_temp_dir/input1.vcf.gz" \ + --input "$meta_temp_dir/input2.vcf.gz" \ + --output "$meta_temp_dir/output1.vcf" -# checks -assert_file_exists "concatenated.vcf" -assert_file_not_empty "concatenated.vcf" -assert_file_contains "concatenated.vcf" "concat -o concatenated.vcf ../example.vcf ../example_2.vcf" -echo "- test1 succeeded -" +check_file_exists "$meta_temp_dir/output1.vcf" "basic concatenation output" +check_file_not_empty "$meta_temp_dir/output1.vcf" "basic concatenation output" +check_file_contains "$meta_temp_dir/output1.vcf" "chr1 1000" "first variant" +check_file_contains "$meta_temp_dir/output1.vcf" "chr1 4000" "last variant" +log "✅ TEST 1 completed successfully" -popd > /dev/null - -# Test 2: Allow overlaps, compact PS and remove duplicates -mkdir "$TMPDIR/test2" && pushd "$TMPDIR/test2" > /dev/null - -echo "> Run bcftools_concat test with allow overlaps, and remove duplicates" +# Test 2: File list input +log "Starting TEST 2: File list input" "$meta_executable" \ - --input "../example.vcf.gz" \ - --input "../example_2.vcf.gz" \ - --output "concatenated.vcf" \ + --file_list "$meta_temp_dir/file_list.txt" \ + --output "$meta_temp_dir/output2.vcf" + +check_file_exists "$meta_temp_dir/output2.vcf" "file list output" +check_file_not_empty "$meta_temp_dir/output2.vcf" "file list output" +check_file_contains "$meta_temp_dir/output2.vcf" "chr1 1000" "first variant from file list" +log "✅ TEST 2 completed successfully" + +# Test 3: Allow overlaps and output type +log "Starting TEST 3: Allow overlaps with compressed output" +"$meta_executable" \ + --input "$meta_temp_dir/input1.vcf.gz" \ + --input "$meta_temp_dir/input2.vcf.gz" \ + --output "$meta_temp_dir/output3.vcf.gz" \ --allow_overlaps \ - --remove_duplicates 'none' \ - &> /dev/null + --output_type "z" -# checks -assert_file_exists "concatenated.vcf" -assert_file_not_empty "concatenated.vcf" -assert_file_contains "concatenated.vcf" "concat -a -d none -o concatenated.vcf ../example.vcf.gz ../example_2.vcf.gz" -echo "- test2 succeeded -" +check_file_exists "$meta_temp_dir/output3.vcf.gz" "compressed output" +check_file_not_empty "$meta_temp_dir/output3.vcf.gz" "compressed output" +log "✅ TEST 3 completed successfully" -popd > /dev/null - - -# Test 3: Ligate, ligate force and ligate warn -mkdir "$TMPDIR/test3" && pushd "$TMPDIR/test3" > /dev/null - -echo "> Run bcftools_concat test with ligate, ligate force and ligate warn" +# Test 4: Remove duplicates +log "Starting TEST 4: Remove duplicates" "$meta_executable" \ - --input "../example.vcf.gz" \ - --input "../example_2.vcf.gz" \ - --output "concatenated.vcf" \ - --ligate \ - --compact_PS \ - &> /dev/null - - -# checks -assert_file_exists "concatenated.vcf" -assert_file_not_empty "concatenated.vcf" -assert_file_contains "concatenated.vcf" "concat -c -l -o concatenated.vcf ../example.vcf.gz ../example_2.vcf.gz" -echo "- test3 succeeded -" - -popd > /dev/null - -# Test 4: file list with ligate force and ligate warn -mkdir "$TMPDIR/test4" && pushd "$TMPDIR/test4" > /dev/null - -echo "> Run bcftools_concat test with file list, ligate force and ligate warn" -"$meta_executable" \ - --file_list "../file_list.txt" \ - --output "concatenated.vcf" \ - --ligate_force \ - &> /dev/null - -# checks -assert_file_exists "concatenated.vcf" -assert_file_not_empty "concatenated.vcf" -assert_file_contains "concatenated.vcf" "concat --ligate-force -o concatenated.vcf -f ../file_list.txt" -echo "- test4 succeeded -" - -popd > /dev/null - -# Test 5: ligate warn and naive -mkdir "$TMPDIR/test5" && pushd "$TMPDIR/test5" > /dev/null - -echo "> Run bcftools_concat test with ligate warn and naive" -"$meta_executable" \ - --input "../example.vcf.gz" \ - --input "../example_2.vcf.gz" \ - --output "concatenated.vcf.gz" \ - --ligate_warn \ - --naive \ - &> /dev/null - -bgzip -d concatenated.vcf.gz - -# checks -assert_file_exists "concatenated.vcf" -assert_file_not_empty "concatenated.vcf" -assert_file_contains "concatenated.vcf" "##fileformat=VCFv4.1" -echo "- test5 succeeded -" - -popd > /dev/null - -# Test 6: minimal PQ -mkdir "$TMPDIR/test6" && pushd "$TMPDIR/test6" > /dev/null - -echo "> Run bcftools_concat test with minimal PQ" -"$meta_executable" \ - --input "../example.vcf.gz" \ - --input "../example_2.vcf.gz" \ - --output "concatenated.vcf" \ - --min_PQ 20 \ - &> /dev/null - -# checks -assert_file_exists "concatenated.vcf" -assert_file_not_empty "concatenated.vcf" -assert_file_contains "concatenated.vcf" "concat -q 20 -o concatenated.vcf ../example.vcf.gz ../example_2.vcf.gz" -echo "- test6 succeeded -" - -popd > /dev/null - -# Test 7: regions -mkdir "$TMPDIR/test7" && pushd "$TMPDIR/test7" > /dev/null - -echo "> Run bcftools_concat test with regions" -"$meta_executable" \ - --input "../example.vcf.gz" \ - --input "../example_2.vcf.gz" \ - --output "concatenated.vcf" \ + --input "$meta_temp_dir/input1.vcf.gz" \ + --input "$meta_temp_dir/input1.vcf.gz" \ + --output "$meta_temp_dir/output4.vcf" \ --allow_overlaps \ - --regions "1:752569-752739" \ - &> /dev/null + --rm_dups "exact" -# checks -assert_file_exists "concatenated.vcf" -assert_file_not_empty "concatenated.vcf" -assert_file_contains "concatenated.vcf" "concat -a -r 1:752569-752739 -o concatenated.vcf ../example.vcf.gz ../example_2.vcf.gz" -echo "- test7 succeeded -" +check_file_exists "$meta_temp_dir/output4.vcf" "deduplicated output" +check_file_not_empty "$meta_temp_dir/output4.vcf" "deduplicated output" +log "✅ TEST 4 completed successfully" -popd > /dev/null - -# Test 8: regions overlap -mkdir "$TMPDIR/test8" && pushd "$TMPDIR/test8" > /dev/null - -echo "> Run bcftools_concat test with regions overlap" +# Test 5: Naive concatenation +log "Starting TEST 5: Naive concatenation" "$meta_executable" \ - --input "../example.vcf.gz" \ - --input "../example_2.vcf.gz" \ - --output "concatenated.vcf" \ + --input "$meta_temp_dir/input1.vcf.gz" \ + --input "$meta_temp_dir/input2.vcf.gz" \ + --output "$meta_temp_dir/output5.vcf" \ + --naive + +check_file_exists "$meta_temp_dir/output5.vcf" "naive concatenation output" +check_file_not_empty "$meta_temp_dir/output5.vcf" "naive concatenation output" +log "✅ TEST 5 completed successfully" + +# Test 6: Drop genotypes +log "Starting TEST 6: Drop genotypes" +"$meta_executable" \ + --input "$meta_temp_dir/input1.vcf.gz" \ + --input "$meta_temp_dir/input2.vcf.gz" \ + --output "$meta_temp_dir/output6.vcf" \ + --drop_genotypes + +check_file_exists "$meta_temp_dir/output6.vcf" "genotype-free output" +check_file_not_empty "$meta_temp_dir/output6.vcf" "genotype-free output" +log "✅ TEST 6 completed successfully" + +# Test 7: Regions filtering +log "Starting TEST 7: Regions filtering" +"$meta_executable" \ + --input "$meta_temp_dir/input1.vcf.gz" \ + --input "$meta_temp_dir/input2.vcf.gz" \ + --output "$meta_temp_dir/output7.vcf" \ --allow_overlaps \ - --regions_overlap 'pos' \ - &> /dev/null - -# checks -assert_file_exists "concatenated.vcf" -assert_file_not_empty "concatenated.vcf" -assert_file_contains "concatenated.vcf" "concat -a --regions-overlap pos -o concatenated.vcf ../example.vcf.gz ../example_2.vcf.gz" -echo "- test8 succeeded -" - -popd > /dev/null - -echo "---- All tests succeeded! ----" -exit 0 + --regions "chr1:1000-2000" +check_file_exists "$meta_temp_dir/output7.vcf" "regions filtered output" +check_file_not_empty "$meta_temp_dir/output7.vcf" "regions filtered output" +check_file_contains "$meta_temp_dir/output7.vcf" "chr1 1000" "variant in region" +log "✅ TEST 7 completed successfully" +# Always end with summary +print_test_summary "All tests completed successfully" diff --git a/src/bcftools/bcftools_norm/config.vsh.yaml b/src/bcftools/bcftools_norm/config.vsh.yaml index 5c525d3a..20d913ef 100644 --- a/src/bcftools/bcftools_norm/config.vsh.yaml +++ b/src/bcftools/bcftools_norm/config.vsh.yaml @@ -22,149 +22,300 @@ argument_groups: - name: Inputs arguments: - name: --input - alternatives: -i type: file - description: Input VCF/BCF file. + description: | + Input VCF/BCF file. + + The file to be normalized, left-aligned, and/or processed. required: true + example: "input.vcf.gz" - name: Outputs arguments: - name: --output - alternatives: -o + alternatives: [-o] direction: output type: file - description: Output normalized VCF/BCF file. + description: | + Write output to a file. + + If not specified, output goes to standard output. required: true + example: "normalized.vcf.gz" - name: Options arguments: - - name: --atomize - alternatives: -a + alternatives: [-a] type: boolean_true description: | Decompose complex variants (e.g., MNVs become consecutive SNVs). + + Breaks down complex variants into simpler components. - name: --atom_overlaps type: string choices: [".", "*"] - description: | + description: | Use the star allele (*) for overlapping alleles or set to missing (.). + + **Options:** + - `*`: Use star allele for overlaps (default) + - `.`: Set overlapping alleles to missing + example: "*" - name: --check_ref - alternatives: -c + alternatives: [-c] type: string choices: ['e', 'w', 'x', 's'] - description: | + description: | Check REF alleles and exit (e), warn (w), exclude (x), or set (s) bad sites. + + **Options:** + - `e`: exit on REF mismatch (default) + - `w`: warn about REF mismatches + - `x`: exclude sites with REF mismatches + - `s`: set/fix REF mismatches + example: "w" - - name: --remove_duplicates - alternatives: -d + - name: --remove_duplicates_flag + alternatives: [-D] + type: boolean_true + description: | + Remove duplicate lines of the same type. + + Shorthand for --rm_dup exact. + + - name: --rm_dup + alternatives: [-d] type: string - choices: ['snps', 'indels', 'both', 'all', 'exact', 'none'] - description: Remove duplicate snps, indels, both, all, exact matches, or none (old -D option). + choices: ['snps', 'indels', 'both', 'all', 'exact'] + description: | + Remove duplicate snps|indels|both|all|exact. + + **Options:** + - `snps`: Remove duplicate SNPs + - `indels`: Remove duplicate indels + - `both`: Remove duplicate SNPs and indels + - `all`: Remove all duplicates + - `exact`: Remove exact duplicates only + example: "exact" + + - name: --exclude + alternatives: [-e] + type: string + description: | + Do not normalize records for which the expression is true. + + Uses bcftools expression syntax (see man page for details). + example: "INFO/DP<10" - name: --fasta_ref - alternatives: -f + alternatives: [-f] type: file - description: Reference fasta sequence file. + description: | + Reference sequence file. + + Required for checking REF alleles and left-alignment. + example: "reference.fa" - name: --force type: boolean_true - description: | - Try to proceed even if malformed tags are encountered. - Experimental, use at your own risk. + description: | + Try to proceed even if malformed tags are encountered. + + **Warning:** Experimental feature, use at your own risk. + + - name: --gff_annot + alternatives: [-g] + type: file + description: | + Follow HGVS 3'rule and right-align variants in transcripts on the forward strand. + + Uses GFF annotation file for transcript information. + example: "genes.gff" + + - name: --include + alternatives: [-i] + type: string + description: | + Normalize only records for which the expression is true. + + Uses bcftools expression syntax (see man page for details). + example: "QUAL>=30" - name: --keep_sum type: string - description: | - Keep vector sum constant when splitting multiallelics (see github issue #360). + description: | + Keep vector sum constant when splitting multiallelics. + + Comma-separated list of INFO tags (see github issue #360). + example: "AC,AF" - name: --multiallelics - alternatives: -m + alternatives: [-m] type: string choices: ['+snps', '+indels', '+both', '+any', '-snps', '-indels', '-both', '-any'] - description: | - Split multiallelics (-) or join biallelics (+), type: snps, indels, both, any [default: both]. + description: | + Split multiallelics (-) or join biallelics (+), type: snps|indels|both|any. + + **Options:** + - `-both`: Split multiallelic sites (default) + - `+both`: Join biallelic sites + - Use `snps`, `indels`, `any` for specific variant types + example: "-both" + + - name: --multi_overlaps + type: string + choices: ['0', '.'] + description: | + Fill in the reference (0) or missing (.) allele when splitting multiallelics. + + **Options:** + - `0`: Fill with reference allele (default) + - `.`: Fill with missing allele + example: "0" - name: --no_version type: boolean_true - description: Do not append version and command line information to the header. + description: | + Do not append version and command line to the header. + + Produces cleaner output headers. - name: --do_not_normalize - alternatives: -N + alternatives: [-N] type: boolean_true - description: Do not normalize indels (with -m or -c s). - - - name: --output_type - alternatives: --O - type: string - choices: ['u', 'z', 'b', 'v'] - description: | - Output type: - u: uncompressed BCF - z: compressed VCF - b: compressed BCF - v: uncompressed VCF + description: | + Do not normalize indels (with -m or -c s). + + Skips indel left-alignment and normalization. - name: --old_rec_tag type: string - description: Annotate modified records with INFO/STR indicating the original variant. + description: | + Annotate modified records with INFO/STR indicating the original variant. + + Adds specified INFO tag to track original variants. + example: "OLD_VARIANT" + + - name: --output_type + alternatives: [-O] + type: string + choices: ['u', 'z', 'b', 'v'] + description: | + Output type and compression level. + + **Options:** + - `u`: uncompressed BCF + - `b`: compressed BCF + - `v`: uncompressed VCF (default) + - `z`: compressed VCF (with optional compression level 0-9) + example: "z" - name: --regions - alternatives: --r + alternatives: [-r] type: string - description: | - Restrict to comma-separated list of regions. - Following formats are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​]. - example: '20:1000000-2000000' + description: | + Restrict to comma-separated list of regions. + + **Formats supported:** chr|chr:pos|chr:beg-end|chr:beg-[,…​] + example: "chr20:1000000-2000000" - name: --regions_file - alternatives: --R + alternatives: [-R] type: file - description: | - Restrict to regions listed in a file. - Regions can be specified either on a VCF, BED, or tab-delimited file (the default). - For more information check manual. + description: | + Restrict to regions listed in a file. + + Regions can be specified in VCF, BED, or tab-delimited format. + example: "regions.bed" - name: --regions_overlap type: string - choices: ['pos', 'record', 'variant', '0', '1', '2'] - description: | - This option controls how overlapping records are determined: - set to 'pos' or '0' if the VCF record has to have POS inside a region (this corresponds to the default behavior of -t/-T); - set to 'record' or '1' if also overlapping records with POS outside a region should be included (this is the default behavior of -r/-R, - and includes indels with POS at the end of a region, which are technically outside the region); - or set to 'variant' or '2' to include only true overlapping variation (compare the full VCF representation "TA>T-" vs the true sequence variation "A>-"). - - - name: --site_win - alternatives: -w - type: integer - description: | - Buffer for sorting lines that changed position during realignment. + choices: ['0', '1', '2'] + description: | + Include if POS in the region (0), record overlaps (1), variant overlaps (2). + + **Options:** + - `0`: POS inside region (default for -t/-T) + - `1`: overlapping records included (default for -r/-R) + - `2`: true overlapping variation only + example: "1" - name: --strict_filter - alternatives: -s + alternatives: [-s] type: boolean_true - description: When merging (-m+), merged site is PASS only if all sites being merged PASS. + description: | + When merging (-m+), merged site is PASS only if all sites being merged PASS. + + Stricter FILTER handling during multiallelic joining. + + - name: --sort + alternatives: [-S] + type: string + choices: ['chr_pos', 'lex'] + description: | + Sort order: chr_pos,lex. + + **Options:** + - `chr_pos`: Sort by chromosome and position (default) + - `lex`: Lexicographic sort + example: "chr_pos" - name: --targets - alternatives: -t + alternatives: [-t] type: string - description: Similar to --regions but streams rather than index-jumps. - example: '20:1000000-2000000' + description: | + Similar to --regions but streams rather than index-jumps. + + More efficient for processing many small regions. + example: "chr20:1000000-2000000" - name: --targets_file - alternatives: -T + alternatives: [-T] type: file - description: Similar to --regions_file but streams rather than index-jumps. + description: | + Similar to --regions_file but streams rather than index-jumps. + + More efficient for processing many regions from file. + example: "targets.bed" - name: --targets_overlap type: string - choices: ['pos', 'record', 'variant', '0', '1', '2'] - description: | + choices: ['0', '1', '2'] + description: | Include if POS in the region (0), record overlaps (1), variant overlaps (2). - Similar to --regions_overlap. + + Similar to --regions_overlap but for streaming mode. + example: "0" + + - name: --verbosity + alternatives: [-v] + type: integer + description: | + Verbosity level. + + Controls amount of diagnostic output. + example: 1 + + - name: --site_win + alternatives: [-w] + type: integer + description: | + Buffer for sorting lines which changed position during realignment. + + Larger values use more memory but handle more complex rearrangements. + example: 1000 + + - name: --write_index + alternatives: [-W] + type: string + description: | + Automatically index the output files. + + **Format:** Specify index format or use default. + example: "tbi" resources: - type: bash_script @@ -173,22 +324,16 @@ resources: test_resources: - type: bash_script path: test.sh + - path: /src/_utils/test_helpers.sh engines: - type: docker - image: debian:stable-slim + image: quay.io/biocontainers/bcftools:1.22--h3a4d415_1 setup: - - type: apt - packages: [bcftools, procps] - type: docker run: | - echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftools //p')\"" > /var/software_versions.txt - test_setup: - - type: apt - packages: [tabix] + bcftools --version 2>&1 | head -1 | sed 's/bcftools /bcftools: /' > /var/software_versions.txt runners: - type: executable - type: nextflow - - diff --git a/src/bcftools/bcftools_norm/help.txt b/src/bcftools/bcftools_norm/help.txt index 02e9761a..e4ee4632 100644 --- a/src/bcftools/bcftools_norm/help.txt +++ b/src/bcftools/bcftools_norm/help.txt @@ -1,5 +1,5 @@ -``` -bcftools norm -h +```bash +docker run --rm quay.io/biocontainers/bcftools:1.22--h3a4d415_1 bcftools norm --help 2>&1 | grep -v unrecognized ``` About: Left-align and normalize indels; check if REF alleles match the reference; @@ -13,10 +13,14 @@ Options: -c, --check-ref e|w|x|s Check REF alleles and exit (e), warn (w), exclude (x), or set (s) bad sites [e] -D, --remove-duplicates Remove duplicate lines of the same type. -d, --rm-dup TYPE Remove duplicate snps|indels|both|all|exact + -e, --exclude EXPR Do not normalize records for which the expression is true (see man page for details) -f, --fasta-ref FILE Reference sequence --force Try to proceed even if malformed tags are encountered. Experimental, use at your own risk + -g, --gff-annot FILE Follow HGVS 3'rule and right-align variants in transcripts on the forward strand + -i, --include EXPR Normalize only records for which the expression is true (see man page for details) --keep-sum TAG,.. Keep vector sum constant when splitting multiallelics (see github issue #360) -m, --multiallelics -|+TYPE Split multiallelics (-) or join biallelics (+), type: snps|indels|both|any [both] + --multi-overlaps 0|. Fill in the reference (0) or missing (.) allele when splitting multiallelics [0] --no-version Do not append version and command line to the header -N, --do-not-normalize Do not normalize indels (with -m or -c s) --old-rec-tag STR Annotate modified records with INFO/STR indicating the original variant @@ -26,11 +30,14 @@ Options: -R, --regions-file FILE Restrict to regions listed in a file --regions-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1] -s, --strict-filter When merging (-m+), merged site is PASS only if all sites being merged PASS + -S, --sort METHOD Sort order: chr_pos,lex [chr_pos] -t, --targets REGION Similar to -r but streams rather than index-jumps -T, --targets-file FILE Similar to -R but streams rather than index-jumps --targets-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0] - --threads INT Use multithreading with worker threads [0] + --threads INT Use multithreading with INT worker threads [0] + -v, --verbosity INT Verbosity level -w, --site-win INT Buffer for sorting lines which changed position during realignment [1000] + -W, --write-index[=FMT] Automatically index the output files [off] Examples: # normalize and left-align indels diff --git a/src/bcftools/bcftools_norm/script.sh b/src/bcftools/bcftools_norm/script.sh index 0f43e593..7e8cde63 100644 --- a/src/bcftools/bcftools_norm/script.sh +++ b/src/bcftools/bcftools_norm/script.sh @@ -3,47 +3,58 @@ ## VIASH START ## VIASH END -# Exit on error set -eo pipefail -# Unset parameters +# Unset false boolean parameters unset_if_false=( - par_atomize - par_remove_duplicates - par_force - par_no_version - par_do_not_normalize - par_strict_filter + par_atomize + par_remove_duplicates_flag + par_force + par_no_version + par_do_not_normalize + par_strict_filter ) for par in ${unset_if_false[@]}; do - test_val="${!par}" - [[ "$test_val" == "false" ]] && unset $par + test_val="${!par}" + [[ "$test_val" == "false" ]] && unset $par done -# Execute bcftools norm with the provided arguments -bcftools norm \ - ${par_atomize:+--atomize} \ - ${par_atom_overlaps:+--atom-overlaps "$par_atom_overlaps"} \ - ${par_check_ref:+-c "$par_check_ref"} \ - ${par_remove_duplicates:+-d "$par_remove_duplicates"} \ - ${par_fasta_ref:+-f "$par_fasta_ref"} \ - ${par_force:+--force} \ - ${par_keep_sum:+--keep-sum "$par_keep_sum"} \ - ${par_multiallelics:+-m "$par_multiallelics"} \ - ${par_no_version:+--no-version} \ - ${par_do_not_normalize:+-N} \ - ${par_old_rec_tag:+--old-rec-tag "$par_old_rec_tag"} \ - ${par_regions:+-r "$par_regions"} \ - ${par_regions_file:+-R "$par_regions_file"} \ - ${par_regions_overlap:+--regions-overlap "$par_regions_overlap"} \ - ${par_site_win:+-w "$par_site_win"} \ - ${par_strict_filter:+-s} \ - ${par_targets:+-t "$par_targets"} \ - ${par_targets_file:+-T "$par_targets_file"} \ - ${par_targets_overlap:+--targets-overlap "$par_targets_overlap"} \ - ${meta_cpus:+--threads "$meta_cpus"} \ - ${par_output_type:+-O "$par_output_type"} \ - -o $par_output \ - $par_input - +# Build command array +cmd_args=( + bcftools norm + ${par_atomize:+--atomize} + ${par_atom_overlaps:+--atom-overlaps "$par_atom_overlaps"} + ${par_check_ref:+--check-ref "$par_check_ref"} + ${par_remove_duplicates_flag:+--remove-duplicates} + ${par_rm_dup:+--rm-dup "$par_rm_dup"} + ${par_exclude:+--exclude "$par_exclude"} + ${par_fasta_ref:+--fasta-ref "$par_fasta_ref"} + ${par_force:+--force} + ${par_gff_annot:+--gff-annot "$par_gff_annot"} + ${par_include:+--include "$par_include"} + ${par_keep_sum:+--keep-sum "$par_keep_sum"} + ${par_multiallelics:+--multiallelics "$par_multiallelics"} + ${par_multi_overlaps:+--multi-overlaps "$par_multi_overlaps"} + ${par_no_version:+--no-version} + ${par_do_not_normalize:+--do-not-normalize} + ${par_old_rec_tag:+--old-rec-tag "$par_old_rec_tag"} + ${par_output_type:+--output-type "$par_output_type"} + ${par_regions:+--regions "$par_regions"} + ${par_regions_file:+--regions-file "$par_regions_file"} + ${par_regions_overlap:+--regions-overlap "$par_regions_overlap"} + ${par_strict_filter:+--strict-filter} + ${par_sort:+--sort "$par_sort"} + ${par_targets:+--targets "$par_targets"} + ${par_targets_file:+--targets-file "$par_targets_file"} + ${par_targets_overlap:+--targets-overlap "$par_targets_overlap"} + ${meta_cpus:+--threads "$meta_cpus"} + ${par_verbosity:+--verbosity "$par_verbosity"} + ${par_site_win:+--site-win "$par_site_win"} + ${par_write_index:+--write-index="$par_write_index"} + ${par_output:+--output "$par_output"} + "$par_input" +) + +# Execute command +"${cmd_args[@]}" diff --git a/src/bcftools/bcftools_norm/test.sh b/src/bcftools/bcftools_norm/test.sh index 254c7176..4a967e01 100644 --- a/src/bcftools/bcftools_norm/test.sh +++ b/src/bcftools/bcftools_norm/test.sh @@ -3,229 +3,145 @@ ## VIASH START ## VIASH END -# Exit on error set -eo pipefail -#test_data="$meta_resources_dir/test_data" +# Always source centralized helpers +source "$meta_resources_dir/test_helpers.sh" -############################################# -# helper functions -assert_file_exists() { - [ -f "$1" ] || { echo "File '$1' does not exist" && exit 1; } -} -assert_file_not_empty() { - [ -s "$1" ] || { echo "File '$1' is empty but shouldn't be" && exit 1; } -} -assert_file_contains() { - grep -q "$2" "$1" || { echo "File '$1' does not contain '$2'" && exit 1; } -} -assert_identical_content() { - diff -a "$2" "$1" \ - || (echo "Files are not identical!" && exit 1) -} -############################################# +# Initialize test environment +setup_test_env -# Create directories for tests -echo "Creating Test Data..." -TMPDIR=$(mktemp -d "$meta_temp_dir/XXXXXX") -function clean_up { - [[ -d "$TMPDIR" ]] && rm -r "$TMPDIR" +log "Starting tests for $meta_name" + +# Create test VCF files using helpers +create_test_vcf() { + local output_file="$1" + local has_multiallelics="$2" + + if [[ "$has_multiallelics" == "true" ]]; then + cat > "$output_file" < +##contig= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE1 +chr1 1000 . G C,A 15 PASS . GT 0/1 +chr1 2000 . ATG A,AT 20 PASS . GT 1/2 +EOF + else + cat > "$output_file" < +##contig= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE1 +chr1 1000 . G C 15 PASS . GT 0/1 +chr1 2000 . A T 20 PASS . GT 1/1 +EOF + fi +} + +create_test_reference() { + local output_file="$1" + cat > "$output_file" <chr1 +ATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCG +CGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGAT +ATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCG +EOF } -trap clean_up EXIT # Create test data -cat < "$TMPDIR/example.vcf" -##fileformat=VCFv4.1 -##contig= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE1 -1 752567 llama G C,A . . . . 1/2 -1 752722 . G A,AAA . . . . ./. -EOF +log "Creating test VCF files and reference" +create_test_vcf "$meta_temp_dir/input.vcf" "false" +create_test_vcf "$meta_temp_dir/multiallelic.vcf" "true" +create_test_reference "$meta_temp_dir/reference.fa" -bgzip -c $TMPDIR/example.vcf > $TMPDIR/example.vcf.gz -tabix -p vcf $TMPDIR/example.vcf.gz +# Compress and index VCF files for bcftools +bgzip -c "$meta_temp_dir/input.vcf" > "$meta_temp_dir/input.vcf.gz" +bgzip -c "$meta_temp_dir/multiallelic.vcf" > "$meta_temp_dir/multiallelic.vcf.gz" +tabix -p vcf "$meta_temp_dir/input.vcf.gz" +tabix -p vcf "$meta_temp_dir/multiallelic.vcf.gz" -cat < "$TMPDIR/reference.fa" ->1 -ATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCG ->2 -CGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGAT -EOF - -# Test 1: Remove ID annotations -mkdir "$TMPDIR/test1" && pushd "$TMPDIR/test1" > /dev/null - -echo "> Run bcftools_norm" +# Test 1: Basic normalization with atomize +log "Starting TEST 1: Basic normalization with atomize" "$meta_executable" \ - --input "../example.vcf" \ - --output "normalized.vcf" \ - --atomize \ - --atom_overlaps "." \ - &> /dev/null + --input "$meta_temp_dir/input.vcf.gz" \ + --output "$meta_temp_dir/output1.vcf" \ + --atomize -# checks -assert_file_exists "normalized.vcf" -assert_file_not_empty "normalized.vcf" -assert_file_contains "normalized.vcf" "bcftools_normCommand=norm --atomize --atom-overlaps . -o normalized.vcf ../example.vcf" -echo "- test1 succeeded -" +check_file_exists "$meta_temp_dir/output1.vcf" "basic normalization output" +check_file_not_empty "$meta_temp_dir/output1.vcf" "basic normalization output" +check_file_contains "$meta_temp_dir/output1.vcf" "chr1 1000" "first variant" +log "✅ TEST 1 completed successfully" -popd > /dev/null - -# Test 2: Check reference -mkdir "$TMPDIR/test2" && pushd "$TMPDIR/test2" > /dev/null - -echo "> Run bcftools_norm with remove duplicates" +# Test 2: Atomize complex variants +log "Starting TEST 2: Atomize complex variants" "$meta_executable" \ - --input "../example.vcf" \ - --output "normalized.vcf" \ - --atomize \ - --remove_duplicates 'all' \ - &> /dev/null + --input "$meta_temp_dir/multiallelic.vcf.gz" \ + --output "$meta_temp_dir/output2.vcf" \ + --atomize -# checks -assert_file_exists "normalized.vcf" -assert_file_not_empty "normalized.vcf" -assert_file_contains "normalized.vcf" "norm --atomize -d all -o normalized.vcf ../example.vcf" -echo "- test2 succeeded -" +check_file_exists "$meta_temp_dir/output2.vcf" "atomized output" +check_file_not_empty "$meta_temp_dir/output2.vcf" "atomized output" +log "✅ TEST 2 completed successfully" -popd > /dev/null - -# Test 3: Check reference and fasta reference -mkdir "$TMPDIR/test3" && pushd "$TMPDIR/test3" > /dev/null - -echo "> Run bcftools_norm with check reference and fasta reference" +# Test 3: Split multiallelics +log "Starting TEST 3: Split multiallelics" "$meta_executable" \ - --input "../example.vcf" \ - --output "normalized.vcf" \ - --atomize \ - --fasta_ref "../reference.fa" \ - --check_ref "e" \ - &> /dev/null + --input "$meta_temp_dir/multiallelic.vcf.gz" \ + --output "$meta_temp_dir/output3.vcf" \ + --multiallelics "-both" -# checks -assert_file_exists "normalized.vcf" -assert_file_not_empty "normalized.vcf" -assert_file_contains "normalized.vcf" "norm --atomize -c e -f ../reference.fa -o normalized.vcf ../example.vcf" -echo "- test3 succeeded -" +check_file_exists "$meta_temp_dir/output3.vcf" "split multiallelic output" +check_file_not_empty "$meta_temp_dir/output3.vcf" "split multiallelic output" +log "✅ TEST 3 completed successfully" -popd > /dev/null - -# Test 4: Multiallelics -mkdir "$TMPDIR/test4" && pushd "$TMPDIR/test4" > /dev/null - -echo "> Run bcftools_norm with multiallelics" +# Test 4: Check reference with fasta +log "Starting TEST 4: Check reference with fasta" "$meta_executable" \ - --input "../example.vcf" \ - --output "normalized.vcf" \ - --multiallelics "-any" \ - --old_rec_tag "wazzaaa" \ - &> /dev/null + --input "$meta_temp_dir/input.vcf.gz" \ + --output "$meta_temp_dir/output4.vcf" \ + --fasta_ref "$meta_temp_dir/reference.fa" \ + --check_ref "w" -# checks -assert_file_exists "normalized.vcf" -assert_file_not_empty "normalized.vcf" -assert_file_contains "normalized.vcf" "norm -m -any --old-rec-tag wazzaaa -o normalized.vcf ../example.vcf" -echo "- test4 succeeded -" +check_file_exists "$meta_temp_dir/output4.vcf" "reference checked output" +check_file_not_empty "$meta_temp_dir/output4.vcf" "reference checked output" +log "✅ TEST 4 completed successfully" -popd > /dev/null - -# Test 5: Regions -mkdir "$TMPDIR/test5" && pushd "$TMPDIR/test5" > /dev/null - -echo "> Run bcftools_norm with regions" +# Test 5: Remove duplicates +log "Starting TEST 5: Remove duplicates" "$meta_executable" \ - --input "../example.vcf.gz" \ - --output "normalized.vcf" \ - --atomize \ - --regions "1:752567-752722" \ - &> /dev/null + --input "$meta_temp_dir/input.vcf.gz" \ + --output "$meta_temp_dir/output5.vcf" \ + --rm_dup "exact" -# checks -assert_file_exists "normalized.vcf" -assert_file_not_empty "normalized.vcf" -assert_file_contains "normalized.vcf" "norm --atomize -r 1:752567-752722 -o normalized.vcf ../example.vcf.gz" -echo "- test5 succeeded -" +check_file_exists "$meta_temp_dir/output5.vcf" "deduplicated output" +check_file_not_empty "$meta_temp_dir/output5.vcf" "deduplicated output" +log "✅ TEST 5 completed successfully" -popd > /dev/null - -# Test 6: Targets -mkdir "$TMPDIR/test6" && pushd "$TMPDIR/test6" > /dev/null - -echo "> Run bcftools_norm with targets" +# Test 6: Output format and compression +log "Starting TEST 6: Output format and compression" "$meta_executable" \ - --input "../example.vcf" \ - --output "normalized.vcf" \ - --atomize \ - --targets "1:752567-752722" \ - &> /dev/null + --input "$meta_temp_dir/input.vcf.gz" \ + --output "$meta_temp_dir/output6.vcf.gz" \ + --output_type "z" \ + --atomize -# checks -assert_file_exists "normalized.vcf" -assert_file_not_empty "normalized.vcf" -assert_file_contains "normalized.vcf" "norm --atomize -t 1:752567-752722 -o normalized.vcf ../example.vcf" -echo "- test6 succeeded -" +check_file_exists "$meta_temp_dir/output6.vcf.gz" "compressed output" +check_file_not_empty "$meta_temp_dir/output6.vcf.gz" "compressed output" +log "✅ TEST 6 completed successfully" -popd > /dev/null - -# Test 7: Regions overlap -mkdir "$TMPDIR/test7" && pushd "$TMPDIR/test7" > /dev/null - -echo "> Run bcftools_norm with regions overlap" +# Test 7: Regions filtering +log "Starting TEST 7: Regions filtering" "$meta_executable" \ - --input "../example.vcf" \ - --output "normalized.vcf" \ - --atomize \ - --regions_overlap "pos" \ - &> /dev/null - -# checks -assert_file_exists "normalized.vcf" -assert_file_not_empty "normalized.vcf" -assert_file_contains "normalized.vcf" "norm --atomize --regions-overlap pos -o normalized.vcf ../example.vcf" -echo "- test7 succeeded -" - -popd > /dev/null - -# Test 8: Strict filter and targets overlap -mkdir "$TMPDIR/test8" && pushd "$TMPDIR/test8" > /dev/null - -echo "> Run bcftools_norm with strict filter and targets overlap" -"$meta_executable" \ - --input "../example.vcf" \ - --output "normalized.vcf" \ - --atomize \ - --strict_filter \ - --targets_overlap "1" \ - &> /dev/null - -# checks -assert_file_exists "normalized.vcf" -assert_file_not_empty "normalized.vcf" -assert_file_contains "normalized.vcf" "norm --atomize -s --targets-overlap 1 -o normalized.vcf ../example.vcf" -echo "- test8 succeeded -" - -popd > /dev/null - -# Test 9: Do not normalize -mkdir "$TMPDIR/test9" && pushd "$TMPDIR/test9" > /dev/null - -echo "> Run bcftools_norm with do not normalize" -"$meta_executable" \ - --input "../example.vcf" \ - --output "normalized.vcf" \ - --do_not_normalize \ - --atomize \ - &> /dev/null - -# checks -assert_file_exists "normalized.vcf" -assert_file_not_empty "normalized.vcf" -assert_file_contains "normalized.vcf" "norm --atomize -N -o normalized.vcf ../example.vcf" -echo "- test9 succeeded -" - -popd > /dev/null - -echo "---- All tests succeeded! ----" -exit 0 + --input "$meta_temp_dir/input.vcf.gz" \ + --output "$meta_temp_dir/output7.vcf" \ + --regions "chr1:1000-1500" \ + --atomize +check_file_exists "$meta_temp_dir/output7.vcf" "regions filtered output" +check_file_not_empty "$meta_temp_dir/output7.vcf" "regions filtered output" +check_file_contains "$meta_temp_dir/output7.vcf" "chr1 1000" "variant in region" +log "✅ TEST 7 completed successfully" +# Always end with summary +print_test_summary "All tests completed successfully" diff --git a/src/bcftools/bcftools_sort/config.vsh.yaml b/src/bcftools/bcftools_sort/config.vsh.yaml index 71a15309..10502309 100644 --- a/src/bcftools/bcftools_sort/config.vsh.yaml +++ b/src/bcftools/bcftools_sort/config.vsh.yaml @@ -1,7 +1,7 @@ name: bcftools_sort namespace: bcftools description: | - Sorts VCF/BCF files. + Sort VCF/BCF file. keywords: [Sort, VCF, BCF] links: homepage: https://samtools.github.io/bcftools/ @@ -15,39 +15,68 @@ requirements: commands: [bcftools] authors: - __merge__: /src/_authors/theodoro_gasperin.yaml - roles: [ author, maintainer ] + roles: [author] argument_groups: - name: Inputs arguments: - name: --input - alternatives: -i type: file - description: Input VCF/BCF file. + description: | + Input VCF/BCF file to sort. + + The file to be sorted by genomic coordinates. required: true + example: "input.vcf.gz" - name: Outputs arguments: - name: --output - alternatives: -o + alternatives: [-o] direction: output type: file - description: Output sorted VCF/BCF file. + description: | + Write output to a file. + + If not specified, output goes to standard output. required: true + example: "sorted.vcf.gz" - name: Options arguments: - name: --output_type - alternatives: -O + alternatives: [-O] type: string - choices: [b, u, z, v] - description: | - Compresses or uncompresses the output. - The options are: - b: compressed BCF, - u: uncompressed BCF, - z: compressed VCF, - v: uncompressed VCF. + description: | + Output file type. + + **Options:** + - u: uncompressed BCF + - b: compressed BCF + - v: uncompressed VCF + - z: compressed VCF + - 0-9: compression level for compressed formats + + **Default:** v (uncompressed VCF) + example: "z" + + - name: --verbosity + alternatives: [-v] + type: integer + description: | + Verbosity level. + + Higher values increase verbosity of output messages. + example: 1 + + - name: --write_index + alternatives: [-W] + type: string + description: | + Automatically index the output files. + + **Format:** Specify index format or use default. + example: "tbi" resources: - type: bash_script @@ -56,17 +85,15 @@ resources: test_resources: - type: bash_script path: test.sh - - path: test_data + - path: /src/_utils/test_helpers.sh engines: - type: docker - image: debian:stable-slim + image: quay.io/biocontainers/bcftools:1.22--h3a4d415_1 setup: - - type: apt - packages: [bcftools, procps] - type: docker run: | - echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftools //p')\"" > /var/software_versions.txt + bcftools --version 2>&1 | head -1 | sed 's/bcftools /bcftools: /' > /var/software_versions.txt runners: - type: executable diff --git a/src/bcftools/bcftools_sort/help.txt b/src/bcftools/bcftools_sort/help.txt index 3b5fa80b..a7b9c0eb 100644 --- a/src/bcftools/bcftools_sort/help.txt +++ b/src/bcftools/bcftools_sort/help.txt @@ -1,14 +1,15 @@ -``` -bcftools sort +```bash +docker run --rm quay.io/biocontainers/bcftools:1.22--h3a4d415_1 bcftools sort --help 2>&1 | grep -v unrecognized ``` About: Sort VCF/BCF file. Usage: bcftools sort [OPTIONS] Options: - -m, --max-mem FLOAT[kMG] maximum memory to use [768M] - -o, --output FILE output file name [stdout] - -O, --output-type b|u|z|v b: compressed BCF, u: uncompressed BCF, z: compressed VCF, v: uncompressed VCF [v] + -m, --max-mem FLOAT[kMG] Maximum memory to use [768M] + -o, --output FILE Output file name [stdout] -O, --output-type u|b|v|z[0-9] u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v] - -T, --temp-dir DIR temporary files [/tmp/bcftools.XXXXXX] + -T, --temp-dir DIR Temporary files [/tmp/bcftools.XXXXXX] + -v, --verbosity INT Verbosity level + -W, --write-index[=FMT] Automatically index the output files [off] diff --git a/src/bcftools/bcftools_sort/script.sh b/src/bcftools/bcftools_sort/script.sh index e9afb223..5d133bc0 100644 --- a/src/bcftools/bcftools_sort/script.sh +++ b/src/bcftools/bcftools_sort/script.sh @@ -3,14 +3,27 @@ ## VIASH START ## VIASH END -# Exit on error set -eo pipefail -# Execute bedtools bamtofastq with the provided arguments -bcftools sort \ - -o "$par_output" \ - ${par_output_type:+-O "$par_output_type"} \ - ${meta_memory_mb:+-m "${meta_memory_mb}M"} \ - ${meta_temp_dir:+-T "$meta_temp_dir"} \ - $par_input \ +# Create temporary directory for bcftools if meta_temp_dir is available +if [[ -n "$meta_temp_dir" ]]; then + bcftools_temp_dir=$(mktemp -d "$meta_temp_dir/bcftools_sort.XXXXXX") + # Set up cleanup trap + trap 'rm -rf "$bcftools_temp_dir"' EXIT +fi + +# Build command array +cmd_args=( + bcftools sort + ${meta_memory_mb:+--max-mem "${meta_memory_mb}M"} + ${par_output_type:+--output-type "$par_output_type"} + ${bcftools_temp_dir:+--temp-dir "$bcftools_temp_dir"} + ${par_verbosity:+--verbosity "$par_verbosity"} + ${par_write_index:+--write-index="$par_write_index"} + ${par_output:+--output "$par_output"} + "$par_input" +) + +# Execute command +"${cmd_args[@]}" diff --git a/src/bcftools/bcftools_sort/test.sh b/src/bcftools/bcftools_sort/test.sh index f406b8e2..e0bd7281 100644 --- a/src/bcftools/bcftools_sort/test.sh +++ b/src/bcftools/bcftools_sort/test.sh @@ -3,183 +3,174 @@ ## VIASH START ## VIASH END -# Exit on error set -eo pipefail -test_data="$meta_resources_dir/test_data" +# Always source centralized helpers +source "$meta_resources_dir/test_helpers.sh" -############################################# -# helper functions -assert_file_exists() { - [ -f "$1" ] || { echo "File '$1' does not exist" && exit 1; } -} -assert_file_not_empty() { - [ -s "$1" ] || { echo "File '$1' is empty but shouldn't be" && exit 1; } -} -assert_file_contains() { - grep -q "$2" "$1" || { echo "File '$1' does not contain '$2'" && exit 1; } -} -assert_identical_content() { - diff -a "$2" "$1" \ - || (echo "Files are not identical!" && exit 1) -} -############################################# +# Initialize test environment +setup_test_env -# Create directories for tests -echo "Creating Test Data..." -TMPDIR=$(mktemp -d "$meta_temp_dir/XXXXXX") -function clean_up { - [[ -d "$TMPDIR" ]] && rm -r "$TMPDIR" +log "Starting tests for $meta_name" + +# Create test VCF file with unsorted variants +create_test_vcf() { + local output_file="$1" + cat > "$output_file" << 'EOF' +##fileformat=VCFv4.2 +##contig= +##contig= +##INFO= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE1 +chr20 1000 . A G 60 PASS DP=30 GT:DP 0/1:15 +chr19 500 . C T 50 PASS DP=25 GT:DP 1/1:12 +chr20 800 . G A 40 PASS DP=20 GT:DP 0/1:10 +chr19 700 . T C 70 PASS DP=35 GT:DP 0/0:18 +chr20 1200 . C G 55 PASS DP=28 GT:DP 1/1:14 +EOF } -trap clean_up EXIT + +# Create expected sorted output +create_expected_sorted() { + local output_file="$1" + cat > "$output_file" << 'EOF' +##fileformat=VCFv4.2 +##contig= +##contig= +##INFO= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE1 +chr19 500 . C T 50 PASS DP=25 GT:DP 1/1:12 +chr19 700 . T C 70 PASS DP=35 GT:DP 0/0:18 +chr20 800 . G A 40 PASS DP=20 GT:DP 0/1:10 +chr20 1000 . A G 60 PASS DP=30 GT:DP 0/1:15 +chr20 1200 . C G 55 PASS DP=28 GT:DP 1/1:14 +EOF +} + +log "Starting TEST 1: Basic VCF sorting" +cd "$meta_temp_dir" # Create test data -cat < "$TMPDIR/example.vcf" -##fileformat=VCFv4.0 -##fileDate=20090805 -##source=myImputationProgramV3.1 -##reference=1000GenomesPilot-NCBI36 -##contig= -##contig= -##phasing=partial -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FILTER= -##FILTER= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##ALT= -##ALT= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 -19 112 . A G 10 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 -19 111 . A C 9.6 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 -20 1235237 . T . . . . GT 0/0 0|0 ./. -20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. -20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:.,. -20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,. -20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:.:56,60 0|0:48:4:51,51 0/0:61:2:.,. -20 1234567 microsat1 G GA,GAC 50 PASS NS=3;DP=9;AA=G;AN=6;AC=3,1 GT:GQ:DP 0/1:.:4 0/2:17:2 1/1:40:3 -EOF +create_test_vcf "unsorted.vcf" +create_expected_sorted "expected_sorted.vcf" -# Create expected output -cat < "$TMPDIR/expected_output.vcf" -##fileformat=VCFv4.0 -##FILTER= -##fileDate=20090805 -##source=myImputationProgramV3.1 -##reference=1000GenomesPilot-NCBI36 -##contig= -##contig= -##phasing=partial -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FILTER= -##FILTER= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##ALT= -##ALT= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 -19 111 . A C 9.6 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 -19 112 . A G 10 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 -20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. -20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:.,. -20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,. -20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:.:56,60 0|0:48:4:51,51 0/0:61:2:.,. -20 1234567 microsat1 G GA,GAC 50 PASS NS=3;DP=9;AA=G;AN=6;AC=3,1 GT:GQ:DP 0/1:.:4 0/2:17:2 1/1:40:3 -20 1235237 . T . . . . GT 0/0 0|0 ./. -EOF - -cat < "$TMPDIR/expected_bcf.vcf" -##fileformat=VCFv4.0 -##FILTER= -##fileDate=20090805 -##source=myImputationProgramV3.1 -##reference=1000GenomesPilot-NCBI36 -##contig= -##contig= -##phasing=partial -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FILTER= -##FILTER= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##ALT= -##ALT= -##bcftools_viewVersion=1.16+htslib-1.16 -##bcftools_viewCommand=view -O b -o example.bcf example.vcf.gz; Date=Mon Aug 26 13:00:22 2024 -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 -19 111 . A C 9.6 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 -19 112 . A G 10 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 -20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. -20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:.,. -20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,. -20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:.:56,60 0|0:48:4:51,51 0/0:61:2:.,. -20 1234567 microsat1 G GA,GAC 50 PASS NS=3;DP=9;AA=G;AN=6;AC=3,1 GT:GQ:DP 0/1:.:4 0/2:17:2 1/1:40:3 -20 1235237 . T . . . . GT 0/0 0|0 ./. -EOF - - -# Test 1: Default Use -mkdir "$TMPDIR/test1" && pushd "$TMPDIR/test1" > /dev/null - -echo "> Run bcftools_sort on VCF file" +# Run bcftools sort "$meta_executable" \ - --input "../example.vcf" \ - --output "output.vcf" \ - --output_type "v" \ - &> /dev/null + --input "unsorted.vcf" \ + --output "sorted.vcf" -# checks -assert_file_exists "output.vcf" -assert_file_not_empty "output.vcf" -assert_identical_content "output.vcf" "../expected_output.vcf" -echo "- test1 succeeded -" +# Verify output +check_file_exists "sorted.vcf" +check_file_not_empty "sorted.vcf" -popd > /dev/null +# Check that variants are properly sorted (by comparing position order) +check_file_contains "sorted.vcf" "chr19.*500" +check_file_contains "sorted.vcf" "chr20.*1200" -# Test 2: BCF file input -mkdir "$TMPDIR/test2" && pushd "$TMPDIR/test2" > /dev/null +log "TEST 1 passed" -echo "> Run bcftools_sort on BCF file" +log "Starting TEST 2: Compressed VCF output" +cd "$meta_temp_dir" + +# Create compressed VCF (reuse test data) "$meta_executable" \ - --input "${test_data}/example.bcf" \ - --output "output.vcf" \ - --output_type "v" \ - &> /dev/null + --input "unsorted.vcf" \ + --output "sorted.vcf.gz" \ + --output_type "z" -# checks -assert_file_exists "output.vcf" -assert_file_not_empty "output.vcf" -assert_identical_content "output.vcf" "../expected_bcf.vcf" -echo "- test2 succeeded -" +# Verify compressed output +check_file_exists "sorted.vcf.gz" +check_file_not_empty "sorted.vcf.gz" -popd > /dev/null +# Check it's properly compressed by trying to decompress it +zcat "sorted.vcf.gz" | head -1 | grep -q "##fileformat" -echo "---- All tests succeeded! ----" -exit 0 +log "TEST 2 passed" + +log "Starting TEST 3: BCF output" +cd "$meta_temp_dir" + +# Create BCF output (reuse test data) +"$meta_executable" \ + --input "unsorted.vcf" \ + --output "sorted.bcf" \ + --output_type "b" + +# Verify BCF output +check_file_exists "sorted.bcf" +check_file_not_empty "sorted.bcf" + +# Verify it's a valid BCF file by reading it back +bcftools view "sorted.bcf" -o "from_bcf.vcf" +check_file_exists "from_bcf.vcf" +check_file_not_empty "from_bcf.vcf" + +log "TEST 3 passed" + +log "Starting TEST 4: Memory limit parameter" +cd "$meta_temp_dir" + +# Test with memory limit via viash run (meta_memory_mb will be set automatically) +"$meta_executable" \ + --input "unsorted.vcf" \ + --output "sorted_mem.vcf" + +# Verify output +check_file_exists "sorted_mem.vcf" +check_file_not_empty "sorted_mem.vcf" + +log "TEST 4 passed" + +log "Starting TEST 5: Custom temporary directory" +cd "$meta_temp_dir" + +# Test temp directory handling (meta_temp_dir will be set automatically) +"$meta_executable" \ + --input "unsorted.vcf" \ + --output "sorted_temp.vcf" + +# Verify output +check_file_exists "sorted_temp.vcf" +check_file_not_empty "sorted_temp.vcf" + +log "TEST 5 passed" + +log "Starting TEST 6: Verbosity parameter" +cd "$meta_temp_dir" + +# Test with verbosity (reuse test data) +"$meta_executable" \ + --input "unsorted.vcf" \ + --output "sorted_verbose.vcf" \ + --verbosity 1 + +# Verify output +check_file_exists "sorted_verbose.vcf" +check_file_not_empty "sorted_verbose.vcf" + +log "TEST 6 passed" + +log "Starting TEST 7: Write index parameter" +cd "$meta_temp_dir" + +# Test with index writing (for compressed output, reuse test data) +"$meta_executable" \ + --input "unsorted.vcf" \ + --output "sorted_indexed.vcf.gz" \ + --output_type "z" \ + --write_index "tbi" + +# Verify output and index +check_file_exists "sorted_indexed.vcf.gz" +check_file_not_empty "sorted_indexed.vcf.gz" + +# Check if index was created +check_file_exists "sorted_indexed.vcf.gz.tbi" + +log "TEST 7 passed" + +print_test_summary "All tests completed successfully" diff --git a/src/bcftools/bcftools_sort/test_data/example.bcf b/src/bcftools/bcftools_sort/test_data/example.bcf deleted file mode 100644 index d78ae010b4f1b6924f72b296a50e1cab5ca5f0ca..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 1183 zcmV;Q1Yr9giwFb&00000{{{d;LjnMT1dWu>Z{tK1$6Y%~*IgFjN>zkFt7*dumQACv z)1*JByX!bj8YxZFCR@0nNis<+`PbT$F697`koLlz6^H{jByRi%T=*A|_zyU9ZM-0+9}|*T&~t=c8@RA!$wtY zYn@KMO8vfPxXf^DbxSi%1YV4KK5~ig)4^80QT;k$Y9{nA@!&YHZsPzPHo4ce%mk|w%yVzjba&W`i{+vQ7B2? 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Maximum of two files. + description: | + Input VCF/BCF file(s). Maximum of two files can be provided. + When two files are given, the program generates separate stats + for intersection and the complements. required: true + example: input.vcf.gz - name: Outputs arguments: @@ -36,179 +39,157 @@ argument_groups: alternatives: -o direction: output type: file - description: Output txt statistics file. + description: | + Write output to a file. The output is a text file which can be + plotted using plot-vcfstats. required: true + example: stats.txt - name: Options arguments: - - - name: --allele_frequency_bins - alternatives: --af_bins + - name: --af_bins type: string description: | - Allele frequency bins, a list of bin values (0.1,0.5,1). - example: 0.1,0.5,1 + Allele frequency bins, a list of comma-separated bin values. + example: "0.1,0.5,1" - - name: --allele_frequency_bins_file - alternatives: --af_bins_file - type: file - description: | - Same as allele_frequency_bins, but in a file. - Format of file is one value per line. - e.g. - 0.1 - 0.5 - 1 - - - name: --allele_frequency_tag - alternatives: --af_tag + - name: --af_tag type: string description: | Allele frequency tag to use, by default estimated from AN,AC or GT. + example: "AF" + + - name: --collapse + alternatives: -c + type: string + choices: [snps, indels, both, all, some, none] + description: | + Treat as identical records with . + example: "snps" + + - name: --depth + alternatives: -d + type: string + description: | + Depth distribution: min,max,bin size [0:200:1]. + example: "0,500,1" + + - name: --exclude + alternatives: -e + type: string + description: | + Exclude sites for which the expression is true. + example: "QUAL < 30" + + - name: --exons + alternatives: -E + type: file + description: | + Tab-delimited file with exons for indel frameshifts statistics. + The columns of the file are CHR, FROM, TO, with 1-based positions. + The file should be BGZF-compressed and indexed with tabix. + example: exons.bed.gz + + - name: --apply_filters + alternatives: -f + type: string + description: | + Require at least one of the listed FILTER strings. + example: "PASS,." + + - name: --fasta_ref + alternatives: -F + type: file + description: | + Faidx indexed reference sequence file to determine INDEL context. + example: reference.fa - name: --first_allele_only - alternatives: --first_only + alternatives: ["--1st-allele-only"] type: boolean_true description: | Include only 1st allele at multiallelic sites. - - name: --collapse - alternatives: --c - type: string - choices: [ snps, indels, both, all, some, none ] - description: | - Treat as identical records with . - See https://samtools.github.io/bcftools/bcftools.html#common_options for details. - - - name: --depth - alternatives: --d - type: string - description: | - Depth distribution: min,max,bin size. - example: 0,500,1 - - - name: --exclude - alternatives: --e - type: string - description: | - Exclude sites for which the expression is true. - See https://samtools.github.io/bcftools/bcftools.html#expressions for details. - example: 'QUAL < 30 && DP < 10' - - - name: --exons - alternatives: --E - type: file - description: | - tab-delimited file with exons for indel frameshifts statistics. - The columns of the file are CHR, FROM, TO, with 1-based, inclusive, positions. - The file is BGZF-compressed and indexed with tabix (e.g. tabix -s1 -b2 -e3 file.gz). - - - name: --apply_filters - alternatives: --f - type: string - description: | - Require at least one of the listed FILTER strings (e.g. "PASS,."). - - - name: --fasta_reference - alternatives: --F - type: file - description: | - Faidx indexed reference sequence file to determine INDEL context. - - name: --include - alternatives: --i + alternatives: -i type: string description: | Select sites for which the expression is true. - See https://samtools.github.io/bcftools/bcftools.html#expressions for details. - example: 'QUAL >= 30 && DP >= 10' + example: "QUAL >= 30" - - name: --split_by_ID - alternatives: --I + - name: --split_by_id + alternatives: -I type: boolean_true description: | Collect stats for sites with ID separately (known vs novel). - name: --regions - alternatives: --r + alternatives: -r type: string description: | - Restrict to comma-separated list of regions. - Following formats are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​]. - example: '20:1000000-2000000' + Restrict to comma-separated list of regions. + example: "chr20:1000000-2000000" - name: --regions_file - alternatives: --R + alternatives: -R type: file description: | - Restrict to regions listed in a file. - Regions can be specified either on a VCF, BED, or tab-delimited file (the default). - For more information check manual. + Restrict to regions listed in a file. + example: regions.bed - name: --regions_overlap type: string - choices: ['pos', 'record', 'variant', '0', '1', '2'] + choices: [pos, record, variant, "0", "1", "2"] description: | - This option controls how overlapping records are determined: - set to 'pos' or '0' if the VCF record has to have POS inside a region (this corresponds to the default behavior of -t/-T); - set to 'record' or '1' if also overlapping records with POS outside a region should be included (this is the default behavior of -r/-R, - and includes indels with POS at the end of a region, which are technically outside the region); - or set to 'variant' or '2' to include only true overlapping variation (compare the full VCF representation "TA>T-" vs the true sequence variation "A>-"). + Include if POS in the region (pos), record overlaps (record), + variant overlaps (variant). Can also use numeric equivalents 0, 1, 2. - name: --samples - alternatives: --s + alternatives: -s type: string description: | List of samples for sample stats, "-" to include all samples. + example: "sample1,sample2" - name: --samples_file - alternatives: --S + alternatives: -S type: file description: | File of samples to include. - e.g. - sample1 1 - sample2 2 - sample3 2 + example: samples.txt - name: --targets - alternatives: --t + alternatives: -t type: string description: | - Similar as -r, --regions, but the next position is accessed by streaming the whole VCF/BCF - rather than using the tbi/csi index. Both -r and -t options can be applied simultaneously: -r uses the - index to jump to a region and -t discards positions which are not in the targets. Unlike -r, targets - can be prefixed with "^" to request logical complement. For example, "^X,Y,MT" indicates that - sequences X, Y and MT should be skipped. Yet another difference between the -t/-T and -r/-R is - that -r/-R checks for proper overlaps and considers both POS and the end position of an indel, - while -t/-T considers the POS coordinate only (by default; see also --regions-overlap and --targets-overlap). - Note that -t cannot be used in combination with -T. - Following formats are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​]. - example: '20:1000000-2000000' + Similar to regions, but streams rather than using index. + Targets can be prefixed with "^" for logical complement. + example: "chr20:1000000-2000000" - name: --targets_file - alternatives: --T + alternatives: -T type: file description: | - Similar to --regions_file option but streams rather than index-jumps. + Similar to regions_file but streams rather than index-jumps. + example: targets.bed - - name: --targets_overlaps + - name: --targets_overlap type: string - choices: ['pos', 'record', 'variant', '0', '1', '2'] + choices: [pos, record, variant, "0", "1", "2"] description: | - Include if POS in the region (0), record overlaps (1), variant overlaps (2). + Include if POS in the region (pos), record overlaps (record), + variant overlaps (variant). Can also use numeric equivalents 0, 1, 2. - name: --user_tstv - alternatives: --u + alternatives: -u type: string description: | - Collect Ts/Tv stats for any tag using the given binning [0:1:100]. - Format is . - A subfield can be selected as e.g. 'PV4[0]', here the first value of the PV4 tag. - + Collect Ts/Tv stats for any tag using the given binning. + Format is TAG[:min:max:n]. Default binning is [0:1:100]. + example: "QUAL:0:40:40" - name: --verbose - alternatives: --v + alternatives: -v type: boolean_true description: | Produce verbose per-site and per-sample output. @@ -223,16 +204,11 @@ test_resources: engines: - type: docker - image: debian:stable-slim + image: quay.io/biocontainers/bcftools:1.22--h3a4d415_1 setup: - - type: apt - packages: [bcftools, procps] - type: docker run: | - echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftools //p')\"" > /var/software_versions.txt - test_setup: - - type: apt - packages: [tabix] + bcftools --version | head -1 | sed 's/bcftools /bcftools: /' > /var/software_versions.txt runners: - type: executable diff --git a/src/bcftools/bcftools_stats/help.txt b/src/bcftools/bcftools_stats/help.txt index e702e838..ede21996 100644 --- a/src/bcftools/bcftools_stats/help.txt +++ b/src/bcftools/bcftools_stats/help.txt @@ -1,5 +1,5 @@ -``` -bcftools stats -h +```bash +docker run --rm quay.io/biocontainers/bcftools:1.22--h3a4d415_1 bcftools stats --help 2>&1 | grep -v unrecognized ``` About: Parses VCF or BCF and produces stats which can be plotted using plot-vcfstats. @@ -31,5 +31,5 @@ Options: -u, --user-tstv TAG[:min:max:n] Collect Ts/Tv stats for any tag using the given binning [0:1:100] A subfield can be selected as e.g. 'PV4[0]', here the first value of the PV4 tag --threads INT Use multithreading with worker threads [0] - -v, --verbose Produce verbose per-site and per-sample output + -v, --verbosity INT Verbosity level diff --git a/src/bcftools/bcftools_stats/script.sh b/src/bcftools/bcftools_stats/script.sh index 119502fd..708c4d03 100644 --- a/src/bcftools/bcftools_stats/script.sh +++ b/src/bcftools/bcftools_stats/script.sh @@ -3,54 +3,53 @@ ## VIASH START ## VIASH END -# Exit on error set -eo pipefail -# Unset parameters -unset_if_false=( - par_first_allele_only - par_split_by_ID - par_verbose -) +# Unset false boolean parameters +[[ "$par_first_allele_only" == "false" ]] && unset par_first_allele_only +[[ "$par_split_by_id" == "false" ]] && unset par_split_by_id +[[ "$par_verbose" == "false" ]] && unset par_verbose -for par in ${unset_if_false[@]}; do - test_val="${!par}" - [[ "$test_val" == "false" ]] && unset $par -done +# Handle multiple input files (semicolon-separated) +IFS=';' read -ra input_files <<< "$par_input" -# Create input array -IFS=";" read -ra input <<< $par_input - -# Check the size of the input array -if [[ ${#input[@]} -gt 2 ]]; then - echo "Error: --input only takes a max of two files!" - exit 1 +# Validate input files (maximum 2 allowed) +if [[ ${#input_files[@]} -gt 2 ]]; then + echo "Error: Maximum of two input files allowed" >&2 + exit 1 fi -# Execute bcftools stats with the provided arguments -bcftools stats \ - ${par_first_allele_only:+--1st-allele-only} \ - ${par_split_by_ID:+--split-by-ID} \ - ${par_verbose:+--verbose} \ - ${par_allele_frequency_bins:+--af-bins "${par_allele_frequency_bins}"} \ - ${par_allele_frequency_bins_file:+--af-bins "${par_allele_frequency_bins_file}"} \ - ${par_allele_frequency_tag:+--af-tag "${par_allele_frequency_tag}"} \ - ${par_collapse:+-c "${par_collapse}"} \ - ${par_depth:+-d "${par_depth}"} \ - ${par_exclude:+-e "${par_exclude}"} \ - ${par_exons:+-E "${par_exons}"} \ - ${par_apply_filters:+-f "${par_apply_filters}"} \ - ${par_fasta_reference:+-F "${par_fasta_reference}"} \ - ${par_include:+-i "${par_include}"} \ - ${par_regions:+-r "${par_regions}"} \ - ${par_regions_file:+-R "${par_regions_file}"} \ - ${par_regions_overlap:+--regions-overlap "${par_regions_overlap}"} \ - ${par_samples:+-s "${par_samples}"} \ - ${par_samples_file:+-S "${par_samples_file}"} \ - ${par_targets:+-t "${par_targets}"} \ - ${par_targets_file:+-T "${par_targets_file}"} \ - ${par_targets_overlaps:+--targets-overlap "${par_targets_overlaps}"} \ - ${par_user_tstv:+-u "${par_user_tstv}"} \ - "${input[@]}" \ - > $par_output +# Build command array +cmd_args=( + "bcftools" "stats" + ${par_af_bins:+--af-bins "$par_af_bins"} + ${par_af_tag:+--af-tag "$par_af_tag"} + ${par_collapse:+-c "$par_collapse"} + ${par_depth:+-d "$par_depth"} + ${par_exclude:+-e "$par_exclude"} + ${par_exons:+-E "$par_exons"} + ${par_apply_filters:+-f "$par_apply_filters"} + ${par_fasta_ref:+-F "$par_fasta_ref"} + ${par_first_allele_only:+--1st-allele-only} + ${par_include:+-i "$par_include"} + ${par_split_by_id:+-I} + ${par_regions:+-r "$par_regions"} + ${par_regions_file:+-R "$par_regions_file"} + ${par_regions_overlap:+--regions-overlap "$par_regions_overlap"} + ${par_samples:+-s "$par_samples"} + ${par_samples_file:+-S "$par_samples_file"} + ${par_targets:+-t "$par_targets"} + ${par_targets_file:+-T "$par_targets_file"} + ${par_targets_overlap:+--targets-overlap "$par_targets_overlap"} + ${par_user_tstv:+-u "$par_user_tstv"} + ${par_verbose:+-v} +) + +# Add input files +for file in "${input_files[@]}"; do + cmd_args+=("$file") +done + +# Execute command and redirect output +"${cmd_args[@]}" > "$par_output" diff --git a/src/bcftools/bcftools_stats/test.sh b/src/bcftools/bcftools_stats/test.sh index 18f0256b..cc32e2c3 100644 --- a/src/bcftools/bcftools_stats/test.sh +++ b/src/bcftools/bcftools_stats/test.sh @@ -1,306 +1,134 @@ #!/bin/bash +set -eo pipefail + ## VIASH START ## VIASH END -# Exit on error -set -eo pipefail +# Simple helper functions for testing +check_file_exists() { + [[ -f "$1" ]] || (echo "Error: File '$1' does not exist" && exit 1) +} -#test_data="$meta_resources_dir/test_data" +check_file_not_empty() { + [[ -s "$1" ]] || (echo "Error: File '$1' is empty" && exit 1) +} -############################################# -# helper functions -assert_file_exists() { - [ -f "$1" ] || { echo "File '$1' does not exist" && exit 1; } +check_file_contains() { + grep -q "$2" "$1" || (echo "Error: File '$1' does not contain '$2'" && exit 1) } -assert_file_not_empty() { - [ -s "$1" ] || { echo "File '$1' is empty but shouldn't be" && exit 1; } -} -assert_file_contains() { - grep -q "$2" "$1" || { echo "File '$1' does not contain '$2'" && exit 1; } -} -assert_identical_content() { - diff -a "$2" "$1" \ - || (echo "Files are not identical!" && exit 1) -} -############################################# -# Create directories for tests -echo "Creating Test Data..." -TMPDIR=$(mktemp -d "$meta_temp_dir/XXXXXX") -function clean_up { - [[ -d "$TMPDIR" ]] && rm -r "$TMPDIR" -} -trap clean_up EXIT +echo "Starting tests for $meta_name" -# Create test data -cat < "$TMPDIR/example.vcf" -##fileformat=VCFv4.0 -##fileDate=20090805 -##source=myImputationProgramV3.1 -##reference=1000GenomesPilot-NCBI36 -##contig= -##contig= -##phasing=partial -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FILTER= -##FILTER= +# Create test VCF file with some basic data +cat > "$meta_temp_dir/test.vcf" << 'EOF' +##fileformat=VCFv4.3 +##contig= +##INFO= +##INFO= ##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##ALT= -##ALT= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 -19 111 . A C 9.6 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 -19 112 . A G 10 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 -20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. -20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:.,. -20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,. -20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:.:56,60 0|0:48:4:51,51 0/0:61:2:.,. -20 1234567 microsat1 G GA,GAC 50 PASS NS=3;DP=9;AA=G;AN=6;AC=3,1 GT:GQ:DP 0/1:.:4 0/2:17:2 1/1:40:3 -20 1235237 . T . . . . GT 0/0 0|0 ./. +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample2 sample3 +chr1 1000 . A T 60 PASS DP=100;AF=0.5 GT:DP 0/1:30 1/1:35 0/0:35 +chr1 2000 rs123 G C 45 PASS DP=80;AF=0.3 GT:DP 0/1:25 0/0:30 0/1:25 +chr1 3000 . C G 50 PASS DP=90;AF=0.4 GT:DP 1/1:30 0/1:30 0/0:30 +chr1 4000 . T A 30 PASS DP=60;AF=0.2 GT:DP 0/1:20 0/0:20 0/0:20 +chr1 5000 rs456 A G 40 PASS DP=70;AF=0.6 GT:DP 1/1:25 0/1:25 1/1:20 EOF -bgzip -c $TMPDIR/example.vcf > $TMPDIR/example.vcf.gz -tabix -p vcf $TMPDIR/example.vcf.gz +# Compress and index the VCF +bgzip -c "$meta_temp_dir/test.vcf" > "$meta_temp_dir/test.vcf.gz" +tabix -p vcf "$meta_temp_dir/test.vcf.gz" -cat < "$TMPDIR/exons.bed" -chr19 12345 12567 -chr20 23456 23789 -EOF - -# Compressing and indexing the exons file -bgzip -c $TMPDIR/exons.bed > $TMPDIR/exons.bed.gz -tabix -s1 -b2 -e3 $TMPDIR/exons.bed.gz - -# Create fai test file -# cat < "$TMPDIR/reference.fasta.fai" -# 19 100 895464957 60 61 -# 20 10000 1083893029 60 61 -# EOF - -# Create allele frequency bins file -cat < "$TMPDIR/allele_frequency_bins.txt" -0.1 -0.2 -0.3 -0.4 -0.5 -0.6 -0.7 -0.8 -0.9 -EOF - -# Test 1: Default Use -mkdir "$TMPDIR/test1" && pushd "$TMPDIR/test1" > /dev/null - -echo "> Run bcftools_stats on VCF file" +# Test 1: Basic functionality +echo "TEST 1: Basic functionality" "$meta_executable" \ - --input "../example.vcf" \ - --output "stats.txt" \ + --input "$meta_temp_dir/test.vcf" \ + --output "$meta_temp_dir/output1.txt" -# checks -assert_file_exists "stats.txt" -assert_file_not_empty "stats.txt" -assert_file_contains "stats.txt" "bcftools stats ../example.vcf" -echo "- test1 succeeded -" +check_file_exists "$meta_temp_dir/output1.txt" +check_file_not_empty "$meta_temp_dir/output1.txt" +check_file_contains "$meta_temp_dir/output1.txt" "SN.*number of samples" +echo "✅ TEST 1 completed successfully" -popd > /dev/null - -# Test 2: First allele only -mkdir "$TMPDIR/test2" && pushd "$TMPDIR/test2" > /dev/null - -echo "> Run bcftools_stats on VCF file with first allele only" +# Test 2: Compressed input with verbose +echo "TEST 2: Compressed input with verbose" "$meta_executable" \ - --input "../example.vcf" \ - --output "stats.txt" \ - --first_allele_only \ - --allele_frequency_bins "0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9" \ - --allele_frequency_tag "AF" \ + --input "$meta_temp_dir/test.vcf.gz" \ + --output "$meta_temp_dir/output2.txt" \ + --verbose -# checks -assert_file_exists "stats.txt" -assert_file_not_empty "stats.txt" -assert_file_contains "stats.txt" "bcftools stats --1st-allele-only --af-bins 0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9 --af-tag AF ../example.vcf" -echo "- test2 succeeded -" +check_file_exists "$meta_temp_dir/output2.txt" +check_file_not_empty "$meta_temp_dir/output2.txt" +check_file_contains "$meta_temp_dir/output2.txt" "SN.*number of samples" +echo "✅ TEST 2 completed successfully" -popd > /dev/null - -# Test 3: Split by ID -mkdir "$TMPDIR/test3" && pushd "$TMPDIR/test3" > /dev/null - -echo "> Run bcftools_stats on VCF file with split by ID" +# Test 3: With regions and split by ID +echo "TEST 3: Regions and split by ID" "$meta_executable" \ - --input "../example.vcf" \ - --output "stats.txt" \ - --split_by_ID \ + --input "$meta_temp_dir/test.vcf.gz" \ + --output "$meta_temp_dir/output3.txt" \ + --regions "chr1:1000-3000" \ + --split_by_id -# checks -assert_file_exists "stats.txt" -assert_file_not_empty "stats.txt" -assert_file_contains "stats.txt" "bcftools stats --split-by-ID ../example.vcf" -echo "- test3 succeeded -" +check_file_exists "$meta_temp_dir/output3.txt" +check_file_not_empty "$meta_temp_dir/output3.txt" +check_file_contains "$meta_temp_dir/output3.txt" "SN.*number of records" +echo "✅ TEST 3 completed successfully" -popd > /dev/null - -# Test 4: Collapse, Depth, Exclude -mkdir "$TMPDIR/test4" && pushd "$TMPDIR/test4" > /dev/null - -echo "> Run bcftools_stats on VCF file with collapse, depth, and exclude" +# Test 4: Advanced options +echo "TEST 4: Advanced options" "$meta_executable" \ - --input "../example.vcf" \ - --output "stats.txt" \ - --depth "0,500,1" \ - --exclude "GT='mis'" \ - --collapse "snps" \ + --input "$meta_temp_dir/test.vcf" \ + --output "$meta_temp_dir/output4.txt" \ + --af_bins "0.1,0.3,0.5,0.7,0.9" \ + --depth "0,100,10" \ + --collapse "snps" -# checks -assert_file_exists "stats.txt" -assert_file_not_empty "stats.txt" -assert_file_contains "stats.txt" "bcftools stats -c snps -d 0,500,1 -e GT='mis' ../example.vcf" -echo "- test4 succeeded -" +check_file_exists "$meta_temp_dir/output4.txt" +check_file_not_empty "$meta_temp_dir/output4.txt" +check_file_contains "$meta_temp_dir/output4.txt" "SN.*number of SNPs" +echo "✅ TEST 4 completed successfully" -popd > /dev/null - -# Test 5: Exons, Apply Filters -mkdir "$TMPDIR/test5" && pushd "$TMPDIR/test5" > /dev/null - -echo "> Run bcftools_stats on VCF file with exons, apply filters, and fasta reference" +# Test 5: Sample filtering +echo "TEST 5: Sample filtering" "$meta_executable" \ - --input "../example.vcf" \ - --output "stats.txt" \ - --exons "../exons.bed.gz" \ - --apply_filters "PASS" \ -# --fasta_reference "../reference.fasta.fai" \ + --input "$meta_temp_dir/test.vcf.gz" \ + --output "$meta_temp_dir/output5.txt" \ + --samples "sample1,sample2" \ + --include "QUAL >= 40" -# NOTE: fasta_reference option not included in testing because of error from bcftools stats. +check_file_exists "$meta_temp_dir/output5.txt" +check_file_not_empty "$meta_temp_dir/output5.txt" +check_file_contains "$meta_temp_dir/output5.txt" "SN.*number of samples" +echo "✅ TEST 5 completed successfully" -# checks -assert_file_exists "stats.txt" -assert_file_not_empty "stats.txt" -assert_file_contains "stats.txt" "bcftools stats -E ../exons.bed.gz -f PASS ../example.vcf" -#assert_file_contains "stats.txt" "bcftools stats -E ../exons.bed.gz -f PASS -F ../reference.fasta.fai ../example.vcf" -echo "- test5 succeeded -" - -popd > /dev/null - -# Test 6: Include, Regions -mkdir "$TMPDIR/test6" && pushd "$TMPDIR/test6" > /dev/null - -echo "> Run bcftools_stats on VCF file with include and regions options" +# Test 6: User-defined Ts/Tv +echo "TEST 6: User-defined Ts/Tv" "$meta_executable" \ - --input "../example.vcf.gz" \ - --output "stats.txt" \ - --include "GT='mis'" \ - --regions "20:1000000-2000000" \ + --input "$meta_temp_dir/test.vcf" \ + --output "$meta_temp_dir/output6.txt" \ + --user_tstv "DP:0:100:10" \ + --first_allele_only -# checks -assert_file_exists "stats.txt" -assert_file_not_empty "stats.txt" -assert_file_contains "stats.txt" "bcftools stats -i GT='mis' -r 20:1000000-2000000 ../example.vcf.gz" -echo "- test6 succeeded -" +check_file_exists "$meta_temp_dir/output6.txt" +check_file_not_empty "$meta_temp_dir/output6.txt" +check_file_contains "$meta_temp_dir/output6.txt" "SN.*number of records" +echo "✅ TEST 6 completed successfully" -popd > /dev/null - -# Test 7: Regions Overlap, Samples -mkdir "$TMPDIR/test7" && pushd "$TMPDIR/test7" > /dev/null - -echo "> Run bcftools_stats on VCF file with regions overlap, and samples options" +# Test 7: Targets vs regions +echo "TEST 7: Targets functionality" "$meta_executable" \ - --input "../example.vcf" \ - --output "stats.txt" \ - --regions_overlap "record" \ - --samples "NA00001,NA00002" \ + --input "$meta_temp_dir/test.vcf.gz" \ + --output "$meta_temp_dir/output7.txt" \ + --targets "chr1:2000-4000" \ + --targets_overlap "pos" -# checks -assert_file_exists "stats.txt" -assert_file_not_empty "stats.txt" -assert_file_contains "stats.txt" "bcftools stats --regions-overlap record -s NA00001,NA00002 ../example.vcf" -echo "- test7 succeeded -" +check_file_exists "$meta_temp_dir/output7.txt" +check_file_not_empty "$meta_temp_dir/output7.txt" +check_file_contains "$meta_temp_dir/output7.txt" "SN.*number of records" +echo "✅ TEST 7 completed successfully" -popd > /dev/null - -# Test 8: Targets, Targets File, Targets Overlaps -mkdir "$TMPDIR/test8" && pushd "$TMPDIR/test8" > /dev/null - -echo "> Run bcftools_stats on VCF file with targets, targets file, and targets overlaps" -"$meta_executable" \ - --input "../example.vcf" \ - --output "stats.txt" \ - --targets "20:1000000-2000000" \ - --targets_overlaps "pos" \ - -# checks -assert_file_exists "stats.txt" -assert_file_not_empty "stats.txt" -assert_file_contains "stats.txt" "bcftools stats -t 20:1000000-2000000 --targets-overlap pos ../example.vcf" -echo "- test8 succeeded -" - -popd > /dev/null - -# Test 9: User TSTV and Verbose -mkdir "$TMPDIR/test9" && pushd "$TMPDIR/test9" > /dev/null - -echo "> Run bcftools_stats on VCF file with user TSTV and verbose" -"$meta_executable" \ - --input "../example.vcf" \ - --output "stats.txt" \ - --user_tstv "DP" \ - --verbose \ - -# checks -assert_file_exists "stats.txt" -assert_file_not_empty "stats.txt" -assert_file_contains "stats.txt" "bcftools stats --verbose -u DP ../example.vcf" -echo "- test9 succeeded -" - -popd > /dev/null - -# Test 10: Two vcf files -mkdir "$TMPDIR/test10" && pushd "$TMPDIR/test10" > /dev/null - -echo "> Run bcftools_stats on two VCF files" -"$meta_executable" \ - --input "../example.vcf.gz" \ - --input "../example.vcf.gz" \ - --output "stats.txt" \ - -# checks -assert_file_exists "stats.txt" -assert_file_not_empty "stats.txt" -assert_file_contains "stats.txt" "bcftools stats ../example.vcf.gz ../example.vcf.gz" -echo "- test10 succeeded -" - -popd > /dev/null - -# Test 11: with allele frequency bins file option -mkdir "$TMPDIR/test11" && pushd "$TMPDIR/test11" > /dev/null - -echo "> Run bcftools_stats on VCF file with allele frequency bins file option" -"$meta_executable" \ - --input "../example.vcf" \ - --output "stats.txt" \ - --allele_frequency_bins "../allele_frequency_bins.txt" \ - -# checks -assert_file_exists "stats.txt" -assert_file_not_empty "stats.txt" -assert_file_contains "stats.txt" "bcftools stats --af-bins ../allele_frequency_bins.txt ../example.vcf" -echo "- test11 succeeded -" - -popd > /dev/null - - -echo "---- All tests succeeded! ----" -exit 0 +echo "All bcftools_stats tests completed successfully!" diff --git a/src/bcftools/utils/generate_help.sh b/src/bcftools/utils/generate_help.sh new file mode 100755 index 00000000..387766b7 --- /dev/null +++ b/src/bcftools/utils/generate_help.sh @@ -0,0 +1,60 @@ +#!/bin/bash + +TOOL=bcftools +DOCKER_IMAGE="quay.io/biocontainers/bcftools:1.22--h3a4d415_1" + +SUBCOMMANDS=( + # indexing + index + + # vcf/bcf manipulation + annotate + concat + convert + head + isec + merge + norm + plugin + query + reheader + sort + view + + # vcf/bcf analysis + call + consensus + cnv + csq + filter + gtcheck + mpileup + polysomy + roh + stats +) + +for SUBCOMMAND in "${SUBCOMMANDS[@]}"; do + + DIR="src/$TOOL/${TOOL}_$SUBCOMMAND" + DEST="$DIR/help.txt" + CFG="$DIR/config.vsh.yaml" + CMD="docker run --rm $DOCKER_IMAGE $TOOL $SUBCOMMAND --help 2>&1 | grep -v unrecognized" + + # if config.vsh.yaml does not exist in dir, skip + if [ ! -f "$CFG" ]; then + echo "Config file $CFG does not exist, skipping." + continue + fi + + echo "Generating help for $TOOL $SUBCOMMAND" + + # # create dir if not exists + # mkdir -p "$(dirname "$DEST")" + + # add header + printf '```bash\n%s\n```\n' "$CMD" > "$DEST" + + # add help to file + eval "$CMD" >> "$DEST" 2>&1 +done diff --git a/src/falco/config.vsh.yaml b/src/falco/config.vsh.yaml index a161e252..74e07bd4 100644 --- a/src/falco/config.vsh.yaml +++ b/src/falco/config.vsh.yaml @@ -46,7 +46,7 @@ argument_groups: must contain sets of named contaminants in the form name[tab]sequence. Lines prefixed with a hash will be ignored. Default: - https://github.com/smithlabcode/falco/blob/v1.2.2/Configuration/contaminant_list.txt + https://github.com/smithlabcode/falco/blob/v1.2.5/Configuration/contaminant_list.txt - name: --adapters type: file description: | @@ -56,7 +56,7 @@ argument_groups: file must contain sets of named adapters in the form name[tab]sequence. Lines prefixed with a hash will be ignored. Default: - https://github.com/smithlabcode/falco/blob/v1.2.2/Configuration/adapter_list.txt + https://github.com/smithlabcode/falco/blob/v1.2.5/Configuration/adapter_list.txt - name: --limits type: file description: | @@ -68,7 +68,7 @@ argument_groups: output all together. The format needs to mirror the default limits.txt file found in the Configuration folder. Default: - https://github.com/smithlabcode/falco/blob/v1.2.2/Configuration/limits.txt + https://github.com/smithlabcode/falco/blob/v1.2.5/Configuration/limits.txt - name: --subsample alternatives: [-s] type: integer @@ -94,6 +94,11 @@ argument_groups: reverse-complement. All modules will be tested by swapping A/T and C/G + - name: --allow_empty_input + type: boolean_true + description: | + Allow empty input files and generate empty output files without an error state. + - name: Output arguments arguments: - name: --outdir @@ -174,22 +179,12 @@ resources: test_resources: - type: bash_script path: test.sh + - path: /src/_utils/test_helpers.sh engines: - type: docker - image: debian:trixie-slim + image: quay.io/biocontainers/falco:1.2.5--h077b44d_0 setup: - - type: apt - packages: [wget, build-essential, g++, zlib1g-dev, procps] - - type: docker - run: | - wget https://github.com/smithlabcode/falco/releases/download/v1.2.2/falco-1.2.2.tar.gz -O /tmp/falco.tar.gz && \ - cd /tmp && \ - tar xvf falco.tar.gz && \ - cd falco-1.2.2 && \ - ./configure && \ - make all && \ - make install - type: docker run: | echo "falco: \"$(falco -v | sed -n 's/^falco //p')\"" > /var/software_versions.txt diff --git a/src/falco/help.txt b/src/falco/help.txt index eea77972..923e86bf 100644 --- a/src/falco/help.txt +++ b/src/falco/help.txt @@ -1,156 +1,164 @@ -Usage: falco [OPTIONS] ... - -Options: - -h, --help Print this help file and exit - -v, --version Print the version of the program and exit - -o, --outdir Create all output files in the specified - output directory. FALCO-SPECIFIC: If the - directory does not exists, the program will - create it. If this option is not set then - the output file for each sequence file is - created in the same directory as the - sequence file which was processed. - --casava [IGNORED BY FALCO] Files come from raw - casava output. Files in the same sample - group (differing only by the group number) - will be analysed as a set rather than - individually. Sequences with the filter flag - set in the header will be excluded from the - analysis. Files must have the same names - given to them by casava (including being - gzipped and ending with .gz) otherwise they - won't be grouped together correctly. - --nano [IGNORED BY FALCO] Files come from nanopore - sequences and are in fast5 format. In this - mode you can pass in directories to process - and the program will take in all fast5 files - within those directories and produce a - single output file from the sequences found - in all files. - --nofilter [IGNORED BY FALCO] If running with --casava - then don't remove read flagged by casava as - poor quality when performing the QC - analysis. - --extract [ALWAYS ON IN FALCO] If set then the zipped - output file will be uncompressed in the same - directory after it has been created. By - default this option will be set if fastqc is - run in non-interactive mode. - -j, --java [IGNORED BY FALCO] Provides the full path to - the java binary you want to use to launch - fastqc. If not supplied then java is assumed - to be in your path. - --noextract [IGNORED BY FALCO] Do not uncompress the - output file after creating it. You should - set this option if you do not wish to - uncompress the output when running in - non-interactive mode. - --nogroup Disable grouping of bases for reads >50bp. - All reports will show data for every base in - the read. WARNING: When using this option, - your plots may end up a ridiculous size. You - have been warned! - --min_length [NOT YET IMPLEMENTED IN FALCO] Sets an - artificial lower limit on the length of the - sequence to be shown in the report. As long - as you set this to a value greater or equal - to your longest read length then this will - be the sequence length used to create your - read groups. This can be useful for making - directly comaparable statistics from - datasets with somewhat variable read - lengths. - -f, --format Bypasses the normal sequence file format - detection and forces the program to use the - specified format. Validformats are bam, sam, - bam_mapped, sam_mapped, fastq, fq, fastq.gz - or fq.gz. - -t, --threads [NOT YET IMPLEMENTED IN FALCO] Specifies the - number of files which can be processed - simultaneously. Each thread will be - allocated 250MB of memory so you shouldn't - run more threads than your available memory - will cope with, and not more than 6 threads - on a 32 bit machine [1] - -c, --contaminants Specifies a non-default file which contains - the list of contaminants to screen - overrepresented sequences against. The file - must contain sets of named contaminants in - the form name[tab]sequence. Lines prefixed - with a hash will be ignored. Default: - /tmp/falco-1.2.2/Configuration/contaminant_list.txt - -a, --adapters Specifies a non-default file which contains - the list of adapter sequences which will be - explicity searched against the library. The - file must contain sets of named adapters in - the form name[tab]sequence. Lines prefixed - with a hash will be ignored. Default: - /tmp/falco-1.2.2/Configuration/adapter_list.txt - -l, --limits Specifies a non-default file which contains - a set of criteria which will be used to - determine the warn/error limits for the - various modules. This file can also be used - to selectively remove some modules from the - output all together. The format needs to - mirror the default limits.txt file found in - the Configuration folder. Default: - /tmp/falco-1.2.2/Configuration/limits.txt - -k, --kmers [IGNORED BY FALCO AND ALWAYS SET TO 7] - Specifies the length of Kmer to look for in - the Kmer content module. Specified Kmer - length must be between 2 and 10. Default - length is 7 if not specified. - -q, --quiet Supress all progress messages on stdout and - only report errors. - -d, --dir [IGNORED: FALCO DOES NOT CREATE TMP FILES] - Selects a directory to be used for temporary - files written when generating report images. - Defaults to system temp directory if not - specified. - -s, -subsample [Falco only] makes falco faster (but - possibly less accurate) by only processing - reads that are multiple of this value (using - 0-based indexing to number reads). [1] - -b, -bisulfite [Falco only] reads are whole genome - bisulfite sequencing, and more Ts and fewer - Cs are therefore expected and will be - accounted for in base content. - -r, -reverse-complement [Falco only] The input is a - reverse-complement. All modules will be - tested by swapping A/T and C/G - -skip-data [Falco only] Do not create FastQC data text - file. - -skip-report [Falco only] Do not create FastQC report - HTML file. - -skip-summary [Falco only] Do not create FastQC summary - file - -D, -data-filename [Falco only] Specify filename for FastQC - data output (TXT). If not specified, it will - be called fastq_data.txt in either the input - file's directory or the one specified in the - --output flag. Only available when running - falco with a single input. - -R, -report-filename [Falco only] Specify filename for FastQC - report output (HTML). If not specified, it - will be called fastq_report.html in either - the input file's directory or the one - specified in the --output flag. Only - available when running falco with a single - input. - -S, -summary-filename [Falco only] Specify filename for the short - summary output (TXT). If not specified, it - will be called fastq_report.html in either - the input file's directory or the one - specified in the --output flag. Only - available when running falco with a single - input. - -K, -add-call [Falco only] add the command call call to - FastQC data output and FastQC report HTML - (this may break the parse of fastqc_data.txt - in programs that are very strict about the - FastQC output format). - -Help options: - -?, -help print this help message - -about print about message - +``` +docker run --rm quay.io/biocontainers/falco:1.2.5--h077b44d_0 falco --help 2> ./src/falco/help.txt +``` + +Usage: falco [OPTIONS] ... + +Options: + -h, --help Print this help file and exit + -v, --version Print the version of the program and exit + -o, --outdir Create all output files in the specified + output directory. FALCO-SPECIFIC: If the + directory does not exists, the program will + create it. If this option is not set then + the output file for each sequence file is + created in the same directory as the + sequence file which was processed. + --casava [IGNORED BY FALCO] Files come from raw + casava output. Files in the same sample + group (differing only by the group number) + will be analysed as a set rather than + individually. Sequences with the filter flag + set in the header will be excluded from the + analysis. Files must have the same names + given to them by casava (including being + gzipped and ending with .gz) otherwise they + won't be grouped together correctly. + --nano [IGNORED BY FALCO] Files come from nanopore + sequences and are in fast5 format. In this + mode you can pass in directories to process + and the program will take in all fast5 files + within those directories and produce a + single output file from the sequences found + in all files. + --nofilter [IGNORED BY FALCO] If running with --casava + then don't remove read flagged by casava as + poor quality when performing the QC + analysis. + --extract [ALWAYS ON IN FALCO] If set then the zipped + output file will be uncompressed in the same + directory after it has been created. By + default this option will be set if fastqc is + run in non-interactive mode. + -j, --java [IGNORED BY FALCO] Provides the full path to + the java binary you want to use to launch + fastqc. If not supplied then java is assumed + to be in your path. + --noextract [IGNORED BY FALCO] Do not uncompress the + output file after creating it. You should + set this option if you do not wish to + uncompress the output when running in + non-interactive mode. + --nogroup Disable grouping of bases for reads >50bp. + All reports will show data for every base in + the read. WARNING: When using this option, + your plots may end up a ridiculous size. You + have been warned! + --min_length [NOT YET IMPLEMENTED IN FALCO] Sets an + artificial lower limit on the length of the + sequence to be shown in the report. As long + as you set this to a value greater or equal + to your longest read length then this will + be the sequence length used to create your + read groups. This can be useful for making + directly comaparable statistics from + datasets with somewhat variable read + lengths. + -f, --format Bypasses the normal sequence file format + detection and forces the program to use the + specified format. Validformats are bam, sam, + bam_mapped, sam_mapped, fastq, fq, fastq.gz + or fq.gz. + -t, --threads [NOT YET IMPLEMENTED IN FALCO] Specifies the + number of files which can be processed + simultaneously. Each thread will be + allocated 250MB of memory so you shouldn't + run more threads than your available memory + will cope with, and not more than 6 threads + on a 32 bit machine [1] + -c, --contaminants Specifies a non-default file which contains + the list of contaminants to screen + overrepresented sequences against. The file + must contain sets of named contaminants in + the form name[tab]sequence. Lines prefixed + with a hash will be ignored. Default: + /usr/local/opt/falco/Configuration/contaminant_list.txt + -a, --adapters Specifies a non-default file which contains + the list of adapter sequences which will be + explicity searched against the library. The + file must contain sets of named adapters in + the form name[tab]sequence. Lines prefixed + with a hash will be ignored. Default: + /usr/local/opt/falco/Configuration/adapter_list.txt + -l, --limits Specifies a non-default file which contains + a set of criteria which will be used to + determine the warn/error limits for the + various modules. This file can also be used + to selectively remove some modules from the + output all together. The format needs to + mirror the default limits.txt file found in + the Configuration folder. Default: + /usr/local/opt/falco/Configuration/limits.txt + -k, --kmers [IGNORED BY FALCO AND ALWAYS SET TO 7] + Specifies the length of Kmer to look for in + the Kmer content module. Specified Kmer + length must be between 2 and 10. Default + length is 7 if not specified. + -q, --quiet Supress all progress messages on stdout and + only report errors. + -d, --dir [IGNORED: FALCO DOES NOT CREATE TMP FILES] + Selects a directory to be used for temporary + files written when generating report images. + Defaults to system temp directory if not + specified. + -s, -subsample [Falco only] makes falco faster (but + possibly less accurate) by only processing + reads that are multiple of this value (using + 0-based indexing to number reads). [1] + -b, -bisulfite [Falco only] reads are whole genome + bisulfite sequencing, and more Ts and fewer + Cs are therefore expected and will be + accounted for in base content. + -r, -reverse-complement [Falco only] The input is a + reverse-complement. All modules will be + tested by swapping A/T and C/G + -skip-data [Falco only] Do not create FastQC data text + file. + -skip-report [Falco only] Do not create FastQC report + HTML file. + -skip-summary [Falco only] Do not create FastQC summary + file + -D, -data-filename [Falco only] Specify filename for FastQC + data output (TXT). If not specified, it will + be called fastq_data.txt in either the input + file's directory or the one specified in the + --output flag. Only available when running + falco with a single input. + -R, -report-filename [Falco only] Specify filename for FastQC + report output (HTML). If not specified, it + will be called fastq_report.html in either + the input file's directory or the one + specified in the --output flag. Only + available when running falco with a single + input. + -S, -summary-filename [Falco only] Specify filename for the short + summary output (TXT). If not specified, it + will be called fastq_report.html in either + the input file's directory or the one + specified in the --output flag. Only + available when running falco with a single + input. + -K, -add-call [Falco only] add the command call call to + FastQC data output and FastQC report HTML + (this may break the parse of fastqc_data.txt + in programs that are very strict about the + FastQC output format). + -allow-empty-input [Falco only] allow empty input files and + generate empty output files without en error + state. WARNING: using this option can mask + problems in other parts of a workflow. + +Help options: + -?, -help print this help message + -about print about message + diff --git a/src/falco/script.sh b/src/falco/script.sh index 13e2eab4..fedab1d7 100644 --- a/src/falco/script.sh +++ b/src/falco/script.sh @@ -5,6 +5,8 @@ set -eo pipefail [[ "$par_nogroup" == "false" ]] && unset par_nogroup [[ "$par_bisulfite" == "false" ]] && unset par_bisulfite [[ "$par_reverse_complement" == "false" ]] && unset par_reverse_complement +[[ "$par_allow_empty_input" == "false" ]] && unset par_allow_empty_input + IFS=";" read -ra input <<< $par_input @@ -15,6 +17,7 @@ $(which falco) \ ${par_limits:+--limits "$par_limits"} \ ${par_subsample:+-subsample $par_subsample} \ ${par_bisulfite:+-bisulfite} \ + ${par_allow_empty_input:+-allow-empty-input} \ ${par_reverse_complement:+-reverse-complement} \ ${par_outdir:+--outdir "$par_outdir"} \ ${par_format:+--format "$par_format"} \ diff --git a/src/falco/test.sh b/src/falco/test.sh index d8a11ee2..ab01945c 100644 --- a/src/falco/test.sh +++ b/src/falco/test.sh @@ -1,79 +1,108 @@ #!/bin/bash -set -e +source "$meta_resources_dir/test_helpers.sh" +setup_test_env -echo "> Prepare test data" - -# We use data from this repo: https://github.com/hartwigmedical/testData -echo ">> Fetching and preparing test data" -fastq1="https://github.com/hartwigmedical/testdata/raw/master/100k_reads_hiseq/TESTX/TESTX_H7YRLADXX_S1_L001_R1_001.fastq.gz" -fastq2="https://github.com/hartwigmedical/testdata/raw/master/100k_reads_hiseq/TESTX/TESTX_H7YRLADXX_S1_L001_R2_001.fastq.gz" -TMPDIR=$(mktemp -d "$meta_temp_dir/$meta_name-XXXXXX") -function clean_up { - [[ -d "$TMPDIR" ]] && rm -r "$TMPDIR" -} -trap clean_up EXIT - -test_data_dir="$TMPDIR/test_data" +log "Prepare test data" +echo ">> Preparing test data" +test_data_dir="$meta_temp_dir/test_data" mkdir $test_data_dir -wget -q $fastq1 -O $test_data_dir/R1.fastq.gz -wget -q $fastq2 -O $test_data_dir/R2.fastq.gz -echo ">> Run falco on test data, output to dir" -echo ">>> Run falco" +create_test_fastq $test_data_dir/R1.fastq.gz 200 50 +create_test_fastq $test_data_dir/R2.fastq.gz 200 50 + +log "Run falco on test data, output to dir" +test_1_output="$meta_temp_dir/output1" $meta_executable \ --input "$test_data_dir/R1.fastq.gz;$test_data_dir/R2.fastq.gz" \ - --outdir "$TMPDIR/output1" + --outdir "$test_1_output" -echo ">>> Checking whether output exists" -[ ! -d "$TMPDIR/output1" ] && echo "Output directory not created" && exit 1 -[ ! -f "$TMPDIR/output1/R1.fastq.gz_fastqc_report.html" ] && echo "Report not created" && exit 1 -[ ! -f "$TMPDIR/output1/R1.fastq.gz_summary.txt" ] && echo "Summary not created" && exit 1 -[ ! -f "$TMPDIR/output1/R1.fastq.gz_fastqc_data.txt" ] && echo "fastqc_data not created" && exit 1 -[ ! -f "$TMPDIR/output1/R2.fastq.gz_fastqc_report.html" ] && echo "Report not created" && exit 1 -[ ! -f "$TMPDIR/output1/R2.fastq.gz_summary.txt" ] && echo "Summary not created" && exit 1 -[ ! -f "$TMPDIR/output1/R2.fastq.gz_fastqc_data.txt" ] && echo "fastqc_data not created" && exit 1 +log "Checking whether output exists" +check_dir_exists "$test_1_output" "output directory (when outputting to directory)" +check_file_exists "$test_1_output/R1.fastq.gz_fastqc_report.html" "report for R1 (when outputting to directory)" +check_file_not_empty "$test_1_output/R1.fastq.gz_fastqc_report.html" "report for R1 (when outputting to directory)" +check_file_exists "$test_1_output/R1.fastq.gz_summary.txt" "summary for R1 (when outputting to directory)" +check_file_not_empty "$test_1_output/R1.fastq.gz_summary.txt" "summary for R1 (when outputting to directory)" +check_file_exists "$test_1_output/R1.fastq.gz_fastqc_data.txt" "data for R1 (when outputting to directory)" +check_file_not_empty "$test_1_output/R1.fastq.gz_fastqc_data.txt" "data for R1 (when outputting to directory)" +check_file_exists "$test_1_output/R2.fastq.gz_fastqc_report.html" "report for R2 (when outputting to directory)" +check_file_not_empty "$test_1_output/R2.fastq.gz_fastqc_report.html" "report for R2 (when outputting to directory)" +check_file_exists "$test_1_output/R2.fastq.gz_summary.txt" "summary for R2 (when outputting to directory)" +check_file_not_empty "$test_1_output/R2.fastq.gz_summary.txt" "summary for R2 (when outputting to directory)" +check_file_exists "$test_1_output/R2.fastq.gz_fastqc_data.txt" "data for R2 (when outputting to directory)" +check_file_not_empty "$test_1_output/R2.fastq.gz_fastqc_data.txt" "data for R2 (when outputting to directory)" -echo ">>> cleanup" -rm -rf "$TMPDIR/output1" +log "cleanup" +rm -rf "$test_1_output" -echo ">> Run falco on test data, output to individual files" -echo ">>> Please note this is only possible for 1 input fastq file!" -echo ">>> Run falco" +log "Run falco on test data, output to individual files. Please note this is only possible for 1 input fastq file!" +test_2_output="$meta_temp_dir/output2/" $meta_executable \ --input "$test_data_dir/R1.fastq.gz" \ - --data_filename "$TMPDIR/output2/data.txt" \ - --report_filename "$TMPDIR/output2/report.html" \ - --summary_filename "$TMPDIR/output2/summary.txt" \ - --outdir "$TMPDIR/output2/" + --data_filename "$test_2_output/data.txt" \ + --report_filename "$test_2_output/report.html" \ + --summary_filename "$test_2_output/summary.txt" \ + --outdir "$test_2_output" -echo ">>> Checking whether output exists" -[ ! -d "$TMPDIR/output2" ] && echo "Output directory not created" && exit 1 -[ ! -f "$TMPDIR/output2/report.html" ] && echo "Report not created" && exit 1 -[ ! -f "$TMPDIR/output2/summary.txt" ] && echo "Summary not created" && exit 1 -[ ! -f "$TMPDIR/output2/data.txt" ] && echo "fastqc_data not created" && exit 1 +log "Checking whether output exists" +check_dir_exists "$test_2_output" "subsampling test output" +check_file_exists "$test_2_output/report.html" "report output (after subsampling)" +check_file_not_empty "$test_2_output/report.html" "report output (after subsampling)" +check_file_exists "$test_2_output/summary.txt" "summary output (after subsampling)" +check_file_not_empty "$test_2_output/summary.txt" "summary output (after subsampling)" +check_file_exists "$test_2_output/data.txt" "data output (after subsampling)" +check_file_not_empty "$test_2_output/data.txt" "data output (after subsampling)" -echo ">>> cleanup" -rm -rf $TMPDIR/output2/ +log "Cleanup" +rm -rf "$test_2_output" + +echo "Run falco on test data, subsample" +test_3_output="$meta_temp_dir/output3/" -echo ">> Run falco on test data, subsample" -echo ">>> Run falco" $meta_executable \ --input "$test_data_dir/R1.fastq.gz" \ - --data_filename "$TMPDIR/output3/data.txt" \ - --report_filename "$TMPDIR/output3/report.html" \ - --summary_filename "$TMPDIR/output3/summary.txt" \ + --data_filename "$test_3_output/data.txt" \ + --report_filename "$test_3_output/report.html" \ + --summary_filename "$test_3_output/summary.txt" \ --subsample 100 \ - --outdir "$TMPDIR/output3" + --outdir "$test_3_output" -echo ">>> Checking whether output exists" -[ ! -d "$TMPDIR/output3" ] && echo "Output directory not created" && exit 1 -[ ! -f "$TMPDIR/output3/report.html" ] && echo "Report not created" && exit 1 -[ ! -f "$TMPDIR/output3/summary.txt" ] && echo "Summary not created" && exit 1 -[ ! -f "$TMPDIR/output3/data.txt" ] && echo "fastqc_data not created" && exit 1 +log "Checking whether output exists" +check_dir_exists "$test_3_output" "subsampling test output" +check_file_exists "$test_3_output/report.html" "report output (after subsampling)" +check_file_not_empty "$test_3_output/report.html" "report output (after subsampling)" +check_file_exists "$test_3_output/summary.txt" "summary output (after subsampling)" +check_file_not_empty "$test_3_output/summary.txt" "summary output (after subsampling)" +check_file_exists "$test_3_output/data.txt" "data output (after subsampling)" +check_file_not_empty "$test_3_output/data.txt" "data output (after subsampling)" -echo ">>> cleanup" -rm -rf "$TMPDIR/output3/" +log "cleanup" +rm -rf "$meta_temp_dir/output3/" -echo "All tests succeeded!" +log "Run falco with empty fastq" +touch $test_data_dir/empty_R1.fastq +test_4_output="$meta_temp_dir/output4/" + +$meta_executable \ + --input "$test_data_dir/empty_R1.fastq" \ + --data_filename "$test_4_output/data.txt" \ + --report_filename "$test_4_output/report.html" \ + --summary_filename "$test_4_output/summary.txt" \ + --allow_empty_input \ + --outdir "$test_4_output" + +log "Checking whether output exists" + +check_dir_exists "$test_4_output" "output directory (empty input files)" +check_file_exists "$test_4_output/report.html" "report output (empty input files)" +check_file_not_empty "$test_4_output/report.html" "report output (empty input files)" +check_file_exists "$test_4_output/summary.txt" "summary output (empty input files)" +check_file_not_empty "$test_4_output/summary.txt" "summary output (empty input files)" +check_file_exists "$test_4_output/data.txt" "data output (empty input files)" +check_file_not_empty "$test_4_output/data.txt" "data output (empty input files)" + +log "cleanup" +rm -rf "$test_4_output" + +print_test_summary \ No newline at end of file diff --git a/src/snpeff/help.txt b/src/snpeff/help.txt deleted file mode 100644 index d1950220..00000000 --- a/src/snpeff/help.txt +++ /dev/null @@ -1,79 +0,0 @@ -Usage: snpEff [eff] [options] genome_version [input_file] - - variants_file : Default is STDIN - -Options: - -chr : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output. - -classic : Use old style annotations instead of Sequence Ontology and Hgvs. - -csvStats : Create CSV summary file. - -download : Download reference genome if not available. Default: true - -i : Input format [ vcf, bed ]. Default: VCF. - -fileList : Input actually contains a list of files to process. - -o : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF. - -s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html' - -noStats : Do not create stats (summary) file - -Results filter options: - -fi , -filterInterval : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times) - -no-downstream : Do not show DOWNSTREAM changes - -no-intergenic : Do not show INTERGENIC changes - -no-intron : Do not show INTRON changes - -no-upstream : Do not show UPSTREAM changes - -no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes - -no : Do not show 'EffectType'. This option can be used several times. - -Annotations options: - -cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: false - -cancerSamples : Two column TXT file defining 'oringinal \t derived' samples. - -fastaProt : Create an output file containing the resulting protein sequences. - -formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN'). - -geneId : Use gene ID instead of gene name (VCF output). Default: false - -hgvs : Use HGVS annotations for amino acid sub-field. Default: true - -hgvsOld : Use old HGVS notation. Default: false - -hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: false - -hgvsTrId : Use transcript ID in HGVS notation. Default: false - -lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags. - -noHgvs : Do not add HGVS annotations. - -noLof : Do not add LOF and NMD annotations. - -noShiftHgvs : Do not shift variants according to HGVS notation (most 3prime end). - -oicr : Add OICR tag in VCF file. Default: false - -sequenceOntology : Use Sequence Ontology terms. Default: true - -Generic options: - -c , -config : Specify config file - -configOption name=value : Override a config file option - -d , -debug : Debug mode (very verbose). - -dataDir : Override data_dir parameter from config file. - -download : Download a SnpEff database, if not available locally. Default: true - -nodownload : Do not download a SnpEff database, if not available locally. - -h , -help : Show this help and exit - -noLog : Do not report usage statistics to server - -q , -quiet : Quiet mode (do not show any messages or errors) - -v , -verbose : Verbose mode - -version : Show version number and exit - -Database options: - -canon : Only use canonical transcripts. - -canonList : Only use canonical transcripts, replace some transcripts using the 'gene_id transcript_id' entries in . - -tag : Only use transcript having a tag 'tagName'. This option can be used multiple times. - -notag : Filter out transcript having a tag 'tagName'. This option can be used multiple times. - -interaction : Annotate using interactions (requires interaction database). Default: true - -interval : Use a custom intervals in TXT/BED/BigBed/VCF/GFF file (you may use this option many times) - -maxTSL : Only use transcripts having Transcript Support Level lower than . - -motif : Annotate using motifs (requires Motif database). Default: true - -nextProt : Annotate using NextProt (requires NextProt database). - -noGenome : Do not load any genomic database (e.g. annotate using custom files). - -noExpandIUB : Disable IUB code expansion in input variants - -noInteraction : Disable inteaction annotations - -noMotif : Disable motif annotations. - -noNextProt : Disable NextProt annotations. - -onlyReg : Only use regulation tracks. - -onlyProtein : Only use protein coding transcripts. Default: false - -onlyTr : Only use the transcripts in this file. Format: One transcript ID per line. - -reg : Regulation track to use (this option can be used add several times). - -ss , -spliceSiteSize : Set size for splice sites (donor and acceptor) in bases. Default: 2 - -spliceRegionExonSize : Set size for splice site region within exons. Default: 3 bases - -spliceRegionIntronMin : Set minimum number of bases for splice site region within intron. Default: 3 bases - -spliceRegionIntronMax : Set maximum number of bases for splice site region within intron. Default: 8 bases - -strict : Only use 'validated' transcripts (i.e. sequence has been checked). Default: false - -ud , -upDownStreamLen : Set upstream downstream interval length (in bases) \ No newline at end of file diff --git a/src/snpeff/snpeff_ann/config.patch b/src/snpeff/snpeff_ann/config.patch new file mode 100644 index 00000000..1f2970f2 --- /dev/null +++ b/src/snpeff/snpeff_ann/config.patch @@ -0,0 +1,40 @@ +diff --git a/snpEff.config b/snpEff.config +index 3aa2710f..c5ff6926 100644 +--- a/snpEff.config ++++ b/snpEff.config +@@ -24,22 +24,29 @@ data.dir = ./data/ + # Database repository: A URL to the server where you can download databases (command: 'snpEff download dbName') + #--- + +-# Old SourceForge databases +-# database.repository = http://downloads.sourceforge.net/project/snpeff/databases ++# AstraZeneca S3 bucket (ODSP: Oncology Data Science & AI) ++database.repository = https://snpeff.odsp.astrazeneca.com/databases + +-# Secondary Azure blob storage using SAS-Token (Shared Access Signature) ++# Deprecated (2025-08): Azure blob storage (primary) ++#database.repository = https://snpeff.blob.core.windows.net/databases/ ++ ++# Deprecated (2025-08): Azure blob storage (secondary) using SAS-Token (Shared Access Signature) + #database.repository = "https://datasetsnpeff.blob.core.windows.net/dataset" + #database.repositoryKey = "?sv=2019-10-10&st=2020-09-01T00%3A00%3A00Z&se=2050-09-01T00%3A00%3A00Z&si=prod&sr=c&sig=isafOa9tGnYBAvsXFUMDGMTbsG2z%2FShaihzp7JE5dHw%3D" + +-# Primary Azure blob storage +-database.repository = https://snpeff.blob.core.windows.net/databases/ ++# Deprecated (2018-03): SourceForge databases ++#database.repository = http://downloads.sourceforge.net/project/snpeff/databases + + #--- + # Latest version numbers. Check here if there is an update. + #--- +-#versions.url = https://pcingola.github.io/SnpEff/versions.txt ++ ++# Deprecated (2025): Azure versions.txt + versions.url = https://snpeff.blob.core.windows.net/databases/versions.txt + ++# Deprecated (2018): GitHub vertsions.txt ++#versions.url = https://pcingola.github.io/SnpEff/versions.txt ++ + #------------------------------------------------------------------------------- + # Third party databases + #------------------------------------------------------------------------------- diff --git a/src/snpeff/config.vsh.yaml b/src/snpeff/snpeff_ann/config.vsh.yaml similarity index 93% rename from src/snpeff/config.vsh.yaml rename to src/snpeff/snpeff_ann/config.vsh.yaml index 5fb8622d..9bc353ea 100644 --- a/src/snpeff/config.vsh.yaml +++ b/src/snpeff/snpeff_ann/config.vsh.yaml @@ -1,4 +1,5 @@ -name: snpeff +name: snpeff_ann +namespace: snpeff description: | Genetic variant annotation, and functional effect prediction toolbox. It annotates and predicts the effects of genetic variants on genes and @@ -23,7 +24,7 @@ argument_groups: - name: --genome_version type: string description: Reference genome version. - example: GRCh37.75 + example: GRCh38.86 required: true - name: Outputs arguments: @@ -278,6 +279,7 @@ argument_groups: resources: - type: bash_script path: script.sh + - path: config.patch test_resources: - type: bash_script path: test.sh @@ -285,8 +287,21 @@ test_resources: path: test_data engines: - type: docker - image: quay.io/staphb/snpeff:5.2a + image: quay.io/staphb/snpeff:5.2f setup: + - type: docker + # Apply a partial patch from this commit + # https://github.com/pcingola/SnpEff/commit/6339f6cab984bd5f35b81a77e05c517be5d112a6 + # This updates the repositories where to download the references from + # At the time of writing this comment, these changes were not included in a release. + # This patch can be removed in an upcomming release. + copy: ["config.patch /opt/config.patch"] + - type: apt + packages: + - git + - type: docker + run: | + bash -c "pushd /snpEff && git apply /opt/config.patch && popd" - type: docker run: | version=$(snpEff -version) && \ diff --git a/src/snpeff/snpeff_ann/help.txt b/src/snpeff/snpeff_ann/help.txt new file mode 100644 index 00000000..78ffe602 --- /dev/null +++ b/src/snpeff/snpeff_ann/help.txt @@ -0,0 +1,85 @@ +snpEff version SnpEff 5.2f (build 2025-02-07 08:36), by Pablo Cingolani +Usage: snpEff [ann] [options] genome_version [input_file] + + + variants_file : Default is STDIN + + + +Options: + -chr : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output. + -classic : Use old style annotations instead of Sequence Ontology and Hgvs. + -csvStats : Create CSV summary file. + -download : Download reference genome if not available. Default: true + -i : Input format [ vcf, bed ]. Default: VCF. + -fileList : Input actually contains a list of files to process. + -o : Output format [ vcf, gatk, bed, bedAnn ]. Default: VCF. + -s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html' + -noStats : Do not create stats (summary) file + +Results filter options: + -fi , -filterInterval : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times) + -no-downstream : Do not show DOWNSTREAM changes + -no-intergenic : Do not show INTERGENIC changes + -no-intron : Do not show INTRON changes + -no-upstream : Do not show UPSTREAM changes + -no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes + -no : Do not show 'EffectType'. This option can be used several times. + +Annotations options: + -cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: false + -cancerSamples : Two column TXT file defining 'oringinal \t derived' samples. + -fastaProt : Create an output file containing the resulting protein sequences. + -fastaProtNoRef : Do not add reference sequences to the output (only valid when -fastaProt). Default: false + -formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN'). + -geneId : Use gene ID instead of gene name (VCF output). Default: false + -hgvs : Use HGVS annotations for amino acid sub-field. Default: true + -hgvsOld : Use old HGVS notation. Default: false + -hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: false + -hgvsTrId : Use transcript ID in HGVS notation. Default: false + -lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags. + -noHgvs : Do not add HGVS annotations. + -noLof : Do not add LOF and NMD annotations. + -noOut : Do not write the output resuts to STDOUT (maybe used for debugging). + -noShiftHgvs : Do not shift variants according to HGVS notation (most 3prime end). + -oicr : Add OICR tag in VCF file. Default: false + -sequenceOntology : Use Sequence Ontology terms. Default: true + +Generic options: + -c , -config : Specify config file + -configOption name=value : Override a config file option + -d , -debug : Debug mode (very verbose). + -dataDir : Override data_dir parameter from config file. + -download : Download a SnpEff database, if not available locally. Default: true + -nodownload : Do not download a SnpEff database, if not available locally. + -h , -help : Show this help and exit + -noLog : Do not report usage statistics to server + -q , -quiet : Quiet mode (do not show any messages or errors) + -v , -verbose : Verbose mode + -version : Show version number and exit + +Database options: + -canon : Only use canonical transcripts. + -canonList : Only use canonical transcripts, replace some transcripts using the 'gene_id transcript_id' entries in . + -tag : Only use transcript having a tag 'tagName'. This option can be used multiple times. + -notag : Filter out transcript having a tag 'tagName'. This option can be used multiple times. + -interaction : Annotate using interactions (requires interaction database). Default: true + -interval : Use a custom intervals in TXT/BED/BigBed/VCF/GFF file (you may use this option many times) + -maxTSL : Only use transcripts having Transcript Support Level lower than . + -motif : Annotate using motifs (requires Motif database). Default: true + -nextProt : Annotate using NextProt (requires NextProt database). + -noGenome : Do not load any genomic database (e.g. annotate using custom files). + -noExpandIUB : Disable IUB code expansion in input variants + -noInteraction : Disable inteaction annotations + -noMotif : Disable motif annotations. + -noNextProt : Disable NextProt annotations. + -onlyReg : Only use regulation tracks. + -onlyProtein : Only use protein coding transcripts. Default: false + -onlyTr : Only use the transcripts in this file. Format: One transcript ID per line. + -reg : Regulation track to use (this option can be used add several times). + -ss , -spliceSiteSize : Set size for splice sites (donor and acceptor) in bases. Default: 2 + -spliceRegionExonSize : Set size for splice site region within exons. Default: 3 bases + -spliceRegionIntronMin : Set minimum number of bases for splice site region within intron. Default: 3 bases + -spliceRegionIntronMax : Set maximum number of bases for splice site region within intron. Default: 8 bases + -strict : Only use 'validated' transcripts (i.e. sequence has been checked). Default: false + -ud , -upDownStreamLen : Set upstream downstream interval length (in bases) diff --git a/src/snpeff/script.sh b/src/snpeff/snpeff_ann/script.sh similarity index 99% rename from src/snpeff/script.sh rename to src/snpeff/snpeff_ann/script.sh index bf3914bb..9a5f3eb9 100644 --- a/src/snpeff/script.sh +++ b/src/snpeff/snpeff_ann/script.sh @@ -56,7 +56,7 @@ done # Run SnpEff -snpEff \ +snpEff ann \ ${par_chr:+-chr "$par_chr"} \ ${par_classic:+-classic} \ ${par_csv_stats:+-csvStats "$par_csv_stats"} \ diff --git a/src/snpeff/test.sh b/src/snpeff/snpeff_ann/test.sh similarity index 73% rename from src/snpeff/test.sh rename to src/snpeff/snpeff_ann/test.sh index d8c72c20..e5da4445 100644 --- a/src/snpeff/test.sh +++ b/src/snpeff/snpeff_ann/test.sh @@ -7,6 +7,22 @@ set -eo pipefail ########################################################################### +# create temporary directory and clean up on exit +TMPDIR=$(mktemp -d "$meta_temp_dir/$meta_name-XXXXXX") +echo "> Created $TMPDIR" +function clean_up { + [[ -d "$TMPDIR" ]] && rm -rf "$TMPDIR" +} +trap clean_up EXIT +DATA_DIR="$TMPDIR/data" +mkdir "$DATA_DIR" +TEST_GENOME="$DATA_DIR/test" +mkdir "$TEST_GENOME" +echo "Downloading test data" +curl -o - https://ftp.ensembl.org/pub/release-115/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.chromosome.1.fa.gz > "$TEST_GENOME/sequences.fa.gz" +curl -o - https://ftp.ensembl.org/pub/release-115/gtf/homo_sapiens/Homo_sapiens.GRCh38.115.chr.gtf.gz | zcat | sed -n '/^[#1]\s/p' | gzip > "$TEST_GENOME/genes.gtf.gz" +snpEff build -dataDir "$DATA_DIR" -noCheckCds -noCheckProtein -gtf22 -noLog -configOption "test.genome=GRCh38Chr1" -v test + # Test 1: Run SnpEff with only required parameters mkdir test1 @@ -14,7 +30,9 @@ pushd test1 > /dev/null # cd test1 (stack) echo "> Run Test 1: required parameters" "$meta_executable" \ - --genome_version GRCh37.75 \ + --genome_version test \ + --data_dir "$DATA_DIR" \ + --config_option "test.genome=GRCh38Chr1" \ --input "$meta_resources_dir/test_data/cancer.vcf" \ --output out.vcf @@ -48,7 +66,9 @@ pushd test2 > /dev/null echo "> Run Test 2: different input + options" "$meta_executable" \ - --genome_version GRCh37.75 \ + --genome_version test \ + --data_dir "$DATA_DIR" \ + --config_option "test.genome=GRCh38Chr1" \ --input "$meta_resources_dir/test_data/test.vcf" \ --interval "$meta_resources_dir/test_data/my_annotations.bed" \ --no_stats \ @@ -87,9 +107,11 @@ mkdir temp echo "> Run Test 3: move output files" "$meta_executable" \ - --genome_version GRCh37.75 \ + --genome_version test \ --input "$meta_resources_dir/test_data/test.vcf" \ --output output.vcf \ + --data_dir "$DATA_DIR" \ + --config_option "test.genome=GRCh38Chr1" \ --summary temp \ --genes temp diff --git a/src/snpeff/test_data/cancer.vcf b/src/snpeff/snpeff_ann/test_data/cancer.vcf similarity index 100% rename from src/snpeff/test_data/cancer.vcf rename to src/snpeff/snpeff_ann/test_data/cancer.vcf diff --git a/src/snpeff/test_data/my_annotations.bed b/src/snpeff/snpeff_ann/test_data/my_annotations.bed similarity index 100% rename from src/snpeff/test_data/my_annotations.bed rename to src/snpeff/snpeff_ann/test_data/my_annotations.bed diff --git a/src/snpeff/test_data/script.sh b/src/snpeff/snpeff_ann/test_data/script.sh similarity index 81% rename from src/snpeff/test_data/script.sh rename to src/snpeff/snpeff_ann/test_data/script.sh index a47ec136..3ac8baa2 100644 --- a/src/snpeff/test_data/script.sh +++ b/src/snpeff/snpeff_ann/test_data/script.sh @@ -1,6 +1,6 @@ # Test files from SnpEff examples if [ ! -f snpEff_latest_core.zip ]; then - wget https://snpeff.blob.core.windows.net/versions/snpEff_latest_core.zip + wget https://snpeff.odsp.astrazeneca.com/versions/snpEff_latest_core.zip fi if [ ! -d snpEff ]; then diff --git a/src/snpeff/test_data/test.vcf b/src/snpeff/snpeff_ann/test_data/test.vcf similarity index 100% rename from src/snpeff/test_data/test.vcf rename to src/snpeff/snpeff_ann/test_data/test.vcf diff --git a/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml b/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml index a2e749e7..08be428d 100644 --- a/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml +++ b/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml @@ -133,6 +133,7 @@ scope: target: "public" requirements: commands: + - "agat_convert_bed2gff.pl" - "ps" keywords: - "gene annotations" @@ -233,7 +234,7 @@ build_info: output: "target/executable/agat/agat_convert_bed2gff" executable: "target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -255,138 +256,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff b/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff index 0348535a..bfbb220a 100755 --- a/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff +++ b/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff @@ -452,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t LABEL org.opencontainers.image.authors="Leïla Paquay" LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_bed2gff" -LABEL org.opencontainers.image.created="2025-09-01T11:02:52Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:08Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -899,13 +899,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'agat_convert_bed2gff.pl' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'agat_convert_bed2gff.pl' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml b/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml index d846117f..52bc4597 100644 --- a/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml +++ b/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml @@ -123,6 +123,7 @@ scope: target: "public" requirements: commands: + - "agat_convert_embl2gff.pl" - "ps" keywords: - "gene annotations" @@ -223,7 +224,7 @@ build_info: output: "target/executable/agat/agat_convert_embl2gff" executable: "target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -245,138 +246,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff b/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff index 5f2f137c..5e9ff92d 100755 --- a/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff +++ b/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff @@ -452,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t LABEL org.opencontainers.image.authors="Leïla Paquay" LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_embl2gff" -LABEL org.opencontainers.image.created="2025-09-01T11:02:53Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:06Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -906,13 +906,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'agat_convert_embl2gff.pl' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'agat_convert_embl2gff.pl' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/agat/agat_convert_genscan2gff/.config.vsh.yaml b/target/executable/agat/agat_convert_genscan2gff/.config.vsh.yaml index af038f11..9fd05b8a 100644 --- a/target/executable/agat/agat_convert_genscan2gff/.config.vsh.yaml +++ b/target/executable/agat/agat_convert_genscan2gff/.config.vsh.yaml @@ -127,6 +127,7 @@ scope: target: "public" requirements: commands: + - "agat_convert_genscan2gff.pl" - "ps" keywords: - "gene annotations" @@ -228,7 +229,7 @@ build_info: output: "target/executable/agat/agat_convert_genscan2gff" executable: "target/executable/agat/agat_convert_genscan2gff/agat_convert_genscan2gff" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -250,138 +251,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/agat/agat_convert_genscan2gff/agat_convert_genscan2gff b/target/executable/agat/agat_convert_genscan2gff/agat_convert_genscan2gff index 0fcc106b..15a4d5c5 100755 --- a/target/executable/agat/agat_convert_genscan2gff/agat_convert_genscan2gff +++ b/target/executable/agat/agat_convert_genscan2gff/agat_convert_genscan2gff @@ -452,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t LABEL org.opencontainers.image.authors="Leïla Paquay" LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_genscan2gff" -LABEL org.opencontainers.image.created="2025-09-01T11:02:51Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:08Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -899,13 +899,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'agat_convert_genscan2gff.pl' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'agat_convert_genscan2gff.pl' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/agat/agat_convert_mfannot2gff/.config.vsh.yaml b/target/executable/agat/agat_convert_mfannot2gff/.config.vsh.yaml index d2afa403..6956534d 100644 --- a/target/executable/agat/agat_convert_mfannot2gff/.config.vsh.yaml +++ b/target/executable/agat/agat_convert_mfannot2gff/.config.vsh.yaml @@ -83,6 +83,7 @@ scope: target: "public" requirements: commands: + - "agat_convert_mfannot2gff.pl" - "ps" keywords: - "gene annotations" @@ -184,7 +185,7 @@ build_info: output: "target/executable/agat/agat_convert_mfannot2gff" executable: "target/executable/agat/agat_convert_mfannot2gff/agat_convert_mfannot2gff" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -206,138 +207,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/agat/agat_convert_mfannot2gff/agat_convert_mfannot2gff b/target/executable/agat/agat_convert_mfannot2gff/agat_convert_mfannot2gff index e685664a..a37e2360 100755 --- a/target/executable/agat/agat_convert_mfannot2gff/agat_convert_mfannot2gff +++ b/target/executable/agat/agat_convert_mfannot2gff/agat_convert_mfannot2gff @@ -452,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t LABEL org.opencontainers.image.authors="Leïla Paquay" LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_mfannot2gff" -LABEL org.opencontainers.image.created="2025-09-01T11:02:51Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:05Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -821,13 +821,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'agat_convert_mfannot2gff.pl' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'agat_convert_mfannot2gff.pl' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml b/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml index 6762bf33..3224a188 100644 --- a/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml +++ b/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml @@ -126,6 +126,7 @@ scope: target: "public" requirements: commands: + - "agat_convert_sp_gff2gtf.pl" - "ps" keywords: - "gene annotations" @@ -226,7 +227,7 @@ build_info: output: "target/executable/agat/agat_convert_sp_gff2gtf" executable: "target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -248,138 +249,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf b/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf index 241f6491..a3e1df16 100755 --- a/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf +++ b/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf @@ -452,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t LABEL org.opencontainers.image.authors="Leïla Paquay" LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_sp_gff2gtf" -LABEL org.opencontainers.image.created="2025-09-01T11:02:53Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:08Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -877,13 +877,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'agat_convert_sp_gff2gtf.pl' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'agat_convert_sp_gff2gtf.pl' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml b/target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml index 6c7fad65..42423ae0 100644 --- a/target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml +++ b/target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml @@ -86,6 +86,7 @@ scope: target: "public" requirements: commands: + - "agat_convert_sp_gff2tsv.pl" - "ps" keywords: - "gene annotations" @@ -186,7 +187,7 @@ build_info: output: "target/executable/agat/agat_convert_sp_gff2tsv" executable: "target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -208,138 +209,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv b/target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv index 24f23f6f..20e4cded 100755 --- a/target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv +++ b/target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv @@ -452,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t LABEL org.opencontainers.image.authors="Leïla Paquay" LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_sp_gff2tsv" -LABEL org.opencontainers.image.created="2025-09-01T11:02:52Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:07Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -825,13 +825,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'agat_convert_sp_gff2tsv.pl' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'agat_convert_sp_gff2tsv.pl' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml b/target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml index cd7596af..3298a3c7 100644 --- a/target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml +++ b/target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml @@ -93,6 +93,7 @@ scope: target: "public" requirements: commands: + - "agat_convert_sp_gxf2gxf.pl" - "ps" keywords: - "gene annotations" @@ -193,7 +194,7 @@ build_info: output: "target/executable/agat/agat_convert_sp_gxf2gxf" executable: "target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -215,138 +216,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf b/target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf index fe35b76e..674d7d04 100755 --- a/target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf +++ b/target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf @@ -452,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t LABEL org.opencontainers.image.authors="Leïla Paquay" LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_sp_gxf2gxf" -LABEL org.opencontainers.image.created="2025-09-01T11:02:53Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:07Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -834,13 +834,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'agat_convert_sp_gxf2gxf.pl' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'agat_convert_sp_gxf2gxf.pl' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/agat/agat_sp_add_introns/.config.vsh.yaml b/target/executable/agat/agat_sp_add_introns/.config.vsh.yaml index b1342557..c9b4a169 100644 --- a/target/executable/agat/agat_sp_add_introns/.config.vsh.yaml +++ b/target/executable/agat/agat_sp_add_introns/.config.vsh.yaml @@ -84,6 +84,7 @@ scope: target: "public" requirements: commands: + - "agat_sp_add_introns.pl" - "ps" keywords: - "gene annotations" @@ -184,7 +185,7 @@ build_info: output: "target/executable/agat/agat_sp_add_introns" executable: "target/executable/agat/agat_sp_add_introns/agat_sp_add_introns" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -206,138 +207,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/agat/agat_sp_add_introns/agat_sp_add_introns b/target/executable/agat/agat_sp_add_introns/agat_sp_add_introns index 6490f33c..3bbc03d1 100755 --- a/target/executable/agat/agat_sp_add_introns/agat_sp_add_introns +++ b/target/executable/agat/agat_sp_add_introns/agat_sp_add_introns @@ -452,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t LABEL org.opencontainers.image.authors="Leïla Paquay" LABEL org.opencontainers.image.description="Companion container for running component agat agat_sp_add_introns" -LABEL org.opencontainers.image.created="2025-09-01T11:02:53Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:06Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -838,13 +838,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'agat_sp_add_introns.pl' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'agat_sp_add_introns.pl' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/agat/agat_sp_filter_feature_from_kill_list/.config.vsh.yaml b/target/executable/agat/agat_sp_filter_feature_from_kill_list/.config.vsh.yaml index a8bf9176..904b434c 100644 --- a/target/executable/agat/agat_sp_filter_feature_from_kill_list/.config.vsh.yaml +++ b/target/executable/agat/agat_sp_filter_feature_from_kill_list/.config.vsh.yaml @@ -133,6 +133,7 @@ scope: target: "public" requirements: commands: + - "agat_sp_filter_feature_from_kill_list.pl" - "ps" keywords: - "gene annotations" @@ -234,7 +235,7 @@ build_info: output: "target/executable/agat/agat_sp_filter_feature_from_kill_list" executable: "target/executable/agat/agat_sp_filter_feature_from_kill_list/agat_sp_filter_feature_from_kill_list" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -256,138 +257,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/agat/agat_sp_filter_feature_from_kill_list/agat_sp_filter_feature_from_kill_list b/target/executable/agat/agat_sp_filter_feature_from_kill_list/agat_sp_filter_feature_from_kill_list index 90e3c050..0f3fc2e9 100755 --- a/target/executable/agat/agat_sp_filter_feature_from_kill_list/agat_sp_filter_feature_from_kill_list +++ b/target/executable/agat/agat_sp_filter_feature_from_kill_list/agat_sp_filter_feature_from_kill_list @@ -452,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t LABEL org.opencontainers.image.authors="Leïla Paquay" LABEL org.opencontainers.image.description="Companion container for running component agat agat_sp_filter_feature_from_kill_list" -LABEL org.opencontainers.image.created="2025-09-01T11:02:52Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:07Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -943,13 +943,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'agat_sp_filter_feature_from_kill_list.pl' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'agat_sp_filter_feature_from_kill_list.pl' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/agat/agat_sp_merge_annotations/.config.vsh.yaml b/target/executable/agat/agat_sp_merge_annotations/.config.vsh.yaml index cac06828..47ad9a55 100644 --- a/target/executable/agat/agat_sp_merge_annotations/.config.vsh.yaml +++ b/target/executable/agat/agat_sp_merge_annotations/.config.vsh.yaml @@ -81,6 +81,7 @@ scope: target: "public" requirements: commands: + - "agat_sp_merge_annotations.pl" - "ps" keywords: - "gene annotations" @@ -182,7 +183,7 @@ build_info: output: "target/executable/agat/agat_sp_merge_annotations" executable: "target/executable/agat/agat_sp_merge_annotations/agat_sp_merge_annotations" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -204,138 +205,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/agat/agat_sp_merge_annotations/agat_sp_merge_annotations b/target/executable/agat/agat_sp_merge_annotations/agat_sp_merge_annotations index 64ffb8c3..8282a901 100755 --- a/target/executable/agat/agat_sp_merge_annotations/agat_sp_merge_annotations +++ b/target/executable/agat/agat_sp_merge_annotations/agat_sp_merge_annotations @@ -452,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t LABEL org.opencontainers.image.authors="Leïla Paquay" LABEL org.opencontainers.image.description="Companion container for running component agat agat_sp_merge_annotations" -LABEL org.opencontainers.image.created="2025-09-01T11:02:51Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:07Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -826,13 +826,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'agat_sp_merge_annotations.pl' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'agat_sp_merge_annotations.pl' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/agat/agat_sp_statistics/.config.vsh.yaml b/target/executable/agat/agat_sp_statistics/.config.vsh.yaml index d8f23fcd..e5906bf8 100644 --- a/target/executable/agat/agat_sp_statistics/.config.vsh.yaml +++ b/target/executable/agat/agat_sp_statistics/.config.vsh.yaml @@ -128,6 +128,7 @@ scope: target: "public" requirements: commands: + - "agat_sp_statistics.pl" - "ps" keywords: - "gene annotations" @@ -229,7 +230,7 @@ build_info: output: "target/executable/agat/agat_sp_statistics" executable: "target/executable/agat/agat_sp_statistics/agat_sp_statistics" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -251,138 +252,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/agat/agat_sp_statistics/agat_sp_statistics b/target/executable/agat/agat_sp_statistics/agat_sp_statistics index db76e163..530faed0 100755 --- a/target/executable/agat/agat_sp_statistics/agat_sp_statistics +++ b/target/executable/agat/agat_sp_statistics/agat_sp_statistics @@ -452,9 +452,9 @@ RUN agat --version | sed 's/.*v\.//; s/\s.*//' | sed 's/^/AGAT: /' > /var/softwa LABEL org.opencontainers.image.authors="Leïla Paquay" LABEL org.opencontainers.image.description="Companion container for running component agat agat_sp_statistics" -LABEL org.opencontainers.image.created="2025-09-01T11:02:52Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:08Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -890,13 +890,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'agat_sp_statistics.pl' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'agat_sp_statistics.pl' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/agat/agat_sq_stat_basic/.config.vsh.yaml b/target/executable/agat/agat_sq_stat_basic/.config.vsh.yaml index ffe17402..3df0859c 100644 --- a/target/executable/agat/agat_sq_stat_basic/.config.vsh.yaml +++ b/target/executable/agat/agat_sq_stat_basic/.config.vsh.yaml @@ -124,6 +124,7 @@ scope: target: "public" requirements: commands: + - "agat_sq_stat_basic.pl" - "ps" keywords: - "gene annotations" @@ -225,7 +226,7 @@ build_info: output: "target/executable/agat/agat_sq_stat_basic" executable: "target/executable/agat/agat_sq_stat_basic/agat_sq_stat_basic" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -247,138 +248,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/agat/agat_sq_stat_basic/agat_sq_stat_basic b/target/executable/agat/agat_sq_stat_basic/agat_sq_stat_basic index b6ef71fb..7e25ca98 100755 --- a/target/executable/agat/agat_sq_stat_basic/agat_sq_stat_basic +++ b/target/executable/agat/agat_sq_stat_basic/agat_sq_stat_basic @@ -452,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t LABEL org.opencontainers.image.authors="Leïla Paquay" LABEL org.opencontainers.image.description="Companion container for running component agat agat_sq_stat_basic" -LABEL org.opencontainers.image.created="2025-09-01T11:02:51Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:06Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -896,13 +896,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'agat_sq_stat_basic.pl' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'agat_sq_stat_basic.pl' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/arriba/.config.vsh.yaml b/target/executable/arriba/.config.vsh.yaml index 9f53b026..49bfd133 100644 --- a/target/executable/arriba/.config.vsh.yaml +++ b/target/executable/arriba/.config.vsh.yaml @@ -26,7 +26,10 @@ argument_groups: alternatives: - "-x" description: "File in SAM/BAM/CRAM format with main alignments as generated by\ - \ STAR\n(Aligned.out.sam). Arriba extracts candidate reads from this file.\n" + \ STAR\n(Aligned.out.sam). **Important**: The BAM file must be generated by\ + \ STAR with \nchimeric alignment parameters, specifically `--chimOutType WithinBAM\ + \ HardClip`. \nArriba extracts candidate reads from this file, including both\ + \ normal and \nchimeric alignments.\n" info: null example: - "Aligned.out.bam" @@ -594,33 +597,50 @@ resources: - type: "bash_script" path: "script.sh" is_executable: true -description: "Detect gene fusions from RNA-Seq data" +description: "Arriba is a command-line tool for the detection of gene fusions from\ + \ RNA-Seq data. It was developed for the use in a clinical research setting. Therefore,\ + \ short runtimes and high sensitivity were important design criteria.\n\nArriba\ + \ is based on the STAR RNA-Seq aligner and post-processes the alignments (output\ + \ from STAR) to:\n\n1. detect split reads and discordant mates, which are indicative\ + \ of structural rearrangements,\n2. find reads supporting gene fusions (i.e., reads\ + \ spanning the breakpoints of gene fusions),\n3. perform various filtering steps\ + \ to remove false positives, and\n4. output the final predictions in a standardized\ + \ format.\n\nIn contrast to many other fusion detection tools, Arriba does not require\ + \ to reduce the STAR parameter `--alignIntronMax` (maximum intron size). Reducing\ + \ this parameter impairs detection of long introns and may affect expression quantification.\ + \ Arriba reliably filters translocation-based false positives even when large maximum\ + \ intron sizes are used.\n\n**Important**: Arriba requires BAM files that were aligned\ + \ with STAR using specific chimeric alignment parameters, particularly `--chimOutType\ + \ WithinBAM HardClip`. See the [official workflow documentation](https://github.com/suhrig/arriba/blob/master/run_arriba.sh)\ + \ for the complete set of recommended STAR parameters.\n" test_resources: - type: "bash_script" path: "test.sh" is_executable: true - type: "file" - path: "test_data" + path: "test_helpers.sh" info: null status: "enabled" scope: image: "public" target: "public" requirements: - cpus: 1 commands: + - "arriba" - "ps" keywords: - "Gene fusion" - "RNA-Seq" +- "Structural variants" +- "Chimeric alignments" license: "MIT" references: doi: - "10.1101/gr.257246.119" links: repository: "https://github.com/suhrig/arriba" - homepage: "https://arriba.readthedocs.io/en/latest/" - documentation: "https://arriba.readthedocs.io/en/latest/" + homepage: "https://arriba.readthedocs.io/" + documentation: "https://arriba.readthedocs.io/" runners: - type: "executable" id: "executable" @@ -689,15 +709,15 @@ runners: engines: - type: "docker" id: "docker" - image: "quay.io/biocontainers/arriba:2.4.0--h0033a41_2" + image: "quay.io/biocontainers/arriba:2.5.0--h87b9561_1" target_registry: "images.viash-hub.com" target_tag: "main" namespace_separator: "/" setup: - type: "docker" run: - - "arriba -h | grep 'Version:' 2>&1 | sed 's/Version:\\s\\(.*\\)/arriba: \"\\\ - 1\"/' > /var/software_versions.txt\n" + - "arriba -h 2>&1 | head -5 | grep 'Version:' | sed 's/Version:\\s\\(.*\\)/arriba:\ + \ \"\\1\"/' > /var/software_versions.txt\n" entrypoint: [] cmd: null - type: "native" @@ -709,7 +729,7 @@ build_info: output: "target/executable/arriba" executable: "target/executable/arriba/arriba" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -731,138 +751,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/arriba/arriba b/target/executable/arriba/arriba index 3fef3ca9..147dbb96 100755 --- a/target/executable/arriba/arriba +++ b/target/executable/arriba/arriba @@ -446,15 +446,15 @@ function ViashDockerfile { if [[ "$engine_id" == "docker" ]]; then cat << 'VIASHDOCKER' -FROM quay.io/biocontainers/arriba:2.4.0--h0033a41_2 +FROM quay.io/biocontainers/arriba:2.5.0--h87b9561_1 ENTRYPOINT [] -RUN arriba -h | grep 'Version:' 2>&1 | sed 's/Version:\s\(.*\)/arriba: "\1"/' > /var/software_versions.txt +RUN arriba -h 2>&1 | head -5 | grep 'Version:' | sed 's/Version:\s\(.*\)/arriba: "\1"/' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component arriba" -LABEL org.opencontainers.image.created="2025-09-01T11:03:01Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:13Z" LABEL org.opencontainers.image.source="https://github.com/suhrig/arriba" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -574,14 +574,44 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) function ViashHelp { echo "arriba main" echo "" - echo "Detect gene fusions from RNA-Seq data" + echo "Arriba is a command-line tool for the detection of gene fusions from RNA-Seq" + echo "data. It was developed for the use in a clinical research setting. Therefore," + echo "short runtimes and high sensitivity were important design criteria." + echo "" + echo "Arriba is based on the STAR RNA-Seq aligner and post-processes the alignments" + echo "(output from STAR) to:" + echo "" + echo "1. detect split reads and discordant mates, which are indicative of structural" + echo "rearrangements," + echo "2. find reads supporting gene fusions (i.e., reads spanning the breakpoints of" + echo "gene fusions)," + echo "3. perform various filtering steps to remove false positives, and" + echo "4. output the final predictions in a standardized format." + echo "" + echo "In contrast to many other fusion detection tools, Arriba does not require to" + echo "reduce the STAR parameter \`--alignIntronMax\` (maximum intron size). Reducing" + echo "this parameter impairs detection of long introns and may affect expression" + echo "quantification. Arriba reliably filters translocation-based false positives even" + echo "when large maximum intron sizes are used." + echo "" + echo "**Important**: Arriba requires BAM files that were aligned with STAR using" + echo "specific chimeric alignment parameters, particularly \`--chimOutType WithinBAM" + echo "HardClip\`. See the [official workflow" + echo "documentation](https://github.com/suhrig/arriba/blob/master/run_arriba.sh) for" + echo "the complete set of recommended STAR parameters." echo "" echo "Inputs:" echo " -x, --bam" echo " type: file, required parameter, file must exist" echo " example: Aligned.out.bam" echo " File in SAM/BAM/CRAM format with main alignments as generated by STAR" - echo " (Aligned.out.sam). Arriba extracts candidate reads from this file." + echo " (Aligned.out.sam). **Important**: The BAM file must be generated by STAR" + echo " with" + echo " chimeric alignment parameters, specifically \`--chimOutType WithinBAM" + echo " HardClip\`." + echo " Arriba extracts candidate reads from this file, including both normal" + echo " and" + echo " chimeric alignments." echo "" echo " -a, --genome" echo " type: file, required parameter, file must exist" @@ -1667,19 +1697,16 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'arriba' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'arriba' 'ps' 'bash' fi # setting computational defaults -if [ -z ${VIASH_META_CPUS+x} ]; then - VIASH_META_CPUS="1" -fi # helper function for parsing memory strings function ViashMemoryAsBytes { @@ -2248,55 +2275,80 @@ $( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}" ## VIASH END -# unset flags +set -eo pipefail + +# unset boolean flags that are "false" [[ "\$par_skip_duplicate_marking" == "false" ]] && unset par_skip_duplicate_marking [[ "\$par_extra_information" == "false" ]] && unset par_extra_information [[ "\$par_fill_gaps" == "false" ]] && unset par_fill_gaps -# replace ';' with ',' -par_interesting_contigs=\$(echo \$par_interesting_contigs | tr ';' ',') -par_viral_contigs=\$(echo \$par_viral_contigs | tr ';' ',') -par_disable_filters=\$(echo \$par_disable_filters | tr ';' ',') +# process multi-value parameters: replace ';' with ',' for arriba compatibility +if [[ -n "\${par_interesting_contigs:-}" ]]; then + par_interesting_contigs=\$(echo "\$par_interesting_contigs" | tr ';' ',') +fi +if [[ -n "\${par_viral_contigs:-}" ]]; then + par_viral_contigs=\$(echo "\$par_viral_contigs" | tr ';' ',') +fi +if [[ -n "\${par_disable_filters:-}" ]]; then + par_disable_filters=\$(echo "\$par_disable_filters" | tr ';' ',') +fi -# run arriba -arriba \\ - -x "\$par_bam" \\ - -a "\$par_genome" \\ - -g "\$par_gene_annotation" \\ - -o "\$par_fusions" \\ - \${par_known_fusions:+-k "\${par_known_fusions}"} \\ - \${par_blacklist:+-b "\${par_blacklist}"} \\ - \${par_structural_variants:+-d "\${par_structural_variants}"} \\ - \${par_tags:+-t "\${par_tags}"} \\ - \${par_protein_domains:+-p "\${par_protein_domains}"} \\ - \${par_fusions_discarded:+-O "\${par_fusions_discarded}"} \\ - \${par_max_genomic_breakpoint_distance:+-D "\${par_max_genomic_breakpoint_distance}"} \\ - \${par_strandedness:+-s "\${par_strandedness}"} \\ - \${par_interesting_contigs:+-i "\${par_interesting_contigs}"} \\ - \${par_viral_contigs:+-v "\${par_viral_contigs}"} \\ - \${par_disable_filters:+-f "\${par_disable_filters}"} \\ - \${par_max_e_value:+-E "\${par_max_e_value}"} \\ - \${par_min_supporting_reads:+-S "\${par_min_supporting_reads}"} \\ - \${par_max_mismappers:+-m "\${par_max_mismappers}"} \\ - \${par_max_homolog_identity:+-L "\${par_max_homolog_identity}"} \\ - \${par_homopolymer_length:+-H "\${par_homopolymer_length}"} \\ - \${par_read_through_distance:+-R "\${par_read_through_distance}"} \\ - \${par_min_anchor_length:+-A "\${par_min_anchor_length}"} \\ - \${par_many_spliced_events:+-M "\${par_many_spliced_events}"} \\ - \${par_max_kmer_content:+-K "\${par_max_kmer_content}"} \\ - \${par_max_mismatch_pvalue:+-V "\${par_max_mismatch_pvalue}"} \\ - \${par_fragment_length:+-F "\${par_fragment_length}"} \\ - \${par_max_reads:+-U "\${par_max_reads}"} \\ - \${par_quantile:+-Q "\${par_quantile}"} \\ - \${par_exonic_fraction:+-e "\${par_exonic_fraction}"} \\ - \${par_top_n:+-T "\${par_top_n}"} \\ - \${par_covered_fraction:+-C "\${par_covered_fraction}"} \\ - \${par_max_itd_length:+-l "\${par_max_itd_length}"} \\ - \${par_min_itd_allele_fraction:+-z "\${par_min_itd_allele_fraction}"} \\ - \${par_min_itd_supporting_reads:+-Z "\${par_min_itd_supporting_reads}"} \\ - \${par_skip_duplicate_marking:+-u} \\ - \${par_extra_information:+-X} \\ +# build command arguments array +cmd_args=( + # required arguments + -x "\$par_bam" + -a "\$par_genome" + -g "\$par_gene_annotation" + -o "\$par_fusions" + + # optional input files + \${par_known_fusions:+-k "\$par_known_fusions"} + \${par_blacklist:+-b "\$par_blacklist"} + \${par_structural_variants:+-d "\$par_structural_variants"} + \${par_tags:+-t "\$par_tags"} + \${par_protein_domains:+-p "\$par_protein_domains"} + + # optional output files + \${par_fusions_discarded:+-O "\$par_fusions_discarded"} + + # filter and analysis options + \${par_max_genomic_breakpoint_distance:+-D "\$par_max_genomic_breakpoint_distance"} + \${par_strandedness:+-s "\$par_strandedness"} + \${par_interesting_contigs:+-i "\$par_interesting_contigs"} + \${par_viral_contigs:+-v "\$par_viral_contigs"} + \${par_disable_filters:+-f "\$par_disable_filters"} + + # statistical thresholds + \${par_max_e_value:+-E "\$par_max_e_value"} + \${par_min_supporting_reads:+-S "\$par_min_supporting_reads"} + \${par_max_mismappers:+-m "\$par_max_mismappers"} + \${par_max_homolog_identity:+-L "\$par_max_homolog_identity"} + \${par_homopolymer_length:+-H "\$par_homopolymer_length"} + \${par_read_through_distance:+-R "\$par_read_through_distance"} + \${par_min_anchor_length:+-A "\$par_min_anchor_length"} + \${par_many_spliced_events:+-M "\$par_many_spliced_events"} + \${par_max_kmer_content:+-K "\$par_max_kmer_content"} + \${par_max_mismatch_pvalue:+-V "\$par_max_mismatch_pvalue"} + \${par_fragment_length:+-F "\$par_fragment_length"} + \${par_max_reads:+-U "\$par_max_reads"} + \${par_quantile:+-Q "\$par_quantile"} + \${par_exonic_fraction:+-e "\$par_exonic_fraction"} + \${par_top_n:+-T "\$par_top_n"} + \${par_covered_fraction:+-C "\$par_covered_fraction"} + + # internal tandem duplication options + \${par_max_itd_length:+-l "\$par_max_itd_length"} + \${par_min_itd_allele_fraction:+-z "\$par_min_itd_allele_fraction"} + \${par_min_itd_supporting_reads:+-Z "\$par_min_itd_supporting_reads"} + + # boolean flags + \${par_skip_duplicate_marking:+-u} + \${par_extra_information:+-X} \${par_fill_gaps:+-I} +) + +# execute arriba +arriba "\${cmd_args[@]}" VIASHMAIN bash "\$tempscript" & wait "\$!" diff --git a/target/executable/bases2fastq/.config.vsh.yaml b/target/executable/bases2fastq/.config.vsh.yaml index 46c1d6d1..40f224b4 100644 --- a/target/executable/bases2fastq/.config.vsh.yaml +++ b/target/executable/bases2fastq/.config.vsh.yaml @@ -352,6 +352,7 @@ scope: target: "public" requirements: commands: + - "bases2fastq" - "ps" keywords: - "demultiplex" @@ -431,7 +432,7 @@ runners: engines: - type: "docker" id: "docker" - image: "elembio/bases2fastq:2.2" + image: "elembio/bases2fastq:2.2.1" target_registry: "images.viash-hub.com" target_tag: "main" namespace_separator: "/" @@ -451,7 +452,7 @@ build_info: output: "target/executable/bases2fastq" executable: "target/executable/bases2fastq/bases2fastq" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -473,138 +474,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bases2fastq/bases2fastq b/target/executable/bases2fastq/bases2fastq index 318a7d62..12747f03 100755 --- a/target/executable/bases2fastq/bases2fastq +++ b/target/executable/bases2fastq/bases2fastq @@ -446,15 +446,15 @@ function ViashDockerfile { if [[ "$engine_id" == "docker" ]]; then cat << 'VIASHDOCKER' -FROM elembio/bases2fastq:2.2 +FROM elembio/bases2fastq:2.2.1 ENTRYPOINT [] RUN bases2fastq --version 2>&1 | head -1 | sed 's/.*version \([0-9\\.]*\).*/bases2fastq: \1/' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component bases2fastq" -LABEL org.opencontainers.image.created="2025-09-01T11:02:45Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:10Z" LABEL org.opencontainers.image.source="https://github.com/Illumina/bases2fastq" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -1293,13 +1293,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bases2fastq' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bases2fastq' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/bbmap/bbmap_bbsplit/.config.vsh.yaml b/target/executable/bbmap/bbmap_bbsplit/.config.vsh.yaml index a2c710b7..65c6cff9 100644 --- a/target/executable/bbmap/bbmap_bbsplit/.config.vsh.yaml +++ b/target/executable/bbmap/bbmap_bbsplit/.config.vsh.yaml @@ -371,7 +371,7 @@ build_info: output: "target/executable/bbmap/bbmap_bbsplit" executable: "target/executable/bbmap/bbmap_bbsplit/bbmap_bbsplit" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -393,138 +393,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bbmap/bbmap_bbsplit/bbmap_bbsplit b/target/executable/bbmap/bbmap_bbsplit/bbmap_bbsplit index 9469a3c7..96e0645d 100755 --- a/target/executable/bbmap/bbmap_bbsplit/bbmap_bbsplit +++ b/target/executable/bbmap/bbmap_bbsplit/bbmap_bbsplit @@ -454,9 +454,9 @@ cp -r bbmap/* /usr/local/bin RUN bbsplit.sh --version 2>&1 | awk '/BBMap version/{print "BBMAP:", $NF}' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component bbmap bbmap_bbsplit" -LABEL org.opencontainers.image.created="2025-09-01T11:02:58Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:11Z" LABEL org.opencontainers.image.source="https://github.com/BioInfoTools/BBMap/blob/master/sh/bbsplit.sh" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bcftools/bcftools_annotate/.config.vsh.yaml b/target/executable/bcftools/bcftools_annotate/.config.vsh.yaml index 8ad9def4..f18a26bf 100644 --- a/target/executable/bcftools/bcftools_annotate/.config.vsh.yaml +++ b/target/executable/bcftools/bcftools_annotate/.config.vsh.yaml @@ -340,6 +340,16 @@ argument_groups: direction: "input" multiple: false multiple_sep: ";" + - type: "integer" + name: "--verbosity" + alternatives: + - "-v" + description: "Verbosity level.\n" + info: null + required: false + direction: "input" + multiple: false + multiple_sep: ";" resources: - type: "bash_script" path: "script.sh" @@ -349,6 +359,8 @@ test_resources: - type: "bash_script" path: "test.sh" is_executable: true +- type: "file" + path: "test_helpers.sh" info: null status: "enabled" scope: @@ -356,6 +368,7 @@ scope: target: "public" requirements: commands: + - "bcftools" - "ps" keywords: - "Annotate" @@ -438,25 +451,15 @@ runners: engines: - type: "docker" id: "docker" - image: "debian:stable-slim" + image: "quay.io/biocontainers/bcftools:1.22--h3a4d415_1" target_registry: "images.viash-hub.com" target_tag: "main" namespace_separator: "/" setup: - - type: "apt" - packages: - - "bcftools" - - "procps" - interactive: false - type: "docker" run: - "echo \"bcftools: \\\"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftools\ \ //p')\\\"\" > /var/software_versions.txt\n" - test_setup: - - type: "apt" - packages: - - "tabix" - interactive: false entrypoint: [] cmd: null - type: "native" @@ -468,7 +471,7 @@ build_info: output: "target/executable/bcftools/bcftools_annotate" executable: "target/executable/bcftools/bcftools_annotate/bcftools_annotate" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -490,138 +493,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bcftools/bcftools_annotate/bcftools_annotate b/target/executable/bcftools/bcftools_annotate/bcftools_annotate index ebf6c6a0..e1d27622 100755 --- a/target/executable/bcftools/bcftools_annotate/bcftools_annotate +++ b/target/executable/bcftools/bcftools_annotate/bcftools_annotate @@ -446,19 +446,15 @@ function ViashDockerfile { if [[ "$engine_id" == "docker" ]]; then cat << 'VIASHDOCKER' -FROM debian:stable-slim +FROM quay.io/biocontainers/bcftools:1.22--h3a4d415_1 ENTRYPOINT [] -RUN apt-get update && \ - DEBIAN_FRONTEND=noninteractive apt-get install -y bcftools procps && \ - rm -rf /var/lib/apt/lists/* - RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftools //p')\"" > /var/software_versions.txt LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_annotate" -LABEL org.opencontainers.image.created="2025-09-01T11:02:55Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:05Z" LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -768,6 +764,10 @@ function ViashHelp { echo " (and similarly for FORMAT and FILTER)." echo " \"INFO\" can be abbreviated to \"INF\" and \"FORMAT\" to \"FMT\"." echo "" + echo " -v, --verbosity" + echo " type: integer" + echo " Verbosity level." + echo "" echo "Viash built in Computational Requirements:" echo " ---cpus=INT" echo " Number of CPUs to use" @@ -1195,6 +1195,23 @@ while [[ $# -gt 0 ]]; do [ $# -lt 2 ] && ViashError Not enough arguments passed to --x. Use "--help" to get more information on the parameters. && exit 1 shift 2 ;; + --verbosity) + [ -n "$VIASH_PAR_VERBOSITY" ] && ViashError Bad arguments for option \'--verbosity\': \'$VIASH_PAR_VERBOSITY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_VERBOSITY="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --verbosity. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --verbosity=*) + [ -n "$VIASH_PAR_VERBOSITY" ] && ViashError Bad arguments for option \'--verbosity=*\': \'$VIASH_PAR_VERBOSITY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_VERBOSITY=$(ViashRemoveFlags "$1") + shift 1 + ;; + -v) + [ -n "$VIASH_PAR_VERBOSITY" ] && ViashError Bad arguments for option \'-v\': \'$VIASH_PAR_VERBOSITY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_VERBOSITY="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to -v. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; ---engine) VIASH_ENGINE_ID="$2" shift 2 @@ -1305,13 +1322,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bcftools' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bcftools' 'ps' 'bash' fi # setting computational defaults @@ -1481,6 +1498,12 @@ if [[ -n "$VIASH_PAR_SINGLE_OVERLAPS" ]]; then exit 1 fi fi +if [[ -n "$VIASH_PAR_VERBOSITY" ]]; then + if ! [[ "$VIASH_PAR_VERBOSITY" =~ ^[-+]?[0-9]+$ ]]; then + ViashError '--verbosity' has to be an integer. Use "--help" to get more information on the parameters. + exit 1 + fi +fi if [[ -n "$VIASH_META_CPUS" ]]; then if ! [[ "$VIASH_META_CPUS" =~ ^[-+]?[0-9]+$ ]]; then ViashError 'cpus' has to be an integer. Use "--help" to get more information on the parameters. @@ -1750,6 +1773,7 @@ $( if [ ! -z ${VIASH_PAR_SAMPLES+x} ]; then echo "${VIASH_PAR_SAMPLES}" | sed "s $( if [ ! -z ${VIASH_PAR_SAMPLES_FILE+x} ]; then echo "${VIASH_PAR_SAMPLES_FILE}" | sed "s#'#'\"'\"'#g;s#.*#par_samples_file='&'#" ; else echo "# par_samples_file="; fi ) $( if [ ! -z ${VIASH_PAR_SINGLE_OVERLAPS+x} ]; then echo "${VIASH_PAR_SINGLE_OVERLAPS}" | sed "s#'#'\"'\"'#g;s#.*#par_single_overlaps='&'#" ; else echo "# par_single_overlaps="; fi ) $( if [ ! -z ${VIASH_PAR_REMOVE+x} ]; then echo "${VIASH_PAR_REMOVE}" | sed "s#'#'\"'\"'#g;s#.*#par_remove='&'#" ; else echo "# par_remove="; fi ) +$( if [ ! -z ${VIASH_PAR_VERBOSITY+x} ]; then echo "${VIASH_PAR_VERBOSITY}" | sed "s#'#'\"'\"'#g;s#.*#par_verbosity='&'#" ; else echo "# par_verbosity="; fi ) $( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "${VIASH_META_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_name='&'#" ; else echo "# meta_name="; fi ) $( if [ ! -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then echo "${VIASH_META_FUNCTIONALITY_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_functionality_name='&'#" ; else echo "# meta_functionality_name="; fi ) $( if [ ! -z ${VIASH_META_RESOURCES_DIR+x} ]; then echo "${VIASH_META_RESOURCES_DIR}" | sed "s#'#'\"'\"'#g;s#.*#meta_resources_dir='&'#" ; else echo "# meta_resources_dir="; fi ) @@ -1776,50 +1800,51 @@ set -eo pipefail # Unset parameters unset_if_false=( - par_force - par_keep_sites - par_no_version - par_single_overlaps + par_force + par_keep_sites + par_no_version + par_single_overlaps ) for par in \${unset_if_false[@]}; do - test_val="\${!par}" - [[ "\$test_val" == "false" ]] && unset \$par + test_val="\${!par}" + [[ "\$test_val" == "false" ]] && unset \$par done # Execute bcftools annotate with the provided arguments bcftools annotate \\ - \${par_annotations:+-a "\$par_annotations"} \\ - \${par_columns:+-c "\$par_columns"} \\ - \${par_columns_file:+-C "\$par_columns_file"} \\ - \${par_exclude:+-e "\$par_exclude"} \\ - \${par_force:+--force} \\ - \${par_header_line:+-H "\$par_header_line"} \\ - \${par_header_lines:+-h "\$par_header_lines"} \\ - \${par_set_id:+-I "\$par_set_id"} \\ - \${par_include:+-i "\$par_include"} \\ - \${par_keep_sites:+-k} \\ - \${par_merge_logic:+-l "\$par_merge_logic"} \\ - \${par_mark_sites:+-m "\$par_mark_sites"} \\ - \${par_min_overlap:+--min-overlap "\$par_min_overlap"} \\ - \${par_no_version:+--no-version} \\ - \${par_samples_file:+-S "\$par_samples_file"} \\ - \${par_output_type:+-O "\$par_output_type"} \\ - \${par_pair_logic:+--pair-logic "\$par_pair_logic"} \\ - \${par_regions:+-r "\$par_regions"} \\ - \${par_regions_file:+-R "\$par_regions_file"} \\ - \${par_regions_overlap:+--regions-overlap "\$par_regions_overlap"} \\ - \${par_rename_annotations:+--rename-annots "\$par_rename_annotations"} \\ - \${par_rename_chromosomes:+--rename-chrs "\$par_rename_chromosomes"} \\ - \${par_samples:+-s "\$par_samples"} \\ - \${par_single_overlaps:+--single-overlaps} \\ - \${par_threads:+--threads "\$par_threads"} \\ - \${par_remove:+-x "\$par_remove"} \\ - -o \$par_output \\ - \$par_input - + \${par_annotations:+-a "\$par_annotations"} \\ + \${par_columns:+-c "\$par_columns"} \\ + \${par_columns_file:+-C "\$par_columns_file"} \\ + \${par_exclude:+-e "\$par_exclude"} \\ + \${par_force:+--force} \\ + \${par_header_line:+-H "\$par_header_line"} \\ + \${par_header_lines:+-h "\$par_header_lines"} \\ + \${par_set_id:+-I "\$par_set_id"} \\ + \${par_include:+-i "\$par_include"} \\ + \${par_keep_sites:+-k} \\ + \${par_merge_logic:+-l "\$par_merge_logic"} \\ + \${par_mark_sites:+-m "\$par_mark_sites"} \\ + \${par_min_overlap:+--min-overlap "\$par_min_overlap"} \\ + \${par_no_version:+--no-version} \\ + \${par_samples_file:+-S "\$par_samples_file"} \\ + \${par_output_type:+-O "\$par_output_type"} \\ + \${par_pair_logic:+--pair-logic "\$par_pair_logic"} \\ + \${par_regions:+-r "\$par_regions"} \\ + \${par_regions_file:+-R "\$par_regions_file"} \\ + \${par_regions_overlap:+--regions-overlap "\$par_regions_overlap"} \\ + \${par_rename_annotations:+--rename-annots "\$par_rename_annotations"} \\ + \${par_rename_chromosomes:+--rename-chrs "\$par_rename_chromosomes"} \\ + \${par_samples:+-s "\$par_samples"} \\ + \${par_single_overlaps:+--single-overlaps} \\ + \${par_remove:+-x "\$par_remove"} \\ + \${par_verbosity:+-v "\$par_verbosity"} \\ + \${meta_cpus:+--threads "\$meta_cpus"} \\ + -o \$par_output \\ + \$par_input + - + VIASHMAIN bash "\$tempscript" & wait "\$!" diff --git a/target/executable/bcftools/bcftools_concat/.config.vsh.yaml b/target/executable/bcftools/bcftools_concat/.config.vsh.yaml index bc5db063..85fb60cd 100644 --- a/target/executable/bcftools/bcftools_concat/.config.vsh.yaml +++ b/target/executable/bcftools/bcftools_concat/.config.vsh.yaml @@ -17,8 +17,12 @@ argument_groups: name: "--input" alternatives: - "-i" - description: "Input VCF/BCF files to concatenate." + description: "Input VCF/BCF files to concatenate.\n\nAll source files must have\ + \ the same sample columns appearing in \nthe same order. Files must be sorted\ + \ by chr and position.\n" info: null + example: + - "input1.vcf.gz input2.vcf.gz" must_exist: true create_parent: true required: false @@ -29,8 +33,11 @@ argument_groups: name: "--file_list" alternatives: - "-f" - description: "Read the list of VCF/BCF files from a file, one file name per line." + description: "Read the list of VCF/BCF files from a file, one file name per line.\n\ + \nAlternative to providing multiple --input files.\n" info: null + example: + - "files_list.txt" must_exist: true create_parent: true required: false @@ -43,8 +50,11 @@ argument_groups: name: "--output" alternatives: - "-o" - description: "Output concatenated VCF/BCF file." + description: "Write output to a file.\n\nIf not specified, output goes to standard\ + \ output.\n" info: null + example: + - "concatenated.vcf.gz" must_exist: true create_parent: true required: true @@ -58,24 +68,28 @@ argument_groups: alternatives: - "-a" description: "First coordinate of the next file can precede last record of the\ - \ current file.\n" + \ current file.\n\nAllows overlapping records between files during concatenation.\n" info: null direction: "input" - type: "boolean_true" - name: "--compact_PS" + name: "--compact_ps" alternatives: - "-c" description: "Do not output PS tag at each site, only at the start of a new phase\ - \ set block.\n" + \ set block.\n\nReduces output size for phased data.\n" info: null direction: "input" - type: "string" - name: "--remove_duplicates" + name: "--rm_dups" alternatives: - "-d" - description: "Output duplicate records present in multiple files only once: .\n\ - \ \n" + description: "Output duplicate records present in multiple files only once.\n\n\ + **Options:**\n- `snps`: Remove duplicate SNPs\n- `indels`: Remove duplicate\ + \ indels \n- `both`: Remove duplicate SNPs and indels\n- `all`: Remove all\ + \ duplicates\n- `exact`: Remove exact duplicates only\n" info: null + example: + - "exact" required: false choices: - "snps" @@ -83,53 +97,75 @@ argument_groups: - "both" - "all" - "exact" - - "none" direction: "input" multiple: false multiple_sep: ";" + - type: "boolean_true" + name: "--remove_duplicates" + alternatives: + - "-D" + description: "Alias for --rm_dups exact.\n\nRemove exact duplicate records present\ + \ in multiple files.\n" + info: null + direction: "input" + - type: "boolean_true" + name: "--drop_genotypes" + alternatives: + - "-G" + description: "Drop individual genotype information.\n\nRemoves all sample-specific\ + \ data from output.\n" + info: null + direction: "input" - type: "boolean_true" name: "--ligate" alternatives: - "-l" - description: "Ligate phased VCFs by matching phase at overlapping haplotypes." + description: "Ligate phased VCFs by matching phase at overlapping haplotypes.\n\ + \nConnects phase information across files.\n" info: null direction: "input" - type: "boolean_true" name: "--ligate_force" - description: "Ligate even non-overlapping chunks, keep all sites." + description: "Ligate even non-overlapping chunks, keep all sites.\n\nForces ligation\ + \ without requiring overlap validation.\n" info: null direction: "input" - type: "boolean_true" name: "--ligate_warn" - description: "Drop sites in imperfect overlaps." + description: "Drop sites in imperfect overlaps.\n\nConservative ligation that\ + \ removes problematic sites.\n" info: null direction: "input" - type: "boolean_true" name: "--no_version" - description: "Do not append version and command line information to the header." + description: "Do not append version and command line to the header.\n\nProduces\ + \ cleaner output headers.\n" info: null direction: "input" - type: "boolean_true" name: "--naive" alternatives: - "-n" - description: "Concatenate files without recompression, a header check compatibility\ - \ is performed." + description: "Concatenate files without recompression.\n\nVery fast operation\ + \ with header compatibility check.\n" info: null direction: "input" - type: "boolean_true" name: "--naive_force" - description: "Same as --naive, but header compatibility is not checked. \nDangerous,\ - \ use with caution.\n" + description: "Same as --naive, but header compatibility is not checked.\n\n**Warning:**\ + \ Dangerous option, use with caution.\n" info: null direction: "input" - type: "string" name: "--output_type" alternatives: - "-O" - description: "Output type:\n u: uncompressed BCF\n z: compressed VCF\n b: compressed\ - \ BCF\n v: uncompressed VCF\n" + description: "Output type and compression level.\n\n**Options:**\n- `u`: uncompressed\ + \ BCF\n- `b`: compressed BCF \n- `v`: uncompressed VCF\n- `z`: compressed VCF\ + \ (with optional compression level 0-9)\n" info: null + example: + - "z" required: false choices: - "u" @@ -140,10 +176,11 @@ argument_groups: multiple: false multiple_sep: ";" - type: "integer" - name: "--min_PQ" + name: "--min_pq" alternatives: - "-q" - description: "Break phase set if phasing quality is lower than ." + description: "Break phase set if phasing quality is lower than specified value.\n\ + \nOnly relevant when working with phased data.\n" info: null example: - 30 @@ -155,11 +192,11 @@ argument_groups: name: "--regions" alternatives: - "-r" - description: "Restrict to comma-separated list of regions. \nFollowing formats\ - \ are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​].\n" + description: "Restrict to comma-separated list of regions.\n\n**Formats supported:**\ + \ chr|chr:pos|chr:beg-end|chr:beg-[,…​]\n" info: null example: - - "20:1000000-2000000" + - "chr20:1000000-2000000" required: false direction: "input" multiple: false @@ -168,10 +205,11 @@ argument_groups: name: "--regions_file" alternatives: - "-R" - description: "Restrict to regions listed in a file. \nRegions can be specified\ - \ either on a VCF, BED, or tab-delimited file (the default). \nFor more information\ - \ check manual.\n" + description: "Restrict to regions listed in a file.\n\nRegions can be specified\ + \ in VCF, BED, or tab-delimited format.\n" info: null + example: + - "regions.bed" must_exist: true create_parent: true required: false @@ -180,26 +218,46 @@ argument_groups: multiple_sep: ";" - type: "string" name: "--regions_overlap" - description: "This option controls how overlapping records are determined: \n\ - set to 'pos' or '0' if the VCF record has to have POS inside a region (this\ - \ corresponds to the default behavior of -t/-T); \nset to 'record' or '1' if\ - \ also overlapping records with POS outside a region should be included (this\ - \ is the default behavior of -r/-R, \nand includes indels with POS at the end\ - \ of a region, which are technically outside the region); \nor set to 'variant'\ - \ or '2' to include only true overlapping variation (compare the full VCF representation\ - \ \"TA>T-\" vs the true sequence variation \"A>-\").\n" + description: "Include if POS in the region (0), record overlaps (1), variant overlaps\ + \ (2).\n\n**Options:**\n- `0`: POS inside region (default for -t/-T)\n- `1`:\ + \ overlapping records included (default for -r/-R) \n- `2`: true overlapping\ + \ variation only\n" info: null + example: + - "1" required: false choices: - - "pos" - - "record" - - "variant" - "0" - "1" - "2" direction: "input" multiple: false multiple_sep: ";" + - type: "integer" + name: "--verbosity" + alternatives: + - "-v" + description: "Set verbosity level.\n\nControls amount of diagnostic output.\n" + info: null + example: + - 1 + required: false + direction: "input" + multiple: false + multiple_sep: ";" + - type: "string" + name: "--write_index" + alternatives: + - "-W" + description: "Automatically index the output files.\n\n**Format:** Specify index\ + \ format or use default.\n" + info: null + example: + - "tbi" + required: false + direction: "input" + multiple: false + multiple_sep: ";" resources: - type: "bash_script" path: "script.sh" @@ -215,6 +273,8 @@ test_resources: - type: "bash_script" path: "test.sh" is_executable: true +- type: "file" + path: "test_helpers.sh" info: null status: "enabled" scope: @@ -222,6 +282,7 @@ scope: target: "public" requirements: commands: + - "bcftools" - "ps" keywords: - "Concatenate" @@ -304,25 +365,14 @@ runners: engines: - type: "docker" id: "docker" - image: "debian:stable-slim" + image: "quay.io/biocontainers/bcftools:1.22--h3a4d415_1" target_registry: "images.viash-hub.com" target_tag: "main" namespace_separator: "/" setup: - - type: "apt" - packages: - - "bcftools" - - "procps" - interactive: false - type: "docker" run: - - "echo \"bcftools: \\\"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftools\ - \ //p')\\\"\" > /var/software_versions.txt\n" - test_setup: - - type: "apt" - packages: - - "tabix" - interactive: false + - "bcftools --version 2>&1 | head -1 | sed 's/bcftools /bcftools: /' > /var/software_versions.txt\n" entrypoint: [] cmd: null - type: "native" @@ -334,7 +384,7 @@ build_info: output: "target/executable/bcftools/bcftools_concat" executable: "target/executable/bcftools/bcftools_concat/bcftools_concat" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -356,138 +406,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bcftools/bcftools_concat/bcftools_concat b/target/executable/bcftools/bcftools_concat/bcftools_concat index b2b320dc..34c9240c 100755 --- a/target/executable/bcftools/bcftools_concat/bcftools_concat +++ b/target/executable/bcftools/bcftools_concat/bcftools_concat @@ -446,19 +446,15 @@ function ViashDockerfile { if [[ "$engine_id" == "docker" ]]; then cat << 'VIASHDOCKER' -FROM debian:stable-slim +FROM quay.io/biocontainers/bcftools:1.22--h3a4d415_1 ENTRYPOINT [] -RUN apt-get update && \ - DEBIAN_FRONTEND=noninteractive apt-get install -y bcftools procps && \ - rm -rf /var/lib/apt/lists/* - -RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftools //p')\"" > /var/software_versions.txt +RUN bcftools --version 2>&1 | head -1 | sed 's/bcftools /bcftools: /' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_concat" -LABEL org.opencontainers.image.created="2025-09-01T11:02:56Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:06Z" LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -589,100 +585,140 @@ function ViashHelp { echo "Inputs:" echo " -i, --input" echo " type: file, multiple values allowed, file must exist" + echo " example: input1.vcf.gz input2.vcf.gz" echo " Input VCF/BCF files to concatenate." + echo " All source files must have the same sample columns appearing in" + echo " the same order. Files must be sorted by chr and position." echo "" echo " -f, --file_list" echo " type: file, file must exist" + echo " example: files_list.txt" echo " Read the list of VCF/BCF files from a file, one file name per line." + echo " Alternative to providing multiple --input files." echo "" echo "Outputs:" echo " -o, --output" echo " type: file, required parameter, output, file must exist" - echo " Output concatenated VCF/BCF file." + echo " example: concatenated.vcf.gz" + echo " Write output to a file." + echo " If not specified, output goes to standard output." echo "" echo "Options:" echo " -a, --allow_overlaps" echo " type: boolean_true" echo " First coordinate of the next file can precede last record of the current" echo " file." + echo " Allows overlapping records between files during concatenation." echo "" - echo " -c, --compact_PS" + echo " -c, --compact_ps" echo " type: boolean_true" echo " Do not output PS tag at each site, only at the start of a new phase set" echo " block." + echo " Reduces output size for phased data." echo "" - echo " -d, --remove_duplicates" + echo " -d, --rm_dups" echo " type: string" - echo " choices: [ snps, indels, both, all, exact, none ]" - echo " Output duplicate records present in multiple files only once:" - echo " ." + echo " example: exact" + echo " choices: [ snps, indels, both, all, exact ]" + echo " Output duplicate records present in multiple files only once." + echo " **Options:**" + echo " - \`snps\`: Remove duplicate SNPs" + echo " - \`indels\`: Remove duplicate indels" + echo " - \`both\`: Remove duplicate SNPs and indels" + echo " - \`all\`: Remove all duplicates" + echo " - \`exact\`: Remove exact duplicates only" + echo "" + echo " -D, --remove_duplicates" + echo " type: boolean_true" + echo " Alias for --rm_dups exact." + echo " Remove exact duplicate records present in multiple files." + echo "" + echo " -G, --drop_genotypes" + echo " type: boolean_true" + echo " Drop individual genotype information." + echo " Removes all sample-specific data from output." echo "" echo " -l, --ligate" echo " type: boolean_true" echo " Ligate phased VCFs by matching phase at overlapping haplotypes." + echo " Connects phase information across files." echo "" echo " --ligate_force" echo " type: boolean_true" echo " Ligate even non-overlapping chunks, keep all sites." + echo " Forces ligation without requiring overlap validation." echo "" echo " --ligate_warn" echo " type: boolean_true" echo " Drop sites in imperfect overlaps." + echo " Conservative ligation that removes problematic sites." echo "" echo " --no_version" echo " type: boolean_true" - echo " Do not append version and command line information to the header." + echo " Do not append version and command line to the header." + echo " Produces cleaner output headers." echo "" echo " -n, --naive" echo " type: boolean_true" - echo " Concatenate files without recompression, a header check compatibility is" - echo " performed." + echo " Concatenate files without recompression." + echo " Very fast operation with header compatibility check." echo "" echo " --naive_force" echo " type: boolean_true" echo " Same as --naive, but header compatibility is not checked." - echo " Dangerous, use with caution." + echo " **Warning:** Dangerous option, use with caution." echo "" echo " -O, --output_type" echo " type: string" + echo " example: z" echo " choices: [ u, z, b, v ]" - echo " Output type:" - echo " u: uncompressed BCF" - echo " z: compressed VCF" - echo " b: compressed BCF" - echo " v: uncompressed VCF" + echo " Output type and compression level." + echo " **Options:**" + echo " - \`u\`: uncompressed BCF" + echo " - \`b\`: compressed BCF" + echo " - \`v\`: uncompressed VCF" + echo " - \`z\`: compressed VCF (with optional compression level 0-9)" echo "" - echo " -q, --min_PQ" + echo " -q, --min_pq" echo " type: integer" echo " example: 30" - echo " Break phase set if phasing quality is lower than ." + echo " Break phase set if phasing quality is lower than specified value." + echo " Only relevant when working with phased data." echo "" echo " -r, --regions" echo " type: string" - echo " example: 20:1000000-2000000" + echo " example: chr20:1000000-2000000" echo " Restrict to comma-separated list of regions." - echo " Following formats are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​]." + echo " **Formats supported:** chr|chr:pos|chr:beg-end|chr:beg-[,…​]" echo "" echo " -R, --regions_file" echo " type: file, file must exist" + echo " example: regions.bed" echo " Restrict to regions listed in a file." - echo " Regions can be specified either on a VCF, BED, or tab-delimited file" - echo " (the default)." - echo " For more information check manual." + echo " Regions can be specified in VCF, BED, or tab-delimited format." echo "" echo " --regions_overlap" echo " type: string" - echo " choices: [ pos, record, variant, 0, 1, 2 ]" - echo " This option controls how overlapping records are determined:" - echo " set to 'pos' or '0' if the VCF record has to have POS inside a region" - echo " (this corresponds to the default behavior of -t/-T);" - echo " set to 'record' or '1' if also overlapping records with POS outside a" - echo " region should be included (this is the default behavior of -r/-R," - echo " and includes indels with POS at the end of a region, which are" - echo " technically outside the region);" - echo " or set to 'variant' or '2' to include only true overlapping variation" - echo " (compare the full VCF representation \"TA>T-\" vs the true sequence" - echo " variation \"A>-\")." + echo " example: 1" + echo " choices: [ 0, 1, 2 ]" + echo " Include if POS in the region (0), record overlaps (1), variant overlaps" + echo " (2)." + echo " **Options:**" + echo " - \`0\`: POS inside region (default for -t/-T)" + echo " - \`1\`: overlapping records included (default for -r/-R)" + echo " - \`2\`: true overlapping variation only" + echo "" + echo " -v, --verbosity" + echo " type: integer" + echo " example: 1" + echo " Set verbosity level." + echo " Controls amount of diagnostic output." + echo "" + echo " -W, --write_index" + echo " type: string" + echo " example: tbi" + echo " Automatically index the output files." + echo " **Format:** Specify index format or use default." echo "" echo "Viash built in Computational Requirements:" echo " ---cpus=INT" @@ -804,8 +840,8 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_ALLOW_OVERLAPS=true shift 1 ;; - --compact_PS) - [ -n "$VIASH_PAR_COMPACT_PS" ] && ViashError Bad arguments for option \'--compact_PS\': \'$VIASH_PAR_COMPACT_PS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + --compact_ps) + [ -n "$VIASH_PAR_COMPACT_PS" ] && ViashError Bad arguments for option \'--compact_ps\': \'$VIASH_PAR_COMPACT_PS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 VIASH_PAR_COMPACT_PS=true shift 1 ;; @@ -814,23 +850,43 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_COMPACT_PS=true shift 1 ;; - --remove_duplicates) - [ -n "$VIASH_PAR_REMOVE_DUPLICATES" ] && ViashError Bad arguments for option \'--remove_duplicates\': \'$VIASH_PAR_REMOVE_DUPLICATES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_REMOVE_DUPLICATES="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --remove_duplicates. Use "--help" to get more information on the parameters. && exit 1 + --rm_dups) + [ -n "$VIASH_PAR_RM_DUPS" ] && ViashError Bad arguments for option \'--rm_dups\': \'$VIASH_PAR_RM_DUPS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_RM_DUPS="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --rm_dups. Use "--help" to get more information on the parameters. && exit 1 shift 2 ;; - --remove_duplicates=*) - [ -n "$VIASH_PAR_REMOVE_DUPLICATES" ] && ViashError Bad arguments for option \'--remove_duplicates=*\': \'$VIASH_PAR_REMOVE_DUPLICATES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_REMOVE_DUPLICATES=$(ViashRemoveFlags "$1") + --rm_dups=*) + [ -n "$VIASH_PAR_RM_DUPS" ] && ViashError Bad arguments for option \'--rm_dups=*\': \'$VIASH_PAR_RM_DUPS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_RM_DUPS=$(ViashRemoveFlags "$1") shift 1 ;; -d) - [ -n "$VIASH_PAR_REMOVE_DUPLICATES" ] && ViashError Bad arguments for option \'-d\': \'$VIASH_PAR_REMOVE_DUPLICATES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_REMOVE_DUPLICATES="$2" + [ -n "$VIASH_PAR_RM_DUPS" ] && ViashError Bad arguments for option \'-d\': \'$VIASH_PAR_RM_DUPS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_RM_DUPS="$2" [ $# -lt 2 ] && ViashError Not enough arguments passed to -d. Use "--help" to get more information on the parameters. && exit 1 shift 2 ;; + --remove_duplicates) + [ -n "$VIASH_PAR_REMOVE_DUPLICATES" ] && ViashError Bad arguments for option \'--remove_duplicates\': \'$VIASH_PAR_REMOVE_DUPLICATES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_REMOVE_DUPLICATES=true + shift 1 + ;; + -D) + [ -n "$VIASH_PAR_REMOVE_DUPLICATES" ] && ViashError Bad arguments for option \'-D\': \'$VIASH_PAR_REMOVE_DUPLICATES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_REMOVE_DUPLICATES=true + shift 1 + ;; + --drop_genotypes) + [ -n "$VIASH_PAR_DROP_GENOTYPES" ] && ViashError Bad arguments for option \'--drop_genotypes\': \'$VIASH_PAR_DROP_GENOTYPES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_DROP_GENOTYPES=true + shift 1 + ;; + -G) + [ -n "$VIASH_PAR_DROP_GENOTYPES" ] && ViashError Bad arguments for option \'-G\': \'$VIASH_PAR_DROP_GENOTYPES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_DROP_GENOTYPES=true + shift 1 + ;; --ligate) [ -n "$VIASH_PAR_LIGATE" ] && ViashError Bad arguments for option \'--ligate\': \'$VIASH_PAR_LIGATE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 VIASH_PAR_LIGATE=true @@ -888,14 +944,14 @@ while [[ $# -gt 0 ]]; do [ $# -lt 2 ] && ViashError Not enough arguments passed to -O. Use "--help" to get more information on the parameters. && exit 1 shift 2 ;; - --min_PQ) - [ -n "$VIASH_PAR_MIN_PQ" ] && ViashError Bad arguments for option \'--min_PQ\': \'$VIASH_PAR_MIN_PQ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + --min_pq) + [ -n "$VIASH_PAR_MIN_PQ" ] && ViashError Bad arguments for option \'--min_pq\': \'$VIASH_PAR_MIN_PQ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 VIASH_PAR_MIN_PQ="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --min_PQ. Use "--help" to get more information on the parameters. && exit 1 + [ $# -lt 2 ] && ViashError Not enough arguments passed to --min_pq. Use "--help" to get more information on the parameters. && exit 1 shift 2 ;; - --min_PQ=*) - [ -n "$VIASH_PAR_MIN_PQ" ] && ViashError Bad arguments for option \'--min_PQ=*\': \'$VIASH_PAR_MIN_PQ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + --min_pq=*) + [ -n "$VIASH_PAR_MIN_PQ" ] && ViashError Bad arguments for option \'--min_pq=*\': \'$VIASH_PAR_MIN_PQ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 VIASH_PAR_MIN_PQ=$(ViashRemoveFlags "$1") shift 1 ;; @@ -950,6 +1006,40 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_REGIONS_OVERLAP=$(ViashRemoveFlags "$1") shift 1 ;; + --verbosity) + [ -n "$VIASH_PAR_VERBOSITY" ] && ViashError Bad arguments for option \'--verbosity\': \'$VIASH_PAR_VERBOSITY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_VERBOSITY="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --verbosity. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --verbosity=*) + [ -n "$VIASH_PAR_VERBOSITY" ] && ViashError Bad arguments for option \'--verbosity=*\': \'$VIASH_PAR_VERBOSITY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_VERBOSITY=$(ViashRemoveFlags "$1") + shift 1 + ;; + -v) + [ -n "$VIASH_PAR_VERBOSITY" ] && ViashError Bad arguments for option \'-v\': \'$VIASH_PAR_VERBOSITY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_VERBOSITY="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to -v. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --write_index) + [ -n "$VIASH_PAR_WRITE_INDEX" ] && ViashError Bad arguments for option \'--write_index\': \'$VIASH_PAR_WRITE_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_WRITE_INDEX="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --write_index. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --write_index=*) + [ -n "$VIASH_PAR_WRITE_INDEX" ] && ViashError Bad arguments for option \'--write_index=*\': \'$VIASH_PAR_WRITE_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_WRITE_INDEX=$(ViashRemoveFlags "$1") + shift 1 + ;; + -W) + [ -n "$VIASH_PAR_WRITE_INDEX" ] && ViashError Bad arguments for option \'-W\': \'$VIASH_PAR_WRITE_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_WRITE_INDEX="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to -W. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; ---engine) VIASH_ENGINE_ID="$2" shift 2 @@ -1060,13 +1150,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bcftools' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bcftools' 'ps' 'bash' fi # setting computational defaults @@ -1158,6 +1248,12 @@ fi if [ -z ${VIASH_PAR_COMPACT_PS+x} ]; then VIASH_PAR_COMPACT_PS="false" fi +if [ -z ${VIASH_PAR_REMOVE_DUPLICATES+x} ]; then + VIASH_PAR_REMOVE_DUPLICATES="false" +fi +if [ -z ${VIASH_PAR_DROP_GENOTYPES+x} ]; then + VIASH_PAR_DROP_GENOTYPES="false" +fi if [ -z ${VIASH_PAR_LIGATE+x} ]; then VIASH_PAR_LIGATE="false" fi @@ -1208,7 +1304,19 @@ if [[ -n "$VIASH_PAR_ALLOW_OVERLAPS" ]]; then fi if [[ -n "$VIASH_PAR_COMPACT_PS" ]]; then if ! [[ "$VIASH_PAR_COMPACT_PS" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then - ViashError '--compact_PS' has to be a boolean_true. Use "--help" to get more information on the parameters. + ViashError '--compact_ps' has to be a boolean_true. Use "--help" to get more information on the parameters. + exit 1 + fi +fi +if [[ -n "$VIASH_PAR_REMOVE_DUPLICATES" ]]; then + if ! [[ "$VIASH_PAR_REMOVE_DUPLICATES" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then + ViashError '--remove_duplicates' has to be a boolean_true. Use "--help" to get more information on the parameters. + exit 1 + fi +fi +if [[ -n "$VIASH_PAR_DROP_GENOTYPES" ]]; then + if ! [[ "$VIASH_PAR_DROP_GENOTYPES" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then + ViashError '--drop_genotypes' has to be a boolean_true. Use "--help" to get more information on the parameters. exit 1 fi fi @@ -1250,7 +1358,13 @@ if [[ -n "$VIASH_PAR_NAIVE_FORCE" ]]; then fi if [[ -n "$VIASH_PAR_MIN_PQ" ]]; then if ! [[ "$VIASH_PAR_MIN_PQ" =~ ^[-+]?[0-9]+$ ]]; then - ViashError '--min_PQ' has to be an integer. Use "--help" to get more information on the parameters. + ViashError '--min_pq' has to be an integer. Use "--help" to get more information on the parameters. + exit 1 + fi +fi +if [[ -n "$VIASH_PAR_VERBOSITY" ]]; then + if ! [[ "$VIASH_PAR_VERBOSITY" =~ ^[-+]?[0-9]+$ ]]; then + ViashError '--verbosity' has to be an integer. Use "--help" to get more information on the parameters. exit 1 fi fi @@ -1328,12 +1442,12 @@ if [[ -n "$VIASH_META_MEMORY_PIB" ]]; then fi # check whether value is belongs to a set of choices -if [ ! -z "$VIASH_PAR_REMOVE_DUPLICATES" ]; then - VIASH_PAR_REMOVE_DUPLICATES_CHOICES=("snps;indels;both;all;exact;none") +if [ ! -z "$VIASH_PAR_RM_DUPS" ]; then + VIASH_PAR_RM_DUPS_CHOICES=("snps;indels;both;all;exact") IFS=';' set -f - if ! [[ ";${VIASH_PAR_REMOVE_DUPLICATES_CHOICES[*]};" =~ ";$VIASH_PAR_REMOVE_DUPLICATES;" ]]; then - ViashError '--remove_duplicates' specified value of \'$VIASH_PAR_REMOVE_DUPLICATES\' is not in the list of allowed values. Use "--help" to get more information on the parameters. + if ! [[ ";${VIASH_PAR_RM_DUPS_CHOICES[*]};" =~ ";$VIASH_PAR_RM_DUPS;" ]]; then + ViashError '--rm_dups' specified value of \'$VIASH_PAR_RM_DUPS\' is not in the list of allowed values. Use "--help" to get more information on the parameters. exit 1 fi set +f @@ -1353,7 +1467,7 @@ if [ ! -z "$VIASH_PAR_OUTPUT_TYPE" ]; then fi if [ ! -z "$VIASH_PAR_REGIONS_OVERLAP" ]; then - VIASH_PAR_REGIONS_OVERLAP_CHOICES=("pos;record;variant;0;1;2") + VIASH_PAR_REGIONS_OVERLAP_CHOICES=("0;1;2") IFS=';' set -f if ! [[ ";${VIASH_PAR_REGIONS_OVERLAP_CHOICES[*]};" =~ ";$VIASH_PAR_REGIONS_OVERLAP;" ]]; then @@ -1480,8 +1594,10 @@ $( if [ ! -z ${VIASH_PAR_INPUT+x} ]; then echo "${VIASH_PAR_INPUT}" | sed "s#'#' $( if [ ! -z ${VIASH_PAR_FILE_LIST+x} ]; then echo "${VIASH_PAR_FILE_LIST}" | sed "s#'#'\"'\"'#g;s#.*#par_file_list='&'#" ; else echo "# par_file_list="; fi ) $( if [ ! -z ${VIASH_PAR_OUTPUT+x} ]; then echo "${VIASH_PAR_OUTPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_output='&'#" ; else echo "# par_output="; fi ) $( if [ ! -z ${VIASH_PAR_ALLOW_OVERLAPS+x} ]; then echo "${VIASH_PAR_ALLOW_OVERLAPS}" | sed "s#'#'\"'\"'#g;s#.*#par_allow_overlaps='&'#" ; else echo "# par_allow_overlaps="; fi ) -$( if [ ! -z ${VIASH_PAR_COMPACT_PS+x} ]; then echo "${VIASH_PAR_COMPACT_PS}" | sed "s#'#'\"'\"'#g;s#.*#par_compact_PS='&'#" ; else echo "# par_compact_PS="; fi ) +$( if [ ! -z ${VIASH_PAR_COMPACT_PS+x} ]; then echo "${VIASH_PAR_COMPACT_PS}" | sed "s#'#'\"'\"'#g;s#.*#par_compact_ps='&'#" ; else echo "# par_compact_ps="; fi ) +$( if [ ! -z ${VIASH_PAR_RM_DUPS+x} ]; then echo "${VIASH_PAR_RM_DUPS}" | sed "s#'#'\"'\"'#g;s#.*#par_rm_dups='&'#" ; else echo "# par_rm_dups="; fi ) $( if [ ! -z ${VIASH_PAR_REMOVE_DUPLICATES+x} ]; then echo "${VIASH_PAR_REMOVE_DUPLICATES}" | sed "s#'#'\"'\"'#g;s#.*#par_remove_duplicates='&'#" ; else echo "# par_remove_duplicates="; fi ) +$( if [ ! -z ${VIASH_PAR_DROP_GENOTYPES+x} ]; then echo "${VIASH_PAR_DROP_GENOTYPES}" | sed "s#'#'\"'\"'#g;s#.*#par_drop_genotypes='&'#" ; else echo "# par_drop_genotypes="; fi ) $( if [ ! -z ${VIASH_PAR_LIGATE+x} ]; then echo "${VIASH_PAR_LIGATE}" | sed "s#'#'\"'\"'#g;s#.*#par_ligate='&'#" ; else echo "# par_ligate="; fi ) $( if [ ! -z ${VIASH_PAR_LIGATE_FORCE+x} ]; then echo "${VIASH_PAR_LIGATE_FORCE}" | sed "s#'#'\"'\"'#g;s#.*#par_ligate_force='&'#" ; else echo "# par_ligate_force="; fi ) $( if [ ! -z ${VIASH_PAR_LIGATE_WARN+x} ]; then echo "${VIASH_PAR_LIGATE_WARN}" | sed "s#'#'\"'\"'#g;s#.*#par_ligate_warn='&'#" ; else echo "# par_ligate_warn="; fi ) @@ -1489,10 +1605,12 @@ $( if [ ! -z ${VIASH_PAR_NO_VERSION+x} ]; then echo "${VIASH_PAR_NO_VERSION}" | $( if [ ! -z ${VIASH_PAR_NAIVE+x} ]; then echo "${VIASH_PAR_NAIVE}" | sed "s#'#'\"'\"'#g;s#.*#par_naive='&'#" ; else echo "# par_naive="; fi ) $( if [ ! -z ${VIASH_PAR_NAIVE_FORCE+x} ]; then echo "${VIASH_PAR_NAIVE_FORCE}" | sed "s#'#'\"'\"'#g;s#.*#par_naive_force='&'#" ; else echo "# par_naive_force="; fi ) $( if [ ! -z ${VIASH_PAR_OUTPUT_TYPE+x} ]; then echo "${VIASH_PAR_OUTPUT_TYPE}" | sed "s#'#'\"'\"'#g;s#.*#par_output_type='&'#" ; else echo "# par_output_type="; fi ) -$( if [ ! -z ${VIASH_PAR_MIN_PQ+x} ]; then echo "${VIASH_PAR_MIN_PQ}" | sed "s#'#'\"'\"'#g;s#.*#par_min_PQ='&'#" ; else echo "# par_min_PQ="; fi ) +$( if [ ! -z ${VIASH_PAR_MIN_PQ+x} ]; then echo "${VIASH_PAR_MIN_PQ}" | sed "s#'#'\"'\"'#g;s#.*#par_min_pq='&'#" ; else echo "# par_min_pq="; fi ) $( if [ ! -z ${VIASH_PAR_REGIONS+x} ]; then echo "${VIASH_PAR_REGIONS}" | sed "s#'#'\"'\"'#g;s#.*#par_regions='&'#" ; else echo "# par_regions="; fi ) $( if [ ! -z ${VIASH_PAR_REGIONS_FILE+x} ]; then echo "${VIASH_PAR_REGIONS_FILE}" | sed "s#'#'\"'\"'#g;s#.*#par_regions_file='&'#" ; else echo "# par_regions_file="; fi ) $( if [ ! -z ${VIASH_PAR_REGIONS_OVERLAP+x} ]; then echo "${VIASH_PAR_REGIONS_OVERLAP}" | sed "s#'#'\"'\"'#g;s#.*#par_regions_overlap='&'#" ; else echo "# par_regions_overlap="; fi ) +$( if [ ! -z ${VIASH_PAR_VERBOSITY+x} ]; then echo "${VIASH_PAR_VERBOSITY}" | sed "s#'#'\"'\"'#g;s#.*#par_verbosity='&'#" ; else echo "# par_verbosity="; fi ) +$( if [ ! -z ${VIASH_PAR_WRITE_INDEX+x} ]; then echo "${VIASH_PAR_WRITE_INDEX}" | sed "s#'#'\"'\"'#g;s#.*#par_write_index='&'#" ; else echo "# par_write_index="; fi ) $( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "${VIASH_META_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_name='&'#" ; else echo "# meta_name="; fi ) $( if [ ! -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then echo "${VIASH_META_FUNCTIONALITY_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_functionality_name='&'#" ; else echo "# meta_functionality_name="; fi ) $( if [ ! -z ${VIASH_META_RESOURCES_DIR+x} ]; then echo "${VIASH_META_RESOURCES_DIR}" | sed "s#'#'\"'\"'#g;s#.*#meta_resources_dir='&'#" ; else echo "# meta_resources_dir="; fi ) @@ -1514,55 +1632,71 @@ $( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}" ## VIASH END -# Exit on error set -eo pipefail -# Unset parameters +# Unset false boolean parameters unset_if_false=( - par_allow_overlaps - par_compact_PS - par_ligate - par_ligate_force - par_ligate_warn - par_no_version - par_naive - par_naive_force + par_allow_overlaps + par_compact_ps + par_remove_duplicates + par_drop_genotypes + par_ligate + par_ligate_force + par_ligate_warn + par_no_version + par_naive + par_naive_force ) for par in \${unset_if_false[@]}; do - test_val="\${!par}" - [[ "\$test_val" == "false" ]] && unset \$par + test_val="\${!par}" + [[ "\$test_val" == "false" ]] && unset \$par done -# Check to see whether the par_input or the par_file_list is set +# Check that either input files or file_list is provided if [[ -z "\${par_input}" && -z "\${par_file_list}" ]]; then - echo "Error: One of the parameters '--input' or '--file_list' must be used." - exit 1 + echo "Error: One of the parameters '--input' or '--file_list' must be used." + exit 1 fi -# Create input array -IFS=";" read -ra input <<< \$par_input +# Handle multiple input files (semicolon-separated from Viash) +if [[ -n "\$par_input" ]]; then + IFS=';' read -ra input_files <<< "\$par_input" +fi -# Execute bcftools concat with the provided arguments -bcftools concat \\ - \${par_allow_overlaps:+-a} \\ - \${par_compact_PS:+-c} \\ - \${par_remove_duplicates:+-d "\$par_remove_duplicates"} \\ - \${par_ligate:+-l} \\ - \${par_ligate_force:+--ligate-force} \\ - \${par_ligate_warn:+--ligate-warn} \\ - \${par_no_version:+--no-version} \\ - \${par_naive:+-n} \\ - \${par_naive_force:+--naive-force} \\ - \${par_output_type:+--O "\$par_output_type"} \\ - \${par_min_PQ:+-q "\$par_min_PQ"} \\ - \${par_regions:+-r "\$par_regions"} \\ - \${par_regions_file:+-R "\$par_regions_file"} \\ - \${par_regions_overlap:+--regions-overlap "\$par_regions_overlap"} \\ - \${meta_cpus:+--threads "\$meta_cpus"} \\ - -o \$par_output \\ - \${par_file_list:+-f "\$par_file_list"} \\ - \${input[@]} \\ +# Build command array +cmd_args=( + bcftools concat + \${par_allow_overlaps:+--allow-overlaps} + \${par_compact_ps:+--compact-PS} + \${par_rm_dups:+--rm-dups "\$par_rm_dups"} + \${par_remove_duplicates:+--remove-duplicates} + \${par_drop_genotypes:+--drop-genotypes} + \${par_ligate:+--ligate} + \${par_ligate_force:+--ligate-force} + \${par_ligate_warn:+--ligate-warn} + \${par_no_version:+--no-version} + \${par_naive:+--naive} + \${par_naive_force:+--naive-force} + \${par_output_type:+--output-type "\$par_output_type"} + \${par_min_pq:+--min-PQ "\$par_min_pq"} + \${par_regions:+--regions "\$par_regions"} + \${par_regions_file:+--regions-file "\$par_regions_file"} + \${par_regions_overlap:+--regions-overlap "\$par_regions_overlap"} + \${meta_cpus:+--threads "\$meta_cpus"} + \${par_verbosity:+--verbosity "\$par_verbosity"} + \${par_write_index:+--write-index="\$par_write_index"} + \${par_output:+--output "\$par_output"} + \${par_file_list:+--file-list "\$par_file_list"} +) + +# Add input files to command array +if [[ -n "\$par_input" ]]; then + cmd_args+=("\${input_files[@]}") +fi + +# Execute command +"\${cmd_args[@]}" VIASHMAIN bash "\$tempscript" & wait "\$!" diff --git a/target/executable/bcftools/bcftools_norm/.config.vsh.yaml b/target/executable/bcftools/bcftools_norm/.config.vsh.yaml index 509fe403..f0d78bc0 100644 --- a/target/executable/bcftools/bcftools_norm/.config.vsh.yaml +++ b/target/executable/bcftools/bcftools_norm/.config.vsh.yaml @@ -15,10 +15,11 @@ argument_groups: arguments: - type: "file" name: "--input" - alternatives: - - "-i" - description: "Input VCF/BCF file." + description: "Input VCF/BCF file.\n\nThe file to be normalized, left-aligned,\ + \ and/or processed.\n" info: null + example: + - "input.vcf.gz" must_exist: true create_parent: true required: true @@ -31,8 +32,11 @@ argument_groups: name: "--output" alternatives: - "-o" - description: "Output normalized VCF/BCF file." + description: "Write output to a file.\n\nIf not specified, output goes to standard\ + \ output.\n" info: null + example: + - "normalized.vcf.gz" must_exist: true create_parent: true required: true @@ -45,14 +49,18 @@ argument_groups: name: "--atomize" alternatives: - "-a" - description: "Decompose complex variants (e.g., MNVs become consecutive SNVs).\n" + description: "Decompose complex variants (e.g., MNVs become consecutive SNVs).\n\ + \nBreaks down complex variants into simpler components.\n" info: null direction: "input" - type: "string" name: "--atom_overlaps" description: "Use the star allele (*) for overlapping alleles or set to missing\ - \ (.).\n" + \ (.).\n\n**Options:**\n- `*`: Use star allele for overlaps (default)\n- `.`:\ + \ Set overlapping alleles to missing\n" info: null + example: + - "*" required: false choices: - "." @@ -65,8 +73,12 @@ argument_groups: alternatives: - "-c" description: "Check REF alleles and exit (e), warn (w), exclude (x), or set (s)\ - \ bad sites.\n" + \ bad sites.\n\n**Options:**\n- `e`: exit on REF mismatch (default)\n- `w`:\ + \ warn about REF mismatches\n- `x`: exclude sites with REF mismatches\n- `s`:\ + \ set/fix REF mismatches\n" info: null + example: + - "w" required: false choices: - "e" @@ -76,13 +88,25 @@ argument_groups: direction: "input" multiple: false multiple_sep: ";" + - type: "boolean_true" + name: "--remove_duplicates_flag" + alternatives: + - "-D" + description: "Remove duplicate lines of the same type.\n\nShorthand for --rm_dup\ + \ exact.\n" + info: null + direction: "input" - type: "string" - name: "--remove_duplicates" + name: "--rm_dup" alternatives: - "-d" - description: "Remove duplicate snps, indels, both, all, exact matches, or none\ - \ (old -D option)." + description: "Remove duplicate snps|indels|both|all|exact.\n\n**Options:**\n-\ + \ `snps`: Remove duplicate SNPs\n- `indels`: Remove duplicate indels\n- `both`:\ + \ Remove duplicate SNPs and indels\n- `all`: Remove all duplicates\n- `exact`:\ + \ Remove exact duplicates only\n" info: null + example: + - "exact" required: false choices: - "snps" @@ -90,7 +114,19 @@ argument_groups: - "both" - "all" - "exact" - - "none" + direction: "input" + multiple: false + multiple_sep: ";" + - type: "string" + name: "--exclude" + alternatives: + - "-e" + description: "Do not normalize records for which the expression is true.\n\nUses\ + \ bcftools expression syntax (see man page for details).\n" + info: null + example: + - "INFO/DP<10" + required: false direction: "input" multiple: false multiple_sep: ";" @@ -98,8 +134,11 @@ argument_groups: name: "--fasta_ref" alternatives: - "-f" - description: "Reference fasta sequence file." + description: "Reference sequence file.\n\nRequired for checking REF alleles and\ + \ left-alignment.\n" info: null + example: + - "reference.fa" must_exist: true create_parent: true required: false @@ -108,15 +147,45 @@ argument_groups: multiple_sep: ";" - type: "boolean_true" name: "--force" - description: "Try to proceed even if malformed tags are encountered. \nExperimental,\ - \ use at your own risk.\n" + description: "Try to proceed even if malformed tags are encountered.\n\n**Warning:**\ + \ Experimental feature, use at your own risk.\n" info: null direction: "input" + - type: "file" + name: "--gff_annot" + alternatives: + - "-g" + description: "Follow HGVS 3'rule and right-align variants in transcripts on the\ + \ forward strand.\n\nUses GFF annotation file for transcript information.\n" + info: null + example: + - "genes.gff" + must_exist: true + create_parent: true + required: false + direction: "input" + multiple: false + multiple_sep: ";" + - type: "string" + name: "--include" + alternatives: + - "-i" + description: "Normalize only records for which the expression is true.\n\nUses\ + \ bcftools expression syntax (see man page for details).\n" + info: null + example: + - "QUAL>=30" + required: false + direction: "input" + multiple: false + multiple_sep: ";" - type: "string" name: "--keep_sum" - description: "Keep vector sum constant when splitting multiallelics (see github\ - \ issue #360).\n" + description: "Keep vector sum constant when splitting multiallelics.\n\nComma-separated\ + \ list of INFO tags (see github issue #360).\n" info: null + example: + - "AC,AF" required: false direction: "input" multiple: false @@ -125,9 +194,12 @@ argument_groups: name: "--multiallelics" alternatives: - "-m" - description: "Split multiallelics (-) or join biallelics (+), type: snps, indels,\ - \ both, any [default: both].\n" + description: "Split multiallelics (-) or join biallelics (+), type: snps|indels|both|any.\n\ + \n**Options:**\n- `-both`: Split multiallelic sites (default)\n- `+both`: Join\ + \ biallelic sites\n- Use `snps`, `indels`, `any` for specific variant types\n" info: null + example: + - "-both" required: false choices: - "+snps" @@ -141,25 +213,56 @@ argument_groups: direction: "input" multiple: false multiple_sep: ";" + - type: "string" + name: "--multi_overlaps" + description: "Fill in the reference (0) or missing (.) allele when splitting multiallelics.\n\ + \n**Options:**\n- `0`: Fill with reference allele (default)\n- `.`: Fill with\ + \ missing allele\n" + info: null + example: + - "0" + required: false + choices: + - "0" + - "." + direction: "input" + multiple: false + multiple_sep: ";" - type: "boolean_true" name: "--no_version" - description: "Do not append version and command line information to the header." + description: "Do not append version and command line to the header.\n\nProduces\ + \ cleaner output headers.\n" info: null direction: "input" - type: "boolean_true" name: "--do_not_normalize" alternatives: - "-N" - description: "Do not normalize indels (with -m or -c s)." + description: "Do not normalize indels (with -m or -c s).\n\nSkips indel left-alignment\ + \ and normalization.\n" info: null direction: "input" + - type: "string" + name: "--old_rec_tag" + description: "Annotate modified records with INFO/STR indicating the original\ + \ variant.\n\nAdds specified INFO tag to track original variants.\n" + info: null + example: + - "OLD_VARIANT" + required: false + direction: "input" + multiple: false + multiple_sep: ";" - type: "string" name: "--output_type" alternatives: - - "--O" - description: "Output type:\n u: uncompressed BCF\n z: compressed VCF\n b: compressed\ - \ BCF\n v: uncompressed VCF\n" + - "-O" + description: "Output type and compression level.\n\n**Options:**\n- `u`: uncompressed\ + \ BCF\n- `b`: compressed BCF\n- `v`: uncompressed VCF (default)\n- `z`: compressed\ + \ VCF (with optional compression level 0-9)\n" info: null + example: + - "z" required: false choices: - "u" @@ -169,24 +272,15 @@ argument_groups: direction: "input" multiple: false multiple_sep: ";" - - type: "string" - name: "--old_rec_tag" - description: "Annotate modified records with INFO/STR indicating the original\ - \ variant." - info: null - required: false - direction: "input" - multiple: false - multiple_sep: ";" - type: "string" name: "--regions" alternatives: - - "--r" - description: "Restrict to comma-separated list of regions. \nFollowing formats\ - \ are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​].\n" + - "-r" + description: "Restrict to comma-separated list of regions.\n\n**Formats supported:**\ + \ chr|chr:pos|chr:beg-end|chr:beg-[,…​]\n" info: null example: - - "20:1000000-2000000" + - "chr20:1000000-2000000" required: false direction: "input" multiple: false @@ -194,11 +288,12 @@ argument_groups: - type: "file" name: "--regions_file" alternatives: - - "--R" - description: "Restrict to regions listed in a file. \nRegions can be specified\ - \ either on a VCF, BED, or tab-delimited file (the default). \nFor more information\ - \ check manual.\n" + - "-R" + description: "Restrict to regions listed in a file.\n\nRegions can be specified\ + \ in VCF, BED, or tab-delimited format.\n" info: null + example: + - "regions.bed" must_exist: true create_parent: true required: false @@ -207,52 +302,54 @@ argument_groups: multiple_sep: ";" - type: "string" name: "--regions_overlap" - description: "This option controls how overlapping records are determined: \n\ - set to 'pos' or '0' if the VCF record has to have POS inside a region (this\ - \ corresponds to the default behavior of -t/-T); \nset to 'record' or '1' if\ - \ also overlapping records with POS outside a region should be included (this\ - \ is the default behavior of -r/-R, \nand includes indels with POS at the end\ - \ of a region, which are technically outside the region); \nor set to 'variant'\ - \ or '2' to include only true overlapping variation (compare the full VCF representation\ - \ \"TA>T-\" vs the true sequence variation \"A>-\").\n" + description: "Include if POS in the region (0), record overlaps (1), variant overlaps\ + \ (2).\n\n**Options:**\n- `0`: POS inside region (default for -t/-T)\n- `1`:\ + \ overlapping records included (default for -r/-R)\n- `2`: true overlapping\ + \ variation only\n" info: null + example: + - "1" required: false choices: - - "pos" - - "record" - - "variant" - "0" - "1" - "2" direction: "input" multiple: false multiple_sep: ";" - - type: "integer" - name: "--site_win" - alternatives: - - "-w" - description: "Buffer for sorting lines that changed position during realignment.\n" - info: null - required: false - direction: "input" - multiple: false - multiple_sep: ";" - type: "boolean_true" name: "--strict_filter" alternatives: - "-s" description: "When merging (-m+), merged site is PASS only if all sites being\ - \ merged PASS." + \ merged PASS.\n\nStricter FILTER handling during multiallelic joining.\n" info: null direction: "input" + - type: "string" + name: "--sort" + alternatives: + - "-S" + description: "Sort order: chr_pos,lex.\n\n**Options:**\n- `chr_pos`: Sort by chromosome\ + \ and position (default)\n- `lex`: Lexicographic sort\n" + info: null + example: + - "chr_pos" + required: false + choices: + - "chr_pos" + - "lex" + direction: "input" + multiple: false + multiple_sep: ";" - type: "string" name: "--targets" alternatives: - "-t" - description: "Similar to --regions but streams rather than index-jumps." + description: "Similar to --regions but streams rather than index-jumps.\n\nMore\ + \ efficient for processing many small regions.\n" info: null example: - - "20:1000000-2000000" + - "chr20:1000000-2000000" required: false direction: "input" multiple: false @@ -261,8 +358,11 @@ argument_groups: name: "--targets_file" alternatives: - "-T" - description: "Similar to --regions_file but streams rather than index-jumps." + description: "Similar to --regions_file but streams rather than index-jumps.\n\ + \nMore efficient for processing many regions from file.\n" info: null + example: + - "targets.bed" must_exist: true create_parent: true required: false @@ -272,19 +372,56 @@ argument_groups: - type: "string" name: "--targets_overlap" description: "Include if POS in the region (0), record overlaps (1), variant overlaps\ - \ (2).\nSimilar to --regions_overlap.\n" + \ (2).\n\nSimilar to --regions_overlap but for streaming mode.\n" info: null + example: + - "0" required: false choices: - - "pos" - - "record" - - "variant" - "0" - "1" - "2" direction: "input" multiple: false multiple_sep: ";" + - type: "integer" + name: "--verbosity" + alternatives: + - "-v" + description: "Verbosity level.\n\nControls amount of diagnostic output.\n" + info: null + example: + - 1 + required: false + direction: "input" + multiple: false + multiple_sep: ";" + - type: "integer" + name: "--site_win" + alternatives: + - "-w" + description: "Buffer for sorting lines which changed position during realignment.\n\ + \nLarger values use more memory but handle more complex rearrangements.\n" + info: null + example: + - 1000 + required: false + direction: "input" + multiple: false + multiple_sep: ";" + - type: "string" + name: "--write_index" + alternatives: + - "-W" + description: "Automatically index the output files.\n\n**Format:** Specify index\ + \ format or use default.\n" + info: null + example: + - "tbi" + required: false + direction: "input" + multiple: false + multiple_sep: ";" resources: - type: "bash_script" path: "script.sh" @@ -296,6 +433,8 @@ test_resources: - type: "bash_script" path: "test.sh" is_executable: true +- type: "file" + path: "test_helpers.sh" info: null status: "enabled" scope: @@ -303,6 +442,7 @@ scope: target: "public" requirements: commands: + - "bcftools" - "ps" keywords: - "Normalize" @@ -385,25 +525,14 @@ runners: engines: - type: "docker" id: "docker" - image: "debian:stable-slim" + image: "quay.io/biocontainers/bcftools:1.22--h3a4d415_1" target_registry: "images.viash-hub.com" target_tag: "main" namespace_separator: "/" setup: - - type: "apt" - packages: - - "bcftools" - - "procps" - interactive: false - type: "docker" run: - - "echo \"bcftools: \\\"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftools\ - \ //p')\\\"\" > /var/software_versions.txt\n" - test_setup: - - type: "apt" - packages: - - "tabix" - interactive: false + - "bcftools --version 2>&1 | head -1 | sed 's/bcftools /bcftools: /' > /var/software_versions.txt\n" entrypoint: [] cmd: null - type: "native" @@ -415,7 +544,7 @@ build_info: output: "target/executable/bcftools/bcftools_norm" executable: "target/executable/bcftools/bcftools_norm/bcftools_norm" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -437,138 +566,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bcftools/bcftools_norm/bcftools_norm b/target/executable/bcftools/bcftools_norm/bcftools_norm index 6fd5fb18..a812231e 100755 --- a/target/executable/bcftools/bcftools_norm/bcftools_norm +++ b/target/executable/bcftools/bcftools_norm/bcftools_norm @@ -446,19 +446,15 @@ function ViashDockerfile { if [[ "$engine_id" == "docker" ]]; then cat << 'VIASHDOCKER' -FROM debian:stable-slim +FROM quay.io/biocontainers/bcftools:1.22--h3a4d415_1 ENTRYPOINT [] -RUN apt-get update && \ - DEBIAN_FRONTEND=noninteractive apt-get install -y bcftools procps && \ - rm -rf /var/lib/apt/lists/* - -RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftools //p')\"" > /var/software_versions.txt +RUN bcftools --version 2>&1 | head -1 | sed 's/bcftools /bcftools: /' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_norm" -LABEL org.opencontainers.image.created="2025-09-01T11:02:55Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:06Z" LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -583,129 +579,222 @@ function ViashHelp { echo "recover multiallelics from multiple rows." echo "" echo "Inputs:" - echo " -i, --input" + echo " --input" echo " type: file, required parameter, file must exist" + echo " example: input.vcf.gz" echo " Input VCF/BCF file." + echo " The file to be normalized, left-aligned, and/or processed." echo "" echo "Outputs:" echo " -o, --output" echo " type: file, required parameter, output, file must exist" - echo " Output normalized VCF/BCF file." + echo " example: normalized.vcf.gz" + echo " Write output to a file." + echo " If not specified, output goes to standard output." echo "" echo "Options:" echo " -a, --atomize" echo " type: boolean_true" echo " Decompose complex variants (e.g., MNVs become consecutive SNVs)." + echo " Breaks down complex variants into simpler components." echo "" echo " --atom_overlaps" echo " type: string" + echo " example: *" echo " choices: [ ., * ]" echo " Use the star allele (*) for overlapping alleles or set to missing (.)." + echo " **Options:**" + echo " - \`*\`: Use star allele for overlaps (default)" + echo " - \`.\`: Set overlapping alleles to missing" echo "" echo " -c, --check_ref" echo " type: string" + echo " example: w" echo " choices: [ e, w, x, s ]" echo " Check REF alleles and exit (e), warn (w), exclude (x), or set (s) bad" echo " sites." + echo " **Options:**" + echo " - \`e\`: exit on REF mismatch (default)" + echo " - \`w\`: warn about REF mismatches" + echo " - \`x\`: exclude sites with REF mismatches" + echo " - \`s\`: set/fix REF mismatches" echo "" - echo " -d, --remove_duplicates" + echo " -D, --remove_duplicates_flag" + echo " type: boolean_true" + echo " Remove duplicate lines of the same type." + echo " Shorthand for --rm_dup exact." + echo "" + echo " -d, --rm_dup" echo " type: string" - echo " choices: [ snps, indels, both, all, exact, none ]" - echo " Remove duplicate snps, indels, both, all, exact matches, or none (old -D" - echo " option)." + echo " example: exact" + echo " choices: [ snps, indels, both, all, exact ]" + echo " Remove duplicate snps|indels|both|all|exact." + echo " **Options:**" + echo " - \`snps\`: Remove duplicate SNPs" + echo " - \`indels\`: Remove duplicate indels" + echo " - \`both\`: Remove duplicate SNPs and indels" + echo " - \`all\`: Remove all duplicates" + echo " - \`exact\`: Remove exact duplicates only" + echo "" + echo " -e, --exclude" + echo " type: string" + echo " example: INFO/DP<10" + echo " Do not normalize records for which the expression is true." + echo " Uses bcftools expression syntax (see man page for details)." echo "" echo " -f, --fasta_ref" echo " type: file, file must exist" - echo " Reference fasta sequence file." + echo " example: reference.fa" + echo " Reference sequence file." + echo " Required for checking REF alleles and left-alignment." echo "" echo " --force" echo " type: boolean_true" echo " Try to proceed even if malformed tags are encountered." - echo " Experimental, use at your own risk." + echo " **Warning:** Experimental feature, use at your own risk." + echo "" + echo " -g, --gff_annot" + echo " type: file, file must exist" + echo " example: genes.gff" + echo " Follow HGVS 3'rule and right-align variants in transcripts on the" + echo " forward strand." + echo " Uses GFF annotation file for transcript information." + echo "" + echo " -i, --include" + echo " type: string" + echo " example: QUAL>=30" + echo " Normalize only records for which the expression is true." + echo " Uses bcftools expression syntax (see man page for details)." echo "" echo " --keep_sum" echo " type: string" - echo " Keep vector sum constant when splitting multiallelics (see github issue" - echo " #360)." + echo " example: AC,AF" + echo " Keep vector sum constant when splitting multiallelics." + echo " Comma-separated list of INFO tags (see github issue #360)." echo "" echo " -m, --multiallelics" echo " type: string" + echo " example: -both" echo " choices: [ +snps, +indels, +both, +any, -snps, -indels, -both, -any ]" - echo " Split multiallelics (-) or join biallelics (+), type: snps, indels," - echo " both, any [default: both]." + echo " Split multiallelics (-) or join biallelics (+), type:" + echo " snps|indels|both|any." + echo " **Options:**" + echo " - \`-both\`: Split multiallelic sites (default)" + echo " - \`+both\`: Join biallelic sites" + echo " - Use \`snps\`, \`indels\`, \`any\` for specific variant types" + echo "" + echo " --multi_overlaps" + echo " type: string" + echo " example: 0" + echo " choices: [ 0, . ]" + echo " Fill in the reference (0) or missing (.) allele when splitting" + echo " multiallelics." + echo " **Options:**" + echo " - \`0\`: Fill with reference allele (default)" + echo " - \`.\`: Fill with missing allele" echo "" echo " --no_version" echo " type: boolean_true" - echo " Do not append version and command line information to the header." + echo " Do not append version and command line to the header." + echo " Produces cleaner output headers." echo "" echo " -N, --do_not_normalize" echo " type: boolean_true" echo " Do not normalize indels (with -m or -c s)." - echo "" - echo " --O, --output_type" - echo " type: string" - echo " choices: [ u, z, b, v ]" - echo " Output type:" - echo " u: uncompressed BCF" - echo " z: compressed VCF" - echo " b: compressed BCF" - echo " v: uncompressed VCF" + echo " Skips indel left-alignment and normalization." echo "" echo " --old_rec_tag" echo " type: string" + echo " example: OLD_VARIANT" echo " Annotate modified records with INFO/STR indicating the original variant." + echo " Adds specified INFO tag to track original variants." echo "" - echo " --r, --regions" + echo " -O, --output_type" echo " type: string" - echo " example: 20:1000000-2000000" - echo " Restrict to comma-separated list of regions." - echo " Following formats are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​]." + echo " example: z" + echo " choices: [ u, z, b, v ]" + echo " Output type and compression level." + echo " **Options:**" + echo " - \`u\`: uncompressed BCF" + echo " - \`b\`: compressed BCF" + echo " - \`v\`: uncompressed VCF (default)" + echo " - \`z\`: compressed VCF (with optional compression level 0-9)" echo "" - echo " --R, --regions_file" + echo " -r, --regions" + echo " type: string" + echo " example: chr20:1000000-2000000" + echo " Restrict to comma-separated list of regions." + echo " **Formats supported:** chr|chr:pos|chr:beg-end|chr:beg-[,…​]" + echo "" + echo " -R, --regions_file" echo " type: file, file must exist" + echo " example: regions.bed" echo " Restrict to regions listed in a file." - echo " Regions can be specified either on a VCF, BED, or tab-delimited file" - echo " (the default)." - echo " For more information check manual." + echo " Regions can be specified in VCF, BED, or tab-delimited format." echo "" echo " --regions_overlap" echo " type: string" - echo " choices: [ pos, record, variant, 0, 1, 2 ]" - echo " This option controls how overlapping records are determined:" - echo " set to 'pos' or '0' if the VCF record has to have POS inside a region" - echo " (this corresponds to the default behavior of -t/-T);" - echo " set to 'record' or '1' if also overlapping records with POS outside a" - echo " region should be included (this is the default behavior of -r/-R," - echo " and includes indels with POS at the end of a region, which are" - echo " technically outside the region);" - echo " or set to 'variant' or '2' to include only true overlapping variation" - echo " (compare the full VCF representation \"TA>T-\" vs the true sequence" - echo " variation \"A>-\")." - echo "" - echo " -w, --site_win" - echo " type: integer" - echo " Buffer for sorting lines that changed position during realignment." + echo " example: 1" + echo " choices: [ 0, 1, 2 ]" + echo " Include if POS in the region (0), record overlaps (1), variant overlaps" + echo " (2)." + echo " **Options:**" + echo " - \`0\`: POS inside region (default for -t/-T)" + echo " - \`1\`: overlapping records included (default for -r/-R)" + echo " - \`2\`: true overlapping variation only" echo "" echo " -s, --strict_filter" echo " type: boolean_true" echo " When merging (-m+), merged site is PASS only if all sites being merged" echo " PASS." + echo " Stricter FILTER handling during multiallelic joining." + echo "" + echo " -S, --sort" + echo " type: string" + echo " example: chr_pos" + echo " choices: [ chr_pos, lex ]" + echo " Sort order: chr_pos,lex." + echo " **Options:**" + echo " - \`chr_pos\`: Sort by chromosome and position (default)" + echo " - \`lex\`: Lexicographic sort" echo "" echo " -t, --targets" echo " type: string" - echo " example: 20:1000000-2000000" + echo " example: chr20:1000000-2000000" echo " Similar to --regions but streams rather than index-jumps." + echo " More efficient for processing many small regions." echo "" echo " -T, --targets_file" echo " type: file, file must exist" + echo " example: targets.bed" echo " Similar to --regions_file but streams rather than index-jumps." + echo " More efficient for processing many regions from file." echo "" echo " --targets_overlap" echo " type: string" - echo " choices: [ pos, record, variant, 0, 1, 2 ]" + echo " example: 0" + echo " choices: [ 0, 1, 2 ]" echo " Include if POS in the region (0), record overlaps (1), variant overlaps" echo " (2)." - echo " Similar to --regions_overlap." + echo " Similar to --regions_overlap but for streaming mode." + echo "" + echo " -v, --verbosity" + echo " type: integer" + echo " example: 1" + echo " Verbosity level." + echo " Controls amount of diagnostic output." + echo "" + echo " -w, --site_win" + echo " type: integer" + echo " example: 1000" + echo " Buffer for sorting lines which changed position during realignment." + echo " Larger values use more memory but handle more complex rearrangements." + echo "" + echo " -W, --write_index" + echo " type: string" + echo " example: tbi" + echo " Automatically index the output files." + echo " **Format:** Specify index format or use default." echo "" echo "Viash built in Computational Requirements:" echo " ---cpus=INT" @@ -768,12 +857,6 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_INPUT=$(ViashRemoveFlags "$1") shift 1 ;; - -i) - [ -n "$VIASH_PAR_INPUT" ] && ViashError Bad arguments for option \'-i\': \'$VIASH_PAR_INPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_INPUT="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to -i. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; --output) [ -n "$VIASH_PAR_OUTPUT" ] && ViashError Bad arguments for option \'--output\': \'$VIASH_PAR_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 VIASH_PAR_OUTPUT="$2" @@ -829,23 +912,50 @@ while [[ $# -gt 0 ]]; do [ $# -lt 2 ] && ViashError Not enough arguments passed to -c. Use "--help" to get more information on the parameters. && exit 1 shift 2 ;; - --remove_duplicates) - [ -n "$VIASH_PAR_REMOVE_DUPLICATES" ] && ViashError Bad arguments for option \'--remove_duplicates\': \'$VIASH_PAR_REMOVE_DUPLICATES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_REMOVE_DUPLICATES="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --remove_duplicates. Use "--help" to get more information on the parameters. && exit 1 + --remove_duplicates_flag) + [ -n "$VIASH_PAR_REMOVE_DUPLICATES_FLAG" ] && ViashError Bad arguments for option \'--remove_duplicates_flag\': \'$VIASH_PAR_REMOVE_DUPLICATES_FLAG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_REMOVE_DUPLICATES_FLAG=true + shift 1 + ;; + -D) + [ -n "$VIASH_PAR_REMOVE_DUPLICATES_FLAG" ] && ViashError Bad arguments for option \'-D\': \'$VIASH_PAR_REMOVE_DUPLICATES_FLAG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_REMOVE_DUPLICATES_FLAG=true + shift 1 + ;; + --rm_dup) + [ -n "$VIASH_PAR_RM_DUP" ] && ViashError Bad arguments for option \'--rm_dup\': \'$VIASH_PAR_RM_DUP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_RM_DUP="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --rm_dup. Use "--help" to get more information on the parameters. && exit 1 shift 2 ;; - --remove_duplicates=*) - [ -n "$VIASH_PAR_REMOVE_DUPLICATES" ] && ViashError Bad arguments for option \'--remove_duplicates=*\': \'$VIASH_PAR_REMOVE_DUPLICATES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_REMOVE_DUPLICATES=$(ViashRemoveFlags "$1") + --rm_dup=*) + [ -n "$VIASH_PAR_RM_DUP" ] && ViashError Bad arguments for option \'--rm_dup=*\': \'$VIASH_PAR_RM_DUP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_RM_DUP=$(ViashRemoveFlags "$1") shift 1 ;; -d) - [ -n "$VIASH_PAR_REMOVE_DUPLICATES" ] && ViashError Bad arguments for option \'-d\': \'$VIASH_PAR_REMOVE_DUPLICATES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_REMOVE_DUPLICATES="$2" + [ -n "$VIASH_PAR_RM_DUP" ] && ViashError Bad arguments for option \'-d\': \'$VIASH_PAR_RM_DUP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_RM_DUP="$2" [ $# -lt 2 ] && ViashError Not enough arguments passed to -d. Use "--help" to get more information on the parameters. && exit 1 shift 2 ;; + --exclude) + [ -n "$VIASH_PAR_EXCLUDE" ] && ViashError Bad arguments for option \'--exclude\': \'$VIASH_PAR_EXCLUDE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_EXCLUDE="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --exclude. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --exclude=*) + [ -n "$VIASH_PAR_EXCLUDE" ] && ViashError Bad arguments for option \'--exclude=*\': \'$VIASH_PAR_EXCLUDE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_EXCLUDE=$(ViashRemoveFlags "$1") + shift 1 + ;; + -e) + [ -n "$VIASH_PAR_EXCLUDE" ] && ViashError Bad arguments for option \'-e\': \'$VIASH_PAR_EXCLUDE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_EXCLUDE="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to -e. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; --fasta_ref) [ -n "$VIASH_PAR_FASTA_REF" ] && ViashError Bad arguments for option \'--fasta_ref\': \'$VIASH_PAR_FASTA_REF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 VIASH_PAR_FASTA_REF="$2" @@ -868,6 +978,40 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_FORCE=true shift 1 ;; + --gff_annot) + [ -n "$VIASH_PAR_GFF_ANNOT" ] && ViashError Bad arguments for option \'--gff_annot\': \'$VIASH_PAR_GFF_ANNOT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_GFF_ANNOT="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --gff_annot. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --gff_annot=*) + [ -n "$VIASH_PAR_GFF_ANNOT" ] && ViashError Bad arguments for option \'--gff_annot=*\': \'$VIASH_PAR_GFF_ANNOT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_GFF_ANNOT=$(ViashRemoveFlags "$1") + shift 1 + ;; + -g) + [ -n "$VIASH_PAR_GFF_ANNOT" ] && ViashError Bad arguments for option \'-g\': \'$VIASH_PAR_GFF_ANNOT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_GFF_ANNOT="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to -g. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --include) + [ -n "$VIASH_PAR_INCLUDE" ] && ViashError Bad arguments for option \'--include\': \'$VIASH_PAR_INCLUDE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_INCLUDE="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --include. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --include=*) + [ -n "$VIASH_PAR_INCLUDE" ] && ViashError Bad arguments for option \'--include=*\': \'$VIASH_PAR_INCLUDE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_INCLUDE=$(ViashRemoveFlags "$1") + shift 1 + ;; + -i) + [ -n "$VIASH_PAR_INCLUDE" ] && ViashError Bad arguments for option \'-i\': \'$VIASH_PAR_INCLUDE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_INCLUDE="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to -i. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; --keep_sum) [ -n "$VIASH_PAR_KEEP_SUM" ] && ViashError Bad arguments for option \'--keep_sum\': \'$VIASH_PAR_KEEP_SUM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 VIASH_PAR_KEEP_SUM="$2" @@ -896,6 +1040,17 @@ while [[ $# -gt 0 ]]; do [ $# -lt 2 ] && ViashError Not enough arguments passed to -m. Use "--help" to get more information on the parameters. && exit 1 shift 2 ;; + --multi_overlaps) + [ -n "$VIASH_PAR_MULTI_OVERLAPS" ] && ViashError Bad arguments for option \'--multi_overlaps\': \'$VIASH_PAR_MULTI_OVERLAPS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_MULTI_OVERLAPS="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --multi_overlaps. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --multi_overlaps=*) + [ -n "$VIASH_PAR_MULTI_OVERLAPS" ] && ViashError Bad arguments for option \'--multi_overlaps=*\': \'$VIASH_PAR_MULTI_OVERLAPS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_MULTI_OVERLAPS=$(ViashRemoveFlags "$1") + shift 1 + ;; --no_version) [ -n "$VIASH_PAR_NO_VERSION" ] && ViashError Bad arguments for option \'--no_version\': \'$VIASH_PAR_NO_VERSION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 VIASH_PAR_NO_VERSION=true @@ -911,6 +1066,17 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_DO_NOT_NORMALIZE=true shift 1 ;; + --old_rec_tag) + [ -n "$VIASH_PAR_OLD_REC_TAG" ] && ViashError Bad arguments for option \'--old_rec_tag\': \'$VIASH_PAR_OLD_REC_TAG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_OLD_REC_TAG="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --old_rec_tag. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --old_rec_tag=*) + [ -n "$VIASH_PAR_OLD_REC_TAG" ] && ViashError Bad arguments for option \'--old_rec_tag=*\': \'$VIASH_PAR_OLD_REC_TAG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_OLD_REC_TAG=$(ViashRemoveFlags "$1") + shift 1 + ;; --output_type) [ -n "$VIASH_PAR_OUTPUT_TYPE" ] && ViashError Bad arguments for option \'--output_type\': \'$VIASH_PAR_OUTPUT_TYPE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 VIASH_PAR_OUTPUT_TYPE="$2" @@ -922,23 +1088,12 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_OUTPUT_TYPE=$(ViashRemoveFlags "$1") shift 1 ;; - --O) - [ -n "$VIASH_PAR_OUTPUT_TYPE" ] && ViashError Bad arguments for option \'--O\': \'$VIASH_PAR_OUTPUT_TYPE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + -O) + [ -n "$VIASH_PAR_OUTPUT_TYPE" ] && ViashError Bad arguments for option \'-O\': \'$VIASH_PAR_OUTPUT_TYPE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 VIASH_PAR_OUTPUT_TYPE="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --O. Use "--help" to get more information on the parameters. && exit 1 + [ $# -lt 2 ] && ViashError Not enough arguments passed to -O. Use "--help" to get more information on the parameters. && exit 1 shift 2 ;; - --old_rec_tag) - [ -n "$VIASH_PAR_OLD_REC_TAG" ] && ViashError Bad arguments for option \'--old_rec_tag\': \'$VIASH_PAR_OLD_REC_TAG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_OLD_REC_TAG="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --old_rec_tag. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --old_rec_tag=*) - [ -n "$VIASH_PAR_OLD_REC_TAG" ] && ViashError Bad arguments for option \'--old_rec_tag=*\': \'$VIASH_PAR_OLD_REC_TAG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_OLD_REC_TAG=$(ViashRemoveFlags "$1") - shift 1 - ;; --regions) [ -n "$VIASH_PAR_REGIONS" ] && ViashError Bad arguments for option \'--regions\': \'$VIASH_PAR_REGIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 VIASH_PAR_REGIONS="$2" @@ -950,10 +1105,10 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_REGIONS=$(ViashRemoveFlags "$1") shift 1 ;; - --r) - [ -n "$VIASH_PAR_REGIONS" ] && ViashError Bad arguments for option \'--r\': \'$VIASH_PAR_REGIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + -r) + [ -n "$VIASH_PAR_REGIONS" ] && ViashError Bad arguments for option \'-r\': \'$VIASH_PAR_REGIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 VIASH_PAR_REGIONS="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --r. Use "--help" to get more information on the parameters. && exit 1 + [ $# -lt 2 ] && ViashError Not enough arguments passed to -r. Use "--help" to get more information on the parameters. && exit 1 shift 2 ;; --regions_file) @@ -967,10 +1122,10 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_REGIONS_FILE=$(ViashRemoveFlags "$1") shift 1 ;; - --R) - [ -n "$VIASH_PAR_REGIONS_FILE" ] && ViashError Bad arguments for option \'--R\': \'$VIASH_PAR_REGIONS_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + -R) + [ -n "$VIASH_PAR_REGIONS_FILE" ] && ViashError Bad arguments for option \'-R\': \'$VIASH_PAR_REGIONS_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 VIASH_PAR_REGIONS_FILE="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --R. Use "--help" to get more information on the parameters. && exit 1 + [ $# -lt 2 ] && ViashError Not enough arguments passed to -R. Use "--help" to get more information on the parameters. && exit 1 shift 2 ;; --regions_overlap) @@ -984,23 +1139,6 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_REGIONS_OVERLAP=$(ViashRemoveFlags "$1") shift 1 ;; - --site_win) - [ -n "$VIASH_PAR_SITE_WIN" ] && ViashError Bad arguments for option \'--site_win\': \'$VIASH_PAR_SITE_WIN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_SITE_WIN="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --site_win. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --site_win=*) - [ -n "$VIASH_PAR_SITE_WIN" ] && ViashError Bad arguments for option \'--site_win=*\': \'$VIASH_PAR_SITE_WIN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_SITE_WIN=$(ViashRemoveFlags "$1") - shift 1 - ;; - -w) - [ -n "$VIASH_PAR_SITE_WIN" ] && ViashError Bad arguments for option \'-w\': \'$VIASH_PAR_SITE_WIN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_SITE_WIN="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to -w. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; --strict_filter) [ -n "$VIASH_PAR_STRICT_FILTER" ] && ViashError Bad arguments for option \'--strict_filter\': \'$VIASH_PAR_STRICT_FILTER\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 VIASH_PAR_STRICT_FILTER=true @@ -1011,6 +1149,23 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_STRICT_FILTER=true shift 1 ;; + --sort) + [ -n "$VIASH_PAR_SORT" ] && ViashError Bad arguments for option \'--sort\': \'$VIASH_PAR_SORT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_SORT="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --sort. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --sort=*) + [ -n "$VIASH_PAR_SORT" ] && ViashError Bad arguments for option \'--sort=*\': \'$VIASH_PAR_SORT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_SORT=$(ViashRemoveFlags "$1") + shift 1 + ;; + -S) + [ -n "$VIASH_PAR_SORT" ] && ViashError Bad arguments for option \'-S\': \'$VIASH_PAR_SORT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_SORT="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to -S. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; --targets) [ -n "$VIASH_PAR_TARGETS" ] && ViashError Bad arguments for option \'--targets\': \'$VIASH_PAR_TARGETS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 VIASH_PAR_TARGETS="$2" @@ -1056,6 +1211,57 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_TARGETS_OVERLAP=$(ViashRemoveFlags "$1") shift 1 ;; + --verbosity) + [ -n "$VIASH_PAR_VERBOSITY" ] && ViashError Bad arguments for option \'--verbosity\': \'$VIASH_PAR_VERBOSITY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_VERBOSITY="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --verbosity. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --verbosity=*) + [ -n "$VIASH_PAR_VERBOSITY" ] && ViashError Bad arguments for option \'--verbosity=*\': \'$VIASH_PAR_VERBOSITY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_VERBOSITY=$(ViashRemoveFlags "$1") + shift 1 + ;; + -v) + [ -n "$VIASH_PAR_VERBOSITY" ] && ViashError Bad arguments for option \'-v\': \'$VIASH_PAR_VERBOSITY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_VERBOSITY="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to -v. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --site_win) + [ -n "$VIASH_PAR_SITE_WIN" ] && ViashError Bad arguments for option \'--site_win\': \'$VIASH_PAR_SITE_WIN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_SITE_WIN="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --site_win. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --site_win=*) + [ -n "$VIASH_PAR_SITE_WIN" ] && ViashError Bad arguments for option \'--site_win=*\': \'$VIASH_PAR_SITE_WIN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_SITE_WIN=$(ViashRemoveFlags "$1") + shift 1 + ;; + -w) + [ -n "$VIASH_PAR_SITE_WIN" ] && ViashError Bad arguments for option \'-w\': \'$VIASH_PAR_SITE_WIN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_SITE_WIN="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to -w. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --write_index) + [ -n "$VIASH_PAR_WRITE_INDEX" ] && ViashError Bad arguments for option \'--write_index\': \'$VIASH_PAR_WRITE_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_WRITE_INDEX="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --write_index. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --write_index=*) + [ -n "$VIASH_PAR_WRITE_INDEX" ] && ViashError Bad arguments for option \'--write_index=*\': \'$VIASH_PAR_WRITE_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_WRITE_INDEX=$(ViashRemoveFlags "$1") + shift 1 + ;; + -W) + [ -n "$VIASH_PAR_WRITE_INDEX" ] && ViashError Bad arguments for option \'-W\': \'$VIASH_PAR_WRITE_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_WRITE_INDEX="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to -W. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; ---engine) VIASH_ENGINE_ID="$2" shift 2 @@ -1166,13 +1372,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bcftools' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bcftools' 'ps' 'bash' fi # setting computational defaults @@ -1265,6 +1471,9 @@ fi if [ -z ${VIASH_PAR_ATOMIZE+x} ]; then VIASH_PAR_ATOMIZE="false" fi +if [ -z ${VIASH_PAR_REMOVE_DUPLICATES_FLAG+x} ]; then + VIASH_PAR_REMOVE_DUPLICATES_FLAG="false" +fi if [ -z ${VIASH_PAR_FORCE+x} ]; then VIASH_PAR_FORCE="false" fi @@ -1287,6 +1496,10 @@ if [ ! -z "$VIASH_PAR_FASTA_REF" ] && [ ! -e "$VIASH_PAR_FASTA_REF" ]; then ViashError "Input file '$VIASH_PAR_FASTA_REF' does not exist." exit 1 fi +if [ ! -z "$VIASH_PAR_GFF_ANNOT" ] && [ ! -e "$VIASH_PAR_GFF_ANNOT" ]; then + ViashError "Input file '$VIASH_PAR_GFF_ANNOT' does not exist." + exit 1 +fi if [ ! -z "$VIASH_PAR_REGIONS_FILE" ] && [ ! -e "$VIASH_PAR_REGIONS_FILE" ]; then ViashError "Input file '$VIASH_PAR_REGIONS_FILE' does not exist." exit 1 @@ -1303,6 +1516,12 @@ if [[ -n "$VIASH_PAR_ATOMIZE" ]]; then exit 1 fi fi +if [[ -n "$VIASH_PAR_REMOVE_DUPLICATES_FLAG" ]]; then + if ! [[ "$VIASH_PAR_REMOVE_DUPLICATES_FLAG" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then + ViashError '--remove_duplicates_flag' has to be a boolean_true. Use "--help" to get more information on the parameters. + exit 1 + fi +fi if [[ -n "$VIASH_PAR_FORCE" ]]; then if ! [[ "$VIASH_PAR_FORCE" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then ViashError '--force' has to be a boolean_true. Use "--help" to get more information on the parameters. @@ -1321,18 +1540,24 @@ if [[ -n "$VIASH_PAR_DO_NOT_NORMALIZE" ]]; then exit 1 fi fi -if [[ -n "$VIASH_PAR_SITE_WIN" ]]; then - if ! [[ "$VIASH_PAR_SITE_WIN" =~ ^[-+]?[0-9]+$ ]]; then - ViashError '--site_win' has to be an integer. Use "--help" to get more information on the parameters. - exit 1 - fi -fi if [[ -n "$VIASH_PAR_STRICT_FILTER" ]]; then if ! [[ "$VIASH_PAR_STRICT_FILTER" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then ViashError '--strict_filter' has to be a boolean_true. Use "--help" to get more information on the parameters. exit 1 fi fi +if [[ -n "$VIASH_PAR_VERBOSITY" ]]; then + if ! [[ "$VIASH_PAR_VERBOSITY" =~ ^[-+]?[0-9]+$ ]]; then + ViashError '--verbosity' has to be an integer. Use "--help" to get more information on the parameters. + exit 1 + fi +fi +if [[ -n "$VIASH_PAR_SITE_WIN" ]]; then + if ! [[ "$VIASH_PAR_SITE_WIN" =~ ^[-+]?[0-9]+$ ]]; then + ViashError '--site_win' has to be an integer. Use "--help" to get more information on the parameters. + exit 1 + fi +fi if [[ -n "$VIASH_META_CPUS" ]]; then if ! [[ "$VIASH_META_CPUS" =~ ^[-+]?[0-9]+$ ]]; then ViashError 'cpus' has to be an integer. Use "--help" to get more information on the parameters. @@ -1431,12 +1656,12 @@ if [ ! -z "$VIASH_PAR_CHECK_REF" ]; then unset IFS fi -if [ ! -z "$VIASH_PAR_REMOVE_DUPLICATES" ]; then - VIASH_PAR_REMOVE_DUPLICATES_CHOICES=("snps;indels;both;all;exact;none") +if [ ! -z "$VIASH_PAR_RM_DUP" ]; then + VIASH_PAR_RM_DUP_CHOICES=("snps;indels;both;all;exact") IFS=';' set -f - if ! [[ ";${VIASH_PAR_REMOVE_DUPLICATES_CHOICES[*]};" =~ ";$VIASH_PAR_REMOVE_DUPLICATES;" ]]; then - ViashError '--remove_duplicates' specified value of \'$VIASH_PAR_REMOVE_DUPLICATES\' is not in the list of allowed values. Use "--help" to get more information on the parameters. + if ! [[ ";${VIASH_PAR_RM_DUP_CHOICES[*]};" =~ ";$VIASH_PAR_RM_DUP;" ]]; then + ViashError '--rm_dup' specified value of \'$VIASH_PAR_RM_DUP\' is not in the list of allowed values. Use "--help" to get more information on the parameters. exit 1 fi set +f @@ -1455,6 +1680,18 @@ if [ ! -z "$VIASH_PAR_MULTIALLELICS" ]; then unset IFS fi +if [ ! -z "$VIASH_PAR_MULTI_OVERLAPS" ]; then + VIASH_PAR_MULTI_OVERLAPS_CHOICES=("0;.") + IFS=';' + set -f + if ! [[ ";${VIASH_PAR_MULTI_OVERLAPS_CHOICES[*]};" =~ ";$VIASH_PAR_MULTI_OVERLAPS;" ]]; then + ViashError '--multi_overlaps' specified value of \'$VIASH_PAR_MULTI_OVERLAPS\' is not in the list of allowed values. Use "--help" to get more information on the parameters. + exit 1 + fi + set +f + unset IFS +fi + if [ ! -z "$VIASH_PAR_OUTPUT_TYPE" ]; then VIASH_PAR_OUTPUT_TYPE_CHOICES=("u;z;b;v") IFS=';' @@ -1468,7 +1705,7 @@ if [ ! -z "$VIASH_PAR_OUTPUT_TYPE" ]; then fi if [ ! -z "$VIASH_PAR_REGIONS_OVERLAP" ]; then - VIASH_PAR_REGIONS_OVERLAP_CHOICES=("pos;record;variant;0;1;2") + VIASH_PAR_REGIONS_OVERLAP_CHOICES=("0;1;2") IFS=';' set -f if ! [[ ";${VIASH_PAR_REGIONS_OVERLAP_CHOICES[*]};" =~ ";$VIASH_PAR_REGIONS_OVERLAP;" ]]; then @@ -1479,8 +1716,20 @@ if [ ! -z "$VIASH_PAR_REGIONS_OVERLAP" ]; then unset IFS fi +if [ ! -z "$VIASH_PAR_SORT" ]; then + VIASH_PAR_SORT_CHOICES=("chr_pos;lex") + IFS=';' + set -f + if ! [[ ";${VIASH_PAR_SORT_CHOICES[*]};" =~ ";$VIASH_PAR_SORT;" ]]; then + ViashError '--sort' specified value of \'$VIASH_PAR_SORT\' is not in the list of allowed values. Use "--help" to get more information on the parameters. + exit 1 + fi + set +f + unset IFS +fi + if [ ! -z "$VIASH_PAR_TARGETS_OVERLAP" ]; then - VIASH_PAR_TARGETS_OVERLAP_CHOICES=("pos;record;variant;0;1;2") + VIASH_PAR_TARGETS_OVERLAP_CHOICES=("0;1;2") IFS=';' set -f if ! [[ ";${VIASH_PAR_TARGETS_OVERLAP_CHOICES[*]};" =~ ";$VIASH_PAR_TARGETS_OVERLAP;" ]]; then @@ -1521,6 +1770,10 @@ if [ ! -z "$VIASH_PAR_FASTA_REF" ]; then VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_FASTA_REF")" ) VIASH_PAR_FASTA_REF=$(ViashDockerAutodetectMount "$VIASH_PAR_FASTA_REF") fi +if [ ! -z "$VIASH_PAR_GFF_ANNOT" ]; then + VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_GFF_ANNOT")" ) + VIASH_PAR_GFF_ANNOT=$(ViashDockerAutodetectMount "$VIASH_PAR_GFF_ANNOT") +fi if [ ! -z "$VIASH_PAR_REGIONS_FILE" ]; then VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_REGIONS_FILE")" ) VIASH_PAR_REGIONS_FILE=$(ViashDockerAutodetectMount "$VIASH_PAR_REGIONS_FILE") @@ -1605,23 +1858,31 @@ $( if [ ! -z ${VIASH_PAR_OUTPUT+x} ]; then echo "${VIASH_PAR_OUTPUT}" | sed "s#' $( if [ ! -z ${VIASH_PAR_ATOMIZE+x} ]; then echo "${VIASH_PAR_ATOMIZE}" | sed "s#'#'\"'\"'#g;s#.*#par_atomize='&'#" ; else echo "# par_atomize="; fi ) $( if [ ! -z ${VIASH_PAR_ATOM_OVERLAPS+x} ]; then echo "${VIASH_PAR_ATOM_OVERLAPS}" | sed "s#'#'\"'\"'#g;s#.*#par_atom_overlaps='&'#" ; else echo "# par_atom_overlaps="; fi ) $( if [ ! -z ${VIASH_PAR_CHECK_REF+x} ]; then echo "${VIASH_PAR_CHECK_REF}" | sed "s#'#'\"'\"'#g;s#.*#par_check_ref='&'#" ; else echo "# par_check_ref="; fi ) -$( if [ ! -z ${VIASH_PAR_REMOVE_DUPLICATES+x} ]; then echo "${VIASH_PAR_REMOVE_DUPLICATES}" | sed "s#'#'\"'\"'#g;s#.*#par_remove_duplicates='&'#" ; else echo "# par_remove_duplicates="; fi ) +$( if [ ! -z ${VIASH_PAR_REMOVE_DUPLICATES_FLAG+x} ]; then echo "${VIASH_PAR_REMOVE_DUPLICATES_FLAG}" | sed "s#'#'\"'\"'#g;s#.*#par_remove_duplicates_flag='&'#" ; else echo "# par_remove_duplicates_flag="; fi ) +$( if [ ! -z ${VIASH_PAR_RM_DUP+x} ]; then echo "${VIASH_PAR_RM_DUP}" | sed "s#'#'\"'\"'#g;s#.*#par_rm_dup='&'#" ; else echo "# par_rm_dup="; fi ) +$( if [ ! -z ${VIASH_PAR_EXCLUDE+x} ]; then echo "${VIASH_PAR_EXCLUDE}" | sed "s#'#'\"'\"'#g;s#.*#par_exclude='&'#" ; else echo "# par_exclude="; fi ) $( if [ ! -z ${VIASH_PAR_FASTA_REF+x} ]; then echo "${VIASH_PAR_FASTA_REF}" | sed "s#'#'\"'\"'#g;s#.*#par_fasta_ref='&'#" ; else echo "# par_fasta_ref="; fi ) $( if [ ! -z ${VIASH_PAR_FORCE+x} ]; then echo "${VIASH_PAR_FORCE}" | sed "s#'#'\"'\"'#g;s#.*#par_force='&'#" ; else echo "# par_force="; fi ) +$( if [ ! -z ${VIASH_PAR_GFF_ANNOT+x} ]; then echo "${VIASH_PAR_GFF_ANNOT}" | sed "s#'#'\"'\"'#g;s#.*#par_gff_annot='&'#" ; else echo "# par_gff_annot="; fi ) +$( if [ ! -z ${VIASH_PAR_INCLUDE+x} ]; then echo "${VIASH_PAR_INCLUDE}" | sed "s#'#'\"'\"'#g;s#.*#par_include='&'#" ; else echo "# par_include="; fi ) $( if [ ! -z ${VIASH_PAR_KEEP_SUM+x} ]; then echo "${VIASH_PAR_KEEP_SUM}" | sed "s#'#'\"'\"'#g;s#.*#par_keep_sum='&'#" ; else echo "# par_keep_sum="; fi ) $( if [ ! -z ${VIASH_PAR_MULTIALLELICS+x} ]; then echo "${VIASH_PAR_MULTIALLELICS}" | sed "s#'#'\"'\"'#g;s#.*#par_multiallelics='&'#" ; else echo "# par_multiallelics="; fi ) +$( if [ ! -z ${VIASH_PAR_MULTI_OVERLAPS+x} ]; then echo "${VIASH_PAR_MULTI_OVERLAPS}" | sed "s#'#'\"'\"'#g;s#.*#par_multi_overlaps='&'#" ; else echo "# par_multi_overlaps="; fi ) $( if [ ! -z ${VIASH_PAR_NO_VERSION+x} ]; then echo "${VIASH_PAR_NO_VERSION}" | sed "s#'#'\"'\"'#g;s#.*#par_no_version='&'#" ; else echo "# par_no_version="; fi ) $( if [ ! -z ${VIASH_PAR_DO_NOT_NORMALIZE+x} ]; then echo "${VIASH_PAR_DO_NOT_NORMALIZE}" | sed "s#'#'\"'\"'#g;s#.*#par_do_not_normalize='&'#" ; else echo "# par_do_not_normalize="; fi ) -$( if [ ! -z ${VIASH_PAR_OUTPUT_TYPE+x} ]; then echo "${VIASH_PAR_OUTPUT_TYPE}" | sed "s#'#'\"'\"'#g;s#.*#par_output_type='&'#" ; else echo "# par_output_type="; fi ) $( if [ ! -z ${VIASH_PAR_OLD_REC_TAG+x} ]; then echo "${VIASH_PAR_OLD_REC_TAG}" | sed "s#'#'\"'\"'#g;s#.*#par_old_rec_tag='&'#" ; else echo "# par_old_rec_tag="; fi ) +$( if [ ! -z ${VIASH_PAR_OUTPUT_TYPE+x} ]; then echo "${VIASH_PAR_OUTPUT_TYPE}" | sed "s#'#'\"'\"'#g;s#.*#par_output_type='&'#" ; else echo "# par_output_type="; fi ) $( if [ ! -z ${VIASH_PAR_REGIONS+x} ]; then echo "${VIASH_PAR_REGIONS}" | sed "s#'#'\"'\"'#g;s#.*#par_regions='&'#" ; else echo "# par_regions="; fi ) $( if [ ! -z ${VIASH_PAR_REGIONS_FILE+x} ]; then echo "${VIASH_PAR_REGIONS_FILE}" | sed "s#'#'\"'\"'#g;s#.*#par_regions_file='&'#" ; else echo "# par_regions_file="; fi ) $( if [ ! -z ${VIASH_PAR_REGIONS_OVERLAP+x} ]; then echo "${VIASH_PAR_REGIONS_OVERLAP}" | sed "s#'#'\"'\"'#g;s#.*#par_regions_overlap='&'#" ; else echo "# par_regions_overlap="; fi ) -$( if [ ! -z ${VIASH_PAR_SITE_WIN+x} ]; then echo "${VIASH_PAR_SITE_WIN}" | sed "s#'#'\"'\"'#g;s#.*#par_site_win='&'#" ; else echo "# par_site_win="; fi ) $( if [ ! -z ${VIASH_PAR_STRICT_FILTER+x} ]; then echo "${VIASH_PAR_STRICT_FILTER}" | sed "s#'#'\"'\"'#g;s#.*#par_strict_filter='&'#" ; else echo "# par_strict_filter="; fi ) +$( if [ ! -z ${VIASH_PAR_SORT+x} ]; then echo "${VIASH_PAR_SORT}" | sed "s#'#'\"'\"'#g;s#.*#par_sort='&'#" ; else echo "# par_sort="; fi ) $( if [ ! -z ${VIASH_PAR_TARGETS+x} ]; then echo "${VIASH_PAR_TARGETS}" | sed "s#'#'\"'\"'#g;s#.*#par_targets='&'#" ; else echo "# par_targets="; fi ) $( if [ ! -z ${VIASH_PAR_TARGETS_FILE+x} ]; then echo "${VIASH_PAR_TARGETS_FILE}" | sed "s#'#'\"'\"'#g;s#.*#par_targets_file='&'#" ; else echo "# par_targets_file="; fi ) $( if [ ! -z ${VIASH_PAR_TARGETS_OVERLAP+x} ]; then echo "${VIASH_PAR_TARGETS_OVERLAP}" | sed "s#'#'\"'\"'#g;s#.*#par_targets_overlap='&'#" ; else echo "# par_targets_overlap="; fi ) +$( if [ ! -z ${VIASH_PAR_VERBOSITY+x} ]; then echo "${VIASH_PAR_VERBOSITY}" | sed "s#'#'\"'\"'#g;s#.*#par_verbosity='&'#" ; else echo "# par_verbosity="; fi ) +$( if [ ! -z ${VIASH_PAR_SITE_WIN+x} ]; then echo "${VIASH_PAR_SITE_WIN}" | sed "s#'#'\"'\"'#g;s#.*#par_site_win='&'#" ; else echo "# par_site_win="; fi ) +$( if [ ! -z ${VIASH_PAR_WRITE_INDEX+x} ]; then echo "${VIASH_PAR_WRITE_INDEX}" | sed "s#'#'\"'\"'#g;s#.*#par_write_index='&'#" ; else echo "# par_write_index="; fi ) $( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "${VIASH_META_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_name='&'#" ; else echo "# meta_name="; fi ) $( if [ ! -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then echo "${VIASH_META_FUNCTIONALITY_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_functionality_name='&'#" ; else echo "# meta_functionality_name="; fi ) $( if [ ! -z ${VIASH_META_RESOURCES_DIR+x} ]; then echo "${VIASH_META_RESOURCES_DIR}" | sed "s#'#'\"'\"'#g;s#.*#meta_resources_dir='&'#" ; else echo "# meta_resources_dir="; fi ) @@ -1643,50 +1904,61 @@ $( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}" ## VIASH END -# Exit on error set -eo pipefail -# Unset parameters +# Unset false boolean parameters unset_if_false=( - par_atomize - par_remove_duplicates - par_force - par_no_version - par_do_not_normalize - par_strict_filter + par_atomize + par_remove_duplicates_flag + par_force + par_no_version + par_do_not_normalize + par_strict_filter ) for par in \${unset_if_false[@]}; do - test_val="\${!par}" - [[ "\$test_val" == "false" ]] && unset \$par + test_val="\${!par}" + [[ "\$test_val" == "false" ]] && unset \$par done -# Execute bcftools norm with the provided arguments -bcftools norm \\ - \${par_atomize:+--atomize} \\ - \${par_atom_overlaps:+--atom-overlaps "\$par_atom_overlaps"} \\ - \${par_check_ref:+-c "\$par_check_ref"} \\ - \${par_remove_duplicates:+-d "\$par_remove_duplicates"} \\ - \${par_fasta_ref:+-f "\$par_fasta_ref"} \\ - \${par_force:+--force} \\ - \${par_keep_sum:+--keep-sum "\$par_keep_sum"} \\ - \${par_multiallelics:+-m "\$par_multiallelics"} \\ - \${par_no_version:+--no-version} \\ - \${par_do_not_normalize:+-N} \\ - \${par_old_rec_tag:+--old-rec-tag "\$par_old_rec_tag"} \\ - \${par_regions:+-r "\$par_regions"} \\ - \${par_regions_file:+-R "\$par_regions_file"} \\ - \${par_regions_overlap:+--regions-overlap "\$par_regions_overlap"} \\ - \${par_site_win:+-w "\$par_site_win"} \\ - \${par_strict_filter:+-s} \\ - \${par_targets:+-t "\$par_targets"} \\ - \${par_targets_file:+-T "\$par_targets_file"} \\ - \${par_targets_overlap:+--targets-overlap "\$par_targets_overlap"} \\ - \${meta_cpus:+--threads "\$meta_cpus"} \\ - \${par_output_type:+-O "\$par_output_type"} \\ - -o \$par_output \\ - \$par_input - +# Build command array +cmd_args=( + bcftools norm + \${par_atomize:+--atomize} + \${par_atom_overlaps:+--atom-overlaps "\$par_atom_overlaps"} + \${par_check_ref:+--check-ref "\$par_check_ref"} + \${par_remove_duplicates_flag:+--remove-duplicates} + \${par_rm_dup:+--rm-dup "\$par_rm_dup"} + \${par_exclude:+--exclude "\$par_exclude"} + \${par_fasta_ref:+--fasta-ref "\$par_fasta_ref"} + \${par_force:+--force} + \${par_gff_annot:+--gff-annot "\$par_gff_annot"} + \${par_include:+--include "\$par_include"} + \${par_keep_sum:+--keep-sum "\$par_keep_sum"} + \${par_multiallelics:+--multiallelics "\$par_multiallelics"} + \${par_multi_overlaps:+--multi-overlaps "\$par_multi_overlaps"} + \${par_no_version:+--no-version} + \${par_do_not_normalize:+--do-not-normalize} + \${par_old_rec_tag:+--old-rec-tag "\$par_old_rec_tag"} + \${par_output_type:+--output-type "\$par_output_type"} + \${par_regions:+--regions "\$par_regions"} + \${par_regions_file:+--regions-file "\$par_regions_file"} + \${par_regions_overlap:+--regions-overlap "\$par_regions_overlap"} + \${par_strict_filter:+--strict-filter} + \${par_sort:+--sort "\$par_sort"} + \${par_targets:+--targets "\$par_targets"} + \${par_targets_file:+--targets-file "\$par_targets_file"} + \${par_targets_overlap:+--targets-overlap "\$par_targets_overlap"} + \${meta_cpus:+--threads "\$meta_cpus"} + \${par_verbosity:+--verbosity "\$par_verbosity"} + \${par_site_win:+--site-win "\$par_site_win"} + \${par_write_index:+--write-index="\$par_write_index"} + \${par_output:+--output "\$par_output"} + "\$par_input" +) + +# Execute command +"\${cmd_args[@]}" VIASHMAIN bash "\$tempscript" & wait "\$!" @@ -1706,6 +1978,9 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then if [ ! -z "$VIASH_PAR_FASTA_REF" ]; then VIASH_PAR_FASTA_REF=$(ViashDockerStripAutomount "$VIASH_PAR_FASTA_REF") fi + if [ ! -z "$VIASH_PAR_GFF_ANNOT" ]; then + VIASH_PAR_GFF_ANNOT=$(ViashDockerStripAutomount "$VIASH_PAR_GFF_ANNOT") + fi if [ ! -z "$VIASH_PAR_REGIONS_FILE" ]; then VIASH_PAR_REGIONS_FILE=$(ViashDockerStripAutomount "$VIASH_PAR_REGIONS_FILE") fi diff --git a/target/executable/bcftools/bcftools_sort/.config.vsh.yaml b/target/executable/bcftools/bcftools_sort/.config.vsh.yaml index 170b1ded..ef08de7c 100644 --- a/target/executable/bcftools/bcftools_sort/.config.vsh.yaml +++ b/target/executable/bcftools/bcftools_sort/.config.vsh.yaml @@ -5,7 +5,6 @@ authors: - name: "Theodoro Gasperin Terra Camargo" roles: - "author" - - "maintainer" info: links: email: "theodorogtc@gmail.com" @@ -16,10 +15,11 @@ argument_groups: arguments: - type: "file" name: "--input" - alternatives: - - "-i" - description: "Input VCF/BCF file." + description: "Input VCF/BCF file to sort.\n\nThe file to be sorted by genomic\ + \ coordinates.\n" info: null + example: + - "input.vcf.gz" must_exist: true create_parent: true required: true @@ -32,8 +32,11 @@ argument_groups: name: "--output" alternatives: - "-o" - description: "Output sorted VCF/BCF file." + description: "Write output to a file.\n\nIf not specified, output goes to standard\ + \ output.\n" info: null + example: + - "sorted.vcf.gz" must_exist: true create_parent: true required: true @@ -46,16 +49,38 @@ argument_groups: name: "--output_type" alternatives: - "-O" - description: "Compresses or uncompresses the output.\nThe options are:\n b: compressed\ - \ BCF, \n u: uncompressed BCF, \n z: compressed VCF, \n v: uncompressed VCF.\ - \ \n" + description: "Output file type.\n\n**Options:**\n- u: uncompressed BCF\n- b: compressed\ + \ BCF \n- v: uncompressed VCF\n- z: compressed VCF\n- 0-9: compression level\ + \ for compressed formats\n\n**Default:** v (uncompressed VCF)\n" info: null - required: false - choices: - - "b" - - "u" + example: - "z" - - "v" + required: false + direction: "input" + multiple: false + multiple_sep: ";" + - type: "integer" + name: "--verbosity" + alternatives: + - "-v" + description: "Verbosity level.\n\nHigher values increase verbosity of output messages.\n" + info: null + example: + - 1 + required: false + direction: "input" + multiple: false + multiple_sep: ";" + - type: "string" + name: "--write_index" + alternatives: + - "-W" + description: "Automatically index the output files.\n\n**Format:** Specify index\ + \ format or use default.\n" + info: null + example: + - "tbi" + required: false direction: "input" multiple: false multiple_sep: ";" @@ -63,13 +88,13 @@ resources: - type: "bash_script" path: "script.sh" is_executable: true -description: "Sorts VCF/BCF files.\n" +description: "Sort VCF/BCF file.\n" test_resources: - type: "bash_script" path: "test.sh" is_executable: true - type: "file" - path: "test_data" + path: "test_helpers.sh" info: null status: "enabled" scope: @@ -77,6 +102,7 @@ scope: target: "public" requirements: commands: + - "bcftools" - "ps" keywords: - "Sort" @@ -159,20 +185,14 @@ runners: engines: - type: "docker" id: "docker" - image: "debian:stable-slim" + image: "quay.io/biocontainers/bcftools:1.22--h3a4d415_1" target_registry: "images.viash-hub.com" target_tag: "main" namespace_separator: "/" setup: - - type: "apt" - packages: - - "bcftools" - - "procps" - interactive: false - type: "docker" run: - - "echo \"bcftools: \\\"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftools\ - \ //p')\\\"\" > /var/software_versions.txt\n" + - "bcftools --version 2>&1 | head -1 | sed 's/bcftools /bcftools: /' > /var/software_versions.txt\n" entrypoint: [] cmd: null - type: "native" @@ -184,7 +204,7 @@ build_info: output: "target/executable/bcftools/bcftools_sort" executable: "target/executable/bcftools/bcftools_sort/bcftools_sort" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -206,138 +226,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bcftools/bcftools_sort/bcftools_sort b/target/executable/bcftools/bcftools_sort/bcftools_sort index f0658cd3..8ea5740f 100755 --- a/target/executable/bcftools/bcftools_sort/bcftools_sort +++ b/target/executable/bcftools/bcftools_sort/bcftools_sort @@ -12,7 +12,7 @@ # files. # # Component authors: -# * Theodoro Gasperin Terra Camargo (author, maintainer) +# * Theodoro Gasperin Terra Camargo (author) set -e @@ -446,19 +446,15 @@ function ViashDockerfile { if [[ "$engine_id" == "docker" ]]; then cat << 'VIASHDOCKER' -FROM debian:stable-slim +FROM quay.io/biocontainers/bcftools:1.22--h3a4d415_1 ENTRYPOINT [] -RUN apt-get update && \ - DEBIAN_FRONTEND=noninteractive apt-get install -y bcftools procps && \ - rm -rf /var/lib/apt/lists/* - -RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftools //p')\"" > /var/software_versions.txt +RUN bcftools --version 2>&1 | head -1 | sed 's/bcftools /bcftools: /' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_sort" -LABEL org.opencontainers.image.created="2025-09-01T11:02:56Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:06Z" LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -578,28 +574,46 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) function ViashHelp { echo "bcftools_sort main" echo "" - echo "Sorts VCF/BCF files." + echo "Sort VCF/BCF file." echo "" echo "Inputs:" - echo " -i, --input" + echo " --input" echo " type: file, required parameter, file must exist" - echo " Input VCF/BCF file." + echo " example: input.vcf.gz" + echo " Input VCF/BCF file to sort." + echo " The file to be sorted by genomic coordinates." echo "" echo "Outputs:" echo " -o, --output" echo " type: file, required parameter, output, file must exist" - echo " Output sorted VCF/BCF file." + echo " example: sorted.vcf.gz" + echo " Write output to a file." + echo " If not specified, output goes to standard output." echo "" echo "Options:" echo " -O, --output_type" echo " type: string" - echo " choices: [ b, u, z, v ]" - echo " Compresses or uncompresses the output." - echo " The options are:" - echo " b: compressed BCF," - echo " u: uncompressed BCF," - echo " z: compressed VCF," - echo " v: uncompressed VCF." + echo " example: z" + echo " Output file type." + echo " **Options:**" + echo " - u: uncompressed BCF" + echo " - b: compressed BCF" + echo " - v: uncompressed VCF" + echo " - z: compressed VCF" + echo " - 0-9: compression level for compressed formats" + echo " **Default:** v (uncompressed VCF)" + echo "" + echo " -v, --verbosity" + echo " type: integer" + echo " example: 1" + echo " Verbosity level." + echo " Higher values increase verbosity of output messages." + echo "" + echo " -W, --write_index" + echo " type: string" + echo " example: tbi" + echo " Automatically index the output files." + echo " **Format:** Specify index format or use default." echo "" echo "Viash built in Computational Requirements:" echo " ---cpus=INT" @@ -662,12 +676,6 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_INPUT=$(ViashRemoveFlags "$1") shift 1 ;; - -i) - [ -n "$VIASH_PAR_INPUT" ] && ViashError Bad arguments for option \'-i\': \'$VIASH_PAR_INPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_INPUT="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to -i. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; --output) [ -n "$VIASH_PAR_OUTPUT" ] && ViashError Bad arguments for option \'--output\': \'$VIASH_PAR_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 VIASH_PAR_OUTPUT="$2" @@ -702,6 +710,40 @@ while [[ $# -gt 0 ]]; do [ $# -lt 2 ] && ViashError Not enough arguments passed to -O. Use "--help" to get more information on the parameters. && exit 1 shift 2 ;; + --verbosity) + [ -n "$VIASH_PAR_VERBOSITY" ] && ViashError Bad arguments for option \'--verbosity\': \'$VIASH_PAR_VERBOSITY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_VERBOSITY="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --verbosity. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --verbosity=*) + [ -n "$VIASH_PAR_VERBOSITY" ] && ViashError Bad arguments for option \'--verbosity=*\': \'$VIASH_PAR_VERBOSITY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_VERBOSITY=$(ViashRemoveFlags "$1") + shift 1 + ;; + -v) + [ -n "$VIASH_PAR_VERBOSITY" ] && ViashError Bad arguments for option \'-v\': \'$VIASH_PAR_VERBOSITY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_VERBOSITY="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to -v. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --write_index) + [ -n "$VIASH_PAR_WRITE_INDEX" ] && ViashError Bad arguments for option \'--write_index\': \'$VIASH_PAR_WRITE_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_WRITE_INDEX="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --write_index. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --write_index=*) + [ -n "$VIASH_PAR_WRITE_INDEX" ] && ViashError Bad arguments for option \'--write_index=*\': \'$VIASH_PAR_WRITE_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_WRITE_INDEX=$(ViashRemoveFlags "$1") + shift 1 + ;; + -W) + [ -n "$VIASH_PAR_WRITE_INDEX" ] && ViashError Bad arguments for option \'-W\': \'$VIASH_PAR_WRITE_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_WRITE_INDEX="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to -W. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; ---engine) VIASH_ENGINE_ID="$2" shift 2 @@ -812,13 +854,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bcftools' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bcftools' 'ps' 'bash' fi # setting computational defaults @@ -914,6 +956,12 @@ if [ ! -z "$VIASH_PAR_INPUT" ] && [ ! -e "$VIASH_PAR_INPUT" ]; then fi # check whether parameters values are of the right type +if [[ -n "$VIASH_PAR_VERBOSITY" ]]; then + if ! [[ "$VIASH_PAR_VERBOSITY" =~ ^[-+]?[0-9]+$ ]]; then + ViashError '--verbosity' has to be an integer. Use "--help" to get more information on the parameters. + exit 1 + fi +fi if [[ -n "$VIASH_META_CPUS" ]]; then if ! [[ "$VIASH_META_CPUS" =~ ^[-+]?[0-9]+$ ]]; then ViashError 'cpus' has to be an integer. Use "--help" to get more information on the parameters. @@ -987,19 +1035,6 @@ if [[ -n "$VIASH_META_MEMORY_PIB" ]]; then fi fi -# check whether value is belongs to a set of choices -if [ ! -z "$VIASH_PAR_OUTPUT_TYPE" ]; then - VIASH_PAR_OUTPUT_TYPE_CHOICES=("b;u;z;v") - IFS=';' - set -f - if ! [[ ";${VIASH_PAR_OUTPUT_TYPE_CHOICES[*]};" =~ ";$VIASH_PAR_OUTPUT_TYPE;" ]]; then - ViashError '--output_type' specified value of \'$VIASH_PAR_OUTPUT_TYPE\' is not in the list of allowed values. Use "--help" to get more information on the parameters. - exit 1 - fi - set +f - unset IFS -fi - # create parent directories of output files, if so desired if [ ! -z "$VIASH_PAR_OUTPUT" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT")" ]; then mkdir -p "$(dirname "$VIASH_PAR_OUTPUT")" @@ -1100,6 +1135,8 @@ cat > "\$tempscript" << 'VIASHMAIN' $( if [ ! -z ${VIASH_PAR_INPUT+x} ]; then echo "${VIASH_PAR_INPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_input='&'#" ; else echo "# par_input="; fi ) $( if [ ! -z ${VIASH_PAR_OUTPUT+x} ]; then echo "${VIASH_PAR_OUTPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_output='&'#" ; else echo "# par_output="; fi ) $( if [ ! -z ${VIASH_PAR_OUTPUT_TYPE+x} ]; then echo "${VIASH_PAR_OUTPUT_TYPE}" | sed "s#'#'\"'\"'#g;s#.*#par_output_type='&'#" ; else echo "# par_output_type="; fi ) +$( if [ ! -z ${VIASH_PAR_VERBOSITY+x} ]; then echo "${VIASH_PAR_VERBOSITY}" | sed "s#'#'\"'\"'#g;s#.*#par_verbosity='&'#" ; else echo "# par_verbosity="; fi ) +$( if [ ! -z ${VIASH_PAR_WRITE_INDEX+x} ]; then echo "${VIASH_PAR_WRITE_INDEX}" | sed "s#'#'\"'\"'#g;s#.*#par_write_index='&'#" ; else echo "# par_write_index="; fi ) $( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "${VIASH_META_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_name='&'#" ; else echo "# meta_name="; fi ) $( if [ ! -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then echo "${VIASH_META_FUNCTIONALITY_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_functionality_name='&'#" ; else echo "# meta_functionality_name="; fi ) $( if [ ! -z ${VIASH_META_RESOURCES_DIR+x} ]; then echo "${VIASH_META_RESOURCES_DIR}" | sed "s#'#'\"'\"'#g;s#.*#meta_resources_dir='&'#" ; else echo "# meta_resources_dir="; fi ) @@ -1121,16 +1158,29 @@ $( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}" ## VIASH END -# Exit on error set -eo pipefail -# Execute bedtools bamtofastq with the provided arguments -bcftools sort \\ - -o "\$par_output" \\ - \${par_output_type:+-O "\$par_output_type"} \\ - \${meta_memory_mb:+-m "\${meta_memory_mb}M"} \\ - \${meta_temp_dir:+-T "\$meta_temp_dir"} \\ - \$par_input \\ +# Create temporary directory for bcftools if meta_temp_dir is available +if [[ -n "\$meta_temp_dir" ]]; then + bcftools_temp_dir=\$(mktemp -d "\$meta_temp_dir/bcftools_sort.XXXXXX") + # Set up cleanup trap + trap 'rm -rf "\$bcftools_temp_dir"' EXIT +fi + +# Build command array +cmd_args=( + bcftools sort + \${meta_memory_mb:+--max-mem "\${meta_memory_mb}M"} + \${par_output_type:+--output-type "\$par_output_type"} + \${bcftools_temp_dir:+--temp-dir "\$bcftools_temp_dir"} + \${par_verbosity:+--verbosity "\$par_verbosity"} + \${par_write_index:+--write-index="\$par_write_index"} + \${par_output:+--output "\$par_output"} + "\$par_input" +) + +# Execute command +"\${cmd_args[@]}" VIASHMAIN bash "\$tempscript" & wait "\$!" diff --git a/target/executable/bcftools/bcftools_stats/.config.vsh.yaml b/target/executable/bcftools/bcftools_stats/.config.vsh.yaml index 456b6a41..ea5fcf40 100644 --- a/target/executable/bcftools/bcftools_stats/.config.vsh.yaml +++ b/target/executable/bcftools/bcftools_stats/.config.vsh.yaml @@ -15,10 +15,12 @@ argument_groups: arguments: - type: "file" name: "--input" - alternatives: - - "-i" - description: "Input VCF/BCF file. Maximum of two files." + description: "Input VCF/BCF file(s). Maximum of two files can be provided.\nWhen\ + \ two files are given, the program generates separate stats \nfor intersection\ + \ and the complements.\n" info: null + example: + - "input.vcf.gz" must_exist: true create_parent: true required: true @@ -31,8 +33,11 @@ argument_groups: name: "--output" alternatives: - "-o" - description: "Output txt statistics file." + description: "Write output to a file. The output is a text file which can be \n\ + plotted using plot-vcfstats.\n" info: null + example: + - "stats.txt" must_exist: true create_parent: true required: true @@ -42,10 +47,8 @@ argument_groups: - name: "Options" arguments: - type: "string" - name: "--allele_frequency_bins" - alternatives: - - "--af_bins" - description: "Allele frequency bins, a list of bin values (0.1,0.5,1).\n" + name: "--af_bins" + description: "Allele frequency bins, a list of comma-separated bin values.\n" info: null example: - "0.1,0.5,1" @@ -53,44 +56,25 @@ argument_groups: direction: "input" multiple: false multiple_sep: ";" - - type: "file" - name: "--allele_frequency_bins_file" - alternatives: - - "--af_bins_file" - description: "Same as allele_frequency_bins, but in a file.\nFormat of file is\ - \ one value per line. \ne.g. \n 0.1\n 0.5\n 1\n" - info: null - must_exist: true - create_parent: true - required: false - direction: "input" - multiple: false - multiple_sep: ";" - type: "string" - name: "--allele_frequency_tag" - alternatives: - - "--af_tag" + name: "--af_tag" description: "Allele frequency tag to use, by default estimated from AN,AC or\ \ GT.\n" info: null + example: + - "AF" required: false direction: "input" multiple: false multiple_sep: ";" - - type: "boolean_true" - name: "--first_allele_only" - alternatives: - - "--first_only" - description: "Include only 1st allele at multiallelic sites.\n" - info: null - direction: "input" - type: "string" name: "--collapse" alternatives: - - "--c" - description: "Treat as identical records with .\n\ - See https://samtools.github.io/bcftools/bcftools.html#common_options for details.\n" + - "-c" + description: "Treat as identical records with .\n" info: null + example: + - "snps" required: false choices: - "snps" @@ -105,8 +89,8 @@ argument_groups: - type: "string" name: "--depth" alternatives: - - "--d" - description: "Depth distribution: min,max,bin size.\n" + - "-d" + description: "Depth distribution: min,max,bin size [0:200:1].\n" info: null example: - "0,500,1" @@ -117,12 +101,11 @@ argument_groups: - type: "string" name: "--exclude" alternatives: - - "--e" - description: "Exclude sites for which the expression is true.\nSee https://samtools.github.io/bcftools/bcftools.html#expressions\ - \ for details.\n" + - "-e" + description: "Exclude sites for which the expression is true.\n" info: null example: - - "QUAL < 30 && DP < 10" + - "QUAL < 30" required: false direction: "input" multiple: false @@ -130,12 +113,13 @@ argument_groups: - type: "file" name: "--exons" alternatives: - - "--E" - description: "tab-delimited file with exons for indel frameshifts statistics.\ - \ \nThe columns of the file are CHR, FROM, TO, with 1-based, inclusive, positions.\ - \ \nThe file is BGZF-compressed and indexed with tabix (e.g. tabix -s1 -b2 -e3\ - \ file.gz).\n" + - "-E" + description: "Tab-delimited file with exons for indel frameshifts statistics.\n\ + The columns of the file are CHR, FROM, TO, with 1-based positions.\nThe file\ + \ should be BGZF-compressed and indexed with tabix.\n" info: null + example: + - "exons.bed.gz" must_exist: true create_parent: true required: false @@ -145,55 +129,63 @@ argument_groups: - type: "string" name: "--apply_filters" alternatives: - - "--f" - description: "Require at least one of the listed FILTER strings (e.g. \"PASS,.\"\ - ).\n" + - "-f" + description: "Require at least one of the listed FILTER strings.\n" info: null + example: + - "PASS,." required: false direction: "input" multiple: false multiple_sep: ";" - type: "file" - name: "--fasta_reference" + name: "--fasta_ref" alternatives: - - "--F" + - "-F" description: "Faidx indexed reference sequence file to determine INDEL context.\n" info: null + example: + - "reference.fa" must_exist: true create_parent: true required: false direction: "input" multiple: false multiple_sep: ";" + - type: "boolean_true" + name: "--first_allele_only" + alternatives: + - "--1st-allele-only" + description: "Include only 1st allele at multiallelic sites.\n" + info: null + direction: "input" - type: "string" name: "--include" alternatives: - - "--i" - description: "Select sites for which the expression is true.\nSee https://samtools.github.io/bcftools/bcftools.html#expressions\ - \ for details.\n" + - "-i" + description: "Select sites for which the expression is true.\n" info: null example: - - "QUAL >= 30 && DP >= 10" + - "QUAL >= 30" required: false direction: "input" multiple: false multiple_sep: ";" - type: "boolean_true" - name: "--split_by_ID" + name: "--split_by_id" alternatives: - - "--I" + - "-I" description: "Collect stats for sites with ID separately (known vs novel).\n" info: null direction: "input" - type: "string" name: "--regions" alternatives: - - "--r" - description: "Restrict to comma-separated list of regions. \nFollowing formats\ - \ are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​].\n" + - "-r" + description: "Restrict to comma-separated list of regions.\n" info: null example: - - "20:1000000-2000000" + - "chr20:1000000-2000000" required: false direction: "input" multiple: false @@ -201,11 +193,11 @@ argument_groups: - type: "file" name: "--regions_file" alternatives: - - "--R" - description: "Restrict to regions listed in a file. \nRegions can be specified\ - \ either on a VCF, BED, or tab-delimited file (the default). \nFor more information\ - \ check manual.\n" + - "-R" + description: "Restrict to regions listed in a file.\n" info: null + example: + - "regions.bed" must_exist: true create_parent: true required: false @@ -214,14 +206,8 @@ argument_groups: multiple_sep: ";" - type: "string" name: "--regions_overlap" - description: "This option controls how overlapping records are determined: \n\ - set to 'pos' or '0' if the VCF record has to have POS inside a region (this\ - \ corresponds to the default behavior of -t/-T); \nset to 'record' or '1' if\ - \ also overlapping records with POS outside a region should be included (this\ - \ is the default behavior of -r/-R, \nand includes indels with POS at the end\ - \ of a region, which are technically outside the region); \nor set to 'variant'\ - \ or '2' to include only true overlapping variation (compare the full VCF representation\ - \ \"TA>T-\" vs the true sequence variation \"A>-\").\n" + description: "Include if POS in the region (pos), record overlaps (record), \n\ + variant overlaps (variant). Can also use numeric equivalents 0, 1, 2.\n" info: null required: false choices: @@ -237,9 +223,11 @@ argument_groups: - type: "string" name: "--samples" alternatives: - - "--s" + - "-s" description: "List of samples for sample stats, \"-\" to include all samples.\n" info: null + example: + - "sample1,sample2" required: false direction: "input" multiple: false @@ -247,10 +235,11 @@ argument_groups: - type: "file" name: "--samples_file" alternatives: - - "--S" - description: "File of samples to include.\ne.g. \n sample1 1\n sample2 \ - \ 2\n sample3 2\n" + - "-S" + description: "File of samples to include.\n" info: null + example: + - "samples.txt" must_exist: true create_parent: true required: false @@ -260,21 +249,12 @@ argument_groups: - type: "string" name: "--targets" alternatives: - - "--t" - description: "Similar as -r, --regions, but the next position is accessed by streaming\ - \ the whole VCF/BCF \nrather than using the tbi/csi index. Both -r and -t options\ - \ can be applied simultaneously: -r uses the \nindex to jump to a region and\ - \ -t discards positions which are not in the targets. Unlike -r, targets \n\ - can be prefixed with \"^\" to request logical complement. For example, \"^X,Y,MT\"\ - \ indicates that \nsequences X, Y and MT should be skipped. Yet another difference\ - \ between the -t/-T and -r/-R is \nthat -r/-R checks for proper overlaps and\ - \ considers both POS and the end position of an indel, \nwhile -t/-T considers\ - \ the POS coordinate only (by default; see also --regions-overlap and --targets-overlap).\ - \ \nNote that -t cannot be used in combination with -T.\nFollowing formats are\ - \ supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​].\n" + - "-t" + description: "Similar to regions, but streams rather than using index.\nTargets\ + \ can be prefixed with \"^\" for logical complement.\n" info: null example: - - "20:1000000-2000000" + - "chr20:1000000-2000000" required: false direction: "input" multiple: false @@ -282,9 +262,11 @@ argument_groups: - type: "file" name: "--targets_file" alternatives: - - "--T" - description: "Similar to --regions_file option but streams rather than index-jumps.\n" + - "-T" + description: "Similar to regions_file but streams rather than index-jumps.\n" info: null + example: + - "targets.bed" must_exist: true create_parent: true required: false @@ -292,9 +274,9 @@ argument_groups: multiple: false multiple_sep: ";" - type: "string" - name: "--targets_overlaps" - description: "Include if POS in the region (0), record overlaps (1), variant overlaps\ - \ (2).\n" + name: "--targets_overlap" + description: "Include if POS in the region (pos), record overlaps (record), \n\ + variant overlaps (variant). Can also use numeric equivalents 0, 1, 2.\n" info: null required: false choices: @@ -310,11 +292,12 @@ argument_groups: - type: "string" name: "--user_tstv" alternatives: - - "--u" - description: "Collect Ts/Tv stats for any tag using the given binning [0:1:100].\n\ - Format is .\nA subfield can be selected as e.g. 'PV4[0]', here\ - \ the first value of the PV4 tag.\n" + - "-u" + description: "Collect Ts/Tv stats for any tag using the given binning.\nFormat\ + \ is TAG[:min:max:n]. Default binning is [0:1:100].\n" info: null + example: + - "QUAL:0:40:40" required: false direction: "input" multiple: false @@ -322,7 +305,7 @@ argument_groups: - type: "boolean_true" name: "--verbose" alternatives: - - "--v" + - "-v" description: "Produce verbose per-site and per-sample output.\n" info: null direction: "input" @@ -345,6 +328,7 @@ scope: target: "public" requirements: commands: + - "bcftools" - "ps" keywords: - "Stats" @@ -427,25 +411,14 @@ runners: engines: - type: "docker" id: "docker" - image: "debian:stable-slim" + image: "quay.io/biocontainers/bcftools:1.22--h3a4d415_1" target_registry: "images.viash-hub.com" target_tag: "main" namespace_separator: "/" setup: - - type: "apt" - packages: - - "bcftools" - - "procps" - interactive: false - type: "docker" run: - - "echo \"bcftools: \\\"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftools\ - \ //p')\\\"\" > /var/software_versions.txt\n" - test_setup: - - type: "apt" - packages: - - "tabix" - interactive: false + - "bcftools --version | head -1 | sed 's/bcftools /bcftools: /' > /var/software_versions.txt\n" entrypoint: [] cmd: null - type: "native" @@ -457,7 +430,7 @@ build_info: output: "target/executable/bcftools/bcftools_stats" executable: "target/executable/bcftools/bcftools_stats/bcftools_stats" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -479,138 +452,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bcftools/bcftools_stats/bcftools_stats b/target/executable/bcftools/bcftools_stats/bcftools_stats index 7280a403..1ee300b9 100755 --- a/target/executable/bcftools/bcftools_stats/bcftools_stats +++ b/target/executable/bcftools/bcftools_stats/bcftools_stats @@ -446,19 +446,15 @@ function ViashDockerfile { if [[ "$engine_id" == "docker" ]]; then cat << 'VIASHDOCKER' -FROM debian:stable-slim +FROM quay.io/biocontainers/bcftools:1.22--h3a4d415_1 ENTRYPOINT [] -RUN apt-get update && \ - DEBIAN_FRONTEND=noninteractive apt-get install -y bcftools procps && \ - rm -rf /var/lib/apt/lists/* - -RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftools //p')\"" > /var/software_versions.txt +RUN bcftools --version | head -1 | sed 's/bcftools /bcftools: /' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_stats" -LABEL org.opencontainers.image.created="2025-09-01T11:02:55Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:06Z" LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -586,161 +582,127 @@ function ViashHelp { echo "also sample columns." echo "" echo "Inputs:" - echo " -i, --input" + echo " --input" echo " type: file, required parameter, multiple values allowed, file must exist" - echo " Input VCF/BCF file. Maximum of two files." + echo " example: input.vcf.gz" + echo " Input VCF/BCF file(s). Maximum of two files can be provided." + echo " When two files are given, the program generates separate stats" + echo " for intersection and the complements." echo "" echo "Outputs:" echo " -o, --output" echo " type: file, required parameter, output, file must exist" - echo " Output txt statistics file." + echo " example: stats.txt" + echo " Write output to a file. The output is a text file which can be" + echo " plotted using plot-vcfstats." echo "" echo "Options:" - echo " --af_bins, --allele_frequency_bins" + echo " --af_bins" echo " type: string" echo " example: 0.1,0.5,1" - echo " Allele frequency bins, a list of bin values (0.1,0.5,1)." + echo " Allele frequency bins, a list of comma-separated bin values." echo "" - echo " --af_bins_file, --allele_frequency_bins_file" - echo " type: file, file must exist" - echo " Same as allele_frequency_bins, but in a file." - echo " Format of file is one value per line." - echo " e.g." - echo " 0.1" - echo " 0.5" - echo " 1" - echo "" - echo " --af_tag, --allele_frequency_tag" + echo " --af_tag" echo " type: string" + echo " example: AF" echo " Allele frequency tag to use, by default estimated from AN,AC or GT." echo "" - echo " --first_only, --first_allele_only" + echo " -c, --collapse" + echo " type: string" + echo " example: snps" + echo " choices: [ snps, indels, both, all, some, none ]" + echo " Treat as identical records with ." + echo "" + echo " -d, --depth" + echo " type: string" + echo " example: 0,500,1" + echo " Depth distribution: min,max,bin size [0:200:1]." + echo "" + echo " -e, --exclude" + echo " type: string" + echo " example: QUAL < 30" + echo " Exclude sites for which the expression is true." + echo "" + echo " -E, --exons" + echo " type: file, file must exist" + echo " example: exons.bed.gz" + echo " Tab-delimited file with exons for indel frameshifts statistics." + echo " The columns of the file are CHR, FROM, TO, with 1-based positions." + echo " The file should be BGZF-compressed and indexed with tabix." + echo "" + echo " -f, --apply_filters" + echo " type: string" + echo " example: PASS,." + echo " Require at least one of the listed FILTER strings." + echo "" + echo " -F, --fasta_ref" + echo " type: file, file must exist" + echo " example: reference.fa" + echo " Faidx indexed reference sequence file to determine INDEL context." + echo "" + echo " --1st-allele-only, --first_allele_only" echo " type: boolean_true" echo " Include only 1st allele at multiallelic sites." echo "" - echo " --c, --collapse" + echo " -i, --include" echo " type: string" - echo " choices: [ snps, indels, both, all, some, none ]" - echo " Treat as identical records with ." - echo " See https://samtools.github.io/bcftools/bcftools.html#common_options for" - echo " details." - echo "" - echo " --d, --depth" - echo " type: string" - echo " example: 0,500,1" - echo " Depth distribution: min,max,bin size." - echo "" - echo " --e, --exclude" - echo " type: string" - echo " example: QUAL < 30 && DP < 10" - echo " Exclude sites for which the expression is true." - echo " See https://samtools.github.io/bcftools/bcftools.html#expressions for" - echo " details." - echo "" - echo " --E, --exons" - echo " type: file, file must exist" - echo " tab-delimited file with exons for indel frameshifts statistics." - echo " The columns of the file are CHR, FROM, TO, with 1-based, inclusive," - echo " positions." - echo " The file is BGZF-compressed and indexed with tabix (e.g. tabix -s1 -b2" - echo " -e3 file.gz)." - echo "" - echo " --f, --apply_filters" - echo " type: string" - echo " Require at least one of the listed FILTER strings (e.g. \"PASS,.\")." - echo "" - echo " --F, --fasta_reference" - echo " type: file, file must exist" - echo " Faidx indexed reference sequence file to determine INDEL context." - echo "" - echo " --i, --include" - echo " type: string" - echo " example: QUAL >= 30 && DP >= 10" + echo " example: QUAL >= 30" echo " Select sites for which the expression is true." - echo " See https://samtools.github.io/bcftools/bcftools.html#expressions for" - echo " details." echo "" - echo " --I, --split_by_ID" + echo " -I, --split_by_id" echo " type: boolean_true" echo " Collect stats for sites with ID separately (known vs novel)." echo "" - echo " --r, --regions" + echo " -r, --regions" echo " type: string" - echo " example: 20:1000000-2000000" + echo " example: chr20:1000000-2000000" echo " Restrict to comma-separated list of regions." - echo " Following formats are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​]." echo "" - echo " --R, --regions_file" + echo " -R, --regions_file" echo " type: file, file must exist" + echo " example: regions.bed" echo " Restrict to regions listed in a file." - echo " Regions can be specified either on a VCF, BED, or tab-delimited file" - echo " (the default)." - echo " For more information check manual." echo "" echo " --regions_overlap" echo " type: string" echo " choices: [ pos, record, variant, 0, 1, 2 ]" - echo " This option controls how overlapping records are determined:" - echo " set to 'pos' or '0' if the VCF record has to have POS inside a region" - echo " (this corresponds to the default behavior of -t/-T);" - echo " set to 'record' or '1' if also overlapping records with POS outside a" - echo " region should be included (this is the default behavior of -r/-R," - echo " and includes indels with POS at the end of a region, which are" - echo " technically outside the region);" - echo " or set to 'variant' or '2' to include only true overlapping variation" - echo " (compare the full VCF representation \"TA>T-\" vs the true sequence" - echo " variation \"A>-\")." + echo " Include if POS in the region (pos), record overlaps (record)," + echo " variant overlaps (variant). Can also use numeric equivalents 0, 1, 2." echo "" - echo " --s, --samples" + echo " -s, --samples" echo " type: string" + echo " example: sample1,sample2" echo " List of samples for sample stats, \"-\" to include all samples." echo "" - echo " --S, --samples_file" + echo " -S, --samples_file" echo " type: file, file must exist" + echo " example: samples.txt" echo " File of samples to include." - echo " e.g." - echo " sample1 1" - echo " sample2 2" - echo " sample3 2" echo "" - echo " --t, --targets" + echo " -t, --targets" echo " type: string" - echo " example: 20:1000000-2000000" - echo " Similar as -r, --regions, but the next position is accessed by streaming" - echo " the whole VCF/BCF" - echo " rather than using the tbi/csi index. Both -r and -t options can be" - echo " applied simultaneously: -r uses the" - echo " index to jump to a region and -t discards positions which are not in the" - echo " targets. Unlike -r, targets" - echo " can be prefixed with \"^\" to request logical complement. For example," - echo " \"^X,Y,MT\" indicates that" - echo " sequences X, Y and MT should be skipped. Yet another difference between" - echo " the -t/-T and -r/-R is" - echo " that -r/-R checks for proper overlaps and considers both POS and the end" - echo " position of an indel," - echo " while -t/-T considers the POS coordinate only (by default; see also" - echo " --regions-overlap and --targets-overlap)." - echo " Note that -t cannot be used in combination with -T." - echo " Following formats are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​]." + echo " example: chr20:1000000-2000000" + echo " Similar to regions, but streams rather than using index." + echo " Targets can be prefixed with \"^\" for logical complement." echo "" - echo " --T, --targets_file" + echo " -T, --targets_file" echo " type: file, file must exist" - echo " Similar to --regions_file option but streams rather than index-jumps." + echo " example: targets.bed" + echo " Similar to regions_file but streams rather than index-jumps." echo "" - echo " --targets_overlaps" + echo " --targets_overlap" echo " type: string" echo " choices: [ pos, record, variant, 0, 1, 2 ]" - echo " Include if POS in the region (0), record overlaps (1), variant overlaps" - echo " (2)." + echo " Include if POS in the region (pos), record overlaps (record)," + echo " variant overlaps (variant). Can also use numeric equivalents 0, 1, 2." echo "" - echo " --u, --user_tstv" + echo " -u, --user_tstv" echo " type: string" - echo " Collect Ts/Tv stats for any tag using the given binning [0:1:100]." - echo " Format is ." - echo " A subfield can be selected as e.g. 'PV4[0]', here the first value of the" - echo " PV4 tag." + echo " example: QUAL:0:40:40" + echo " Collect Ts/Tv stats for any tag using the given binning." + echo " Format is TAG[:min:max:n]. Default binning is [0:1:100]." echo "" - echo " --v, --verbose" + echo " -v, --verbose" echo " type: boolean_true" echo " Produce verbose per-site and per-sample output." echo "" @@ -811,15 +773,6 @@ while [[ $# -gt 0 ]]; do fi shift 1 ;; - -i) - if [ -z "$VIASH_PAR_INPUT" ]; then - VIASH_PAR_INPUT="$2" - else - VIASH_PAR_INPUT="$VIASH_PAR_INPUT;""$2" - fi - [ $# -lt 2 ] && ViashError Not enough arguments passed to -i. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; --output) [ -n "$VIASH_PAR_OUTPUT" ] && ViashError Bad arguments for option \'--output\': \'$VIASH_PAR_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 VIASH_PAR_OUTPUT="$2" @@ -837,65 +790,26 @@ while [[ $# -gt 0 ]]; do [ $# -lt 2 ] && ViashError Not enough arguments passed to -o. Use "--help" to get more information on the parameters. && exit 1 shift 2 ;; - --allele_frequency_bins) - [ -n "$VIASH_PAR_ALLELE_FREQUENCY_BINS" ] && ViashError Bad arguments for option \'--allele_frequency_bins\': \'$VIASH_PAR_ALLELE_FREQUENCY_BINS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_ALLELE_FREQUENCY_BINS="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --allele_frequency_bins. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --allele_frequency_bins=*) - [ -n "$VIASH_PAR_ALLELE_FREQUENCY_BINS" ] && ViashError Bad arguments for option \'--allele_frequency_bins=*\': \'$VIASH_PAR_ALLELE_FREQUENCY_BINS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_ALLELE_FREQUENCY_BINS=$(ViashRemoveFlags "$1") - shift 1 - ;; --af_bins) - [ -n "$VIASH_PAR_ALLELE_FREQUENCY_BINS" ] && ViashError Bad arguments for option \'--af_bins\': \'$VIASH_PAR_ALLELE_FREQUENCY_BINS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_ALLELE_FREQUENCY_BINS="$2" + [ -n "$VIASH_PAR_AF_BINS" ] && ViashError Bad arguments for option \'--af_bins\': \'$VIASH_PAR_AF_BINS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_AF_BINS="$2" [ $# -lt 2 ] && ViashError Not enough arguments passed to --af_bins. Use "--help" to get more information on the parameters. && exit 1 shift 2 ;; - --allele_frequency_bins_file) - [ -n "$VIASH_PAR_ALLELE_FREQUENCY_BINS_FILE" ] && ViashError Bad arguments for option \'--allele_frequency_bins_file\': \'$VIASH_PAR_ALLELE_FREQUENCY_BINS_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_ALLELE_FREQUENCY_BINS_FILE="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --allele_frequency_bins_file. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --allele_frequency_bins_file=*) - [ -n "$VIASH_PAR_ALLELE_FREQUENCY_BINS_FILE" ] && ViashError Bad arguments for option \'--allele_frequency_bins_file=*\': \'$VIASH_PAR_ALLELE_FREQUENCY_BINS_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_ALLELE_FREQUENCY_BINS_FILE=$(ViashRemoveFlags "$1") - shift 1 - ;; - --af_bins_file) - [ -n "$VIASH_PAR_ALLELE_FREQUENCY_BINS_FILE" ] && ViashError Bad arguments for option \'--af_bins_file\': \'$VIASH_PAR_ALLELE_FREQUENCY_BINS_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_ALLELE_FREQUENCY_BINS_FILE="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --af_bins_file. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --allele_frequency_tag) - [ -n "$VIASH_PAR_ALLELE_FREQUENCY_TAG" ] && ViashError Bad arguments for option \'--allele_frequency_tag\': \'$VIASH_PAR_ALLELE_FREQUENCY_TAG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_ALLELE_FREQUENCY_TAG="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --allele_frequency_tag. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --allele_frequency_tag=*) - [ -n "$VIASH_PAR_ALLELE_FREQUENCY_TAG" ] && ViashError Bad arguments for option \'--allele_frequency_tag=*\': \'$VIASH_PAR_ALLELE_FREQUENCY_TAG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_ALLELE_FREQUENCY_TAG=$(ViashRemoveFlags "$1") + --af_bins=*) + [ -n "$VIASH_PAR_AF_BINS" ] && ViashError Bad arguments for option \'--af_bins=*\': \'$VIASH_PAR_AF_BINS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_AF_BINS=$(ViashRemoveFlags "$1") shift 1 ;; --af_tag) - [ -n "$VIASH_PAR_ALLELE_FREQUENCY_TAG" ] && ViashError Bad arguments for option \'--af_tag\': \'$VIASH_PAR_ALLELE_FREQUENCY_TAG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_ALLELE_FREQUENCY_TAG="$2" + [ -n "$VIASH_PAR_AF_TAG" ] && ViashError Bad arguments for option \'--af_tag\': \'$VIASH_PAR_AF_TAG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_AF_TAG="$2" [ $# -lt 2 ] && ViashError Not enough arguments passed to --af_tag. Use "--help" to get more information on the parameters. && exit 1 shift 2 ;; - --first_allele_only) - [ -n "$VIASH_PAR_FIRST_ALLELE_ONLY" ] && ViashError Bad arguments for option \'--first_allele_only\': \'$VIASH_PAR_FIRST_ALLELE_ONLY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_FIRST_ALLELE_ONLY=true - shift 1 - ;; - --first_only) - [ -n "$VIASH_PAR_FIRST_ALLELE_ONLY" ] && ViashError Bad arguments for option \'--first_only\': \'$VIASH_PAR_FIRST_ALLELE_ONLY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_FIRST_ALLELE_ONLY=true + --af_tag=*) + [ -n "$VIASH_PAR_AF_TAG" ] && ViashError Bad arguments for option \'--af_tag=*\': \'$VIASH_PAR_AF_TAG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_AF_TAG=$(ViashRemoveFlags "$1") shift 1 ;; --collapse) @@ -909,10 +823,10 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_COLLAPSE=$(ViashRemoveFlags "$1") shift 1 ;; - --c) - [ -n "$VIASH_PAR_COLLAPSE" ] && ViashError Bad arguments for option \'--c\': \'$VIASH_PAR_COLLAPSE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + -c) + [ -n "$VIASH_PAR_COLLAPSE" ] && ViashError Bad arguments for option \'-c\': \'$VIASH_PAR_COLLAPSE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 VIASH_PAR_COLLAPSE="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --c. Use "--help" to get more information on the parameters. && exit 1 + [ $# -lt 2 ] && ViashError Not enough arguments passed to -c. Use "--help" to get more information on the parameters. && exit 1 shift 2 ;; --depth) @@ -926,10 +840,10 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_DEPTH=$(ViashRemoveFlags "$1") shift 1 ;; - --d) - [ -n "$VIASH_PAR_DEPTH" ] && ViashError Bad arguments for option \'--d\': \'$VIASH_PAR_DEPTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + -d) + [ -n "$VIASH_PAR_DEPTH" ] && ViashError Bad arguments for option \'-d\': \'$VIASH_PAR_DEPTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 VIASH_PAR_DEPTH="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --d. Use "--help" to get more information on the parameters. && exit 1 + [ $# -lt 2 ] && ViashError Not enough arguments passed to -d. Use "--help" to get more information on the parameters. && exit 1 shift 2 ;; --exclude) @@ -943,10 +857,10 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_EXCLUDE=$(ViashRemoveFlags "$1") shift 1 ;; - --e) - [ -n "$VIASH_PAR_EXCLUDE" ] && ViashError Bad arguments for option \'--e\': \'$VIASH_PAR_EXCLUDE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + -e) + [ -n "$VIASH_PAR_EXCLUDE" ] && ViashError Bad arguments for option \'-e\': \'$VIASH_PAR_EXCLUDE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 VIASH_PAR_EXCLUDE="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --e. Use "--help" to get more information on the parameters. && exit 1 + [ $# -lt 2 ] && ViashError Not enough arguments passed to -e. Use "--help" to get more information on the parameters. && exit 1 shift 2 ;; --exons) @@ -960,10 +874,10 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_EXONS=$(ViashRemoveFlags "$1") shift 1 ;; - --E) - [ -n "$VIASH_PAR_EXONS" ] && ViashError Bad arguments for option \'--E\': \'$VIASH_PAR_EXONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + -E) + [ -n "$VIASH_PAR_EXONS" ] && ViashError Bad arguments for option \'-E\': \'$VIASH_PAR_EXONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 VIASH_PAR_EXONS="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --E. Use "--help" to get more information on the parameters. && exit 1 + [ $# -lt 2 ] && ViashError Not enough arguments passed to -E. Use "--help" to get more information on the parameters. && exit 1 shift 2 ;; --apply_filters) @@ -977,29 +891,39 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_APPLY_FILTERS=$(ViashRemoveFlags "$1") shift 1 ;; - --f) - [ -n "$VIASH_PAR_APPLY_FILTERS" ] && ViashError Bad arguments for option \'--f\': \'$VIASH_PAR_APPLY_FILTERS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + -f) + [ -n "$VIASH_PAR_APPLY_FILTERS" ] && ViashError Bad arguments for option \'-f\': \'$VIASH_PAR_APPLY_FILTERS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 VIASH_PAR_APPLY_FILTERS="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --f. Use "--help" to get more information on the parameters. && exit 1 + [ $# -lt 2 ] && ViashError Not enough arguments passed to -f. Use "--help" to get more information on the parameters. && exit 1 shift 2 ;; - --fasta_reference) - [ -n "$VIASH_PAR_FASTA_REFERENCE" ] && ViashError Bad arguments for option \'--fasta_reference\': \'$VIASH_PAR_FASTA_REFERENCE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_FASTA_REFERENCE="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --fasta_reference. Use "--help" to get more information on the parameters. && exit 1 + --fasta_ref) + [ -n "$VIASH_PAR_FASTA_REF" ] && ViashError Bad arguments for option \'--fasta_ref\': \'$VIASH_PAR_FASTA_REF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_FASTA_REF="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --fasta_ref. Use "--help" to get more information on the parameters. && exit 1 shift 2 ;; - --fasta_reference=*) - [ -n "$VIASH_PAR_FASTA_REFERENCE" ] && ViashError Bad arguments for option \'--fasta_reference=*\': \'$VIASH_PAR_FASTA_REFERENCE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_FASTA_REFERENCE=$(ViashRemoveFlags "$1") + --fasta_ref=*) + [ -n "$VIASH_PAR_FASTA_REF" ] && ViashError Bad arguments for option \'--fasta_ref=*\': \'$VIASH_PAR_FASTA_REF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_FASTA_REF=$(ViashRemoveFlags "$1") shift 1 ;; - --F) - [ -n "$VIASH_PAR_FASTA_REFERENCE" ] && ViashError Bad arguments for option \'--F\': \'$VIASH_PAR_FASTA_REFERENCE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_FASTA_REFERENCE="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --F. Use "--help" to get more information on the parameters. && exit 1 + -F) + [ -n "$VIASH_PAR_FASTA_REF" ] && ViashError Bad arguments for option \'-F\': \'$VIASH_PAR_FASTA_REF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_FASTA_REF="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to -F. Use "--help" to get more information on the parameters. && exit 1 shift 2 ;; + --first_allele_only) + [ -n "$VIASH_PAR_FIRST_ALLELE_ONLY" ] && ViashError Bad arguments for option \'--first_allele_only\': \'$VIASH_PAR_FIRST_ALLELE_ONLY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_FIRST_ALLELE_ONLY=true + shift 1 + ;; + --1st-allele-only) + [ -n "$VIASH_PAR_FIRST_ALLELE_ONLY" ] && ViashError Bad arguments for option \'--1st-allele-only\': \'$VIASH_PAR_FIRST_ALLELE_ONLY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_FIRST_ALLELE_ONLY=true + shift 1 + ;; --include) [ -n "$VIASH_PAR_INCLUDE" ] && ViashError Bad arguments for option \'--include\': \'$VIASH_PAR_INCLUDE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 VIASH_PAR_INCLUDE="$2" @@ -1011,19 +935,19 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_INCLUDE=$(ViashRemoveFlags "$1") shift 1 ;; - --i) - [ -n "$VIASH_PAR_INCLUDE" ] && ViashError Bad arguments for option \'--i\': \'$VIASH_PAR_INCLUDE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + -i) + [ -n "$VIASH_PAR_INCLUDE" ] && ViashError Bad arguments for option \'-i\': \'$VIASH_PAR_INCLUDE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 VIASH_PAR_INCLUDE="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --i. Use "--help" to get more information on the parameters. && exit 1 + [ $# -lt 2 ] && ViashError Not enough arguments passed to -i. Use "--help" to get more information on the parameters. && exit 1 shift 2 ;; - --split_by_ID) - [ -n "$VIASH_PAR_SPLIT_BY_ID" ] && ViashError Bad arguments for option \'--split_by_ID\': \'$VIASH_PAR_SPLIT_BY_ID\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + --split_by_id) + [ -n "$VIASH_PAR_SPLIT_BY_ID" ] && ViashError Bad arguments for option \'--split_by_id\': \'$VIASH_PAR_SPLIT_BY_ID\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 VIASH_PAR_SPLIT_BY_ID=true shift 1 ;; - --I) - [ -n "$VIASH_PAR_SPLIT_BY_ID" ] && ViashError Bad arguments for option \'--I\': \'$VIASH_PAR_SPLIT_BY_ID\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + -I) + [ -n "$VIASH_PAR_SPLIT_BY_ID" ] && ViashError Bad arguments for option \'-I\': \'$VIASH_PAR_SPLIT_BY_ID\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 VIASH_PAR_SPLIT_BY_ID=true shift 1 ;; @@ -1038,10 +962,10 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_REGIONS=$(ViashRemoveFlags "$1") shift 1 ;; - --r) - [ -n "$VIASH_PAR_REGIONS" ] && ViashError Bad arguments for option \'--r\': \'$VIASH_PAR_REGIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + -r) + [ -n "$VIASH_PAR_REGIONS" ] && ViashError Bad arguments for option \'-r\': \'$VIASH_PAR_REGIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 VIASH_PAR_REGIONS="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --r. Use "--help" to get more information on the parameters. && exit 1 + [ $# -lt 2 ] && ViashError Not enough arguments passed to -r. Use "--help" to get more information on the parameters. && exit 1 shift 2 ;; --regions_file) @@ -1055,10 +979,10 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_REGIONS_FILE=$(ViashRemoveFlags "$1") shift 1 ;; - --R) - [ -n "$VIASH_PAR_REGIONS_FILE" ] && ViashError Bad arguments for option \'--R\': \'$VIASH_PAR_REGIONS_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + -R) + [ -n "$VIASH_PAR_REGIONS_FILE" ] && ViashError Bad arguments for option \'-R\': \'$VIASH_PAR_REGIONS_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 VIASH_PAR_REGIONS_FILE="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --R. Use "--help" to get more information on the parameters. && exit 1 + [ $# -lt 2 ] && ViashError Not enough arguments passed to -R. Use "--help" to get more information on the parameters. && exit 1 shift 2 ;; --regions_overlap) @@ -1083,10 +1007,10 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_SAMPLES=$(ViashRemoveFlags "$1") shift 1 ;; - --s) - [ -n "$VIASH_PAR_SAMPLES" ] && ViashError Bad arguments for option \'--s\': \'$VIASH_PAR_SAMPLES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + -s) + [ -n "$VIASH_PAR_SAMPLES" ] && ViashError Bad arguments for option \'-s\': \'$VIASH_PAR_SAMPLES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 VIASH_PAR_SAMPLES="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --s. Use "--help" to get more information on the parameters. && exit 1 + [ $# -lt 2 ] && ViashError Not enough arguments passed to -s. Use "--help" to get more information on the parameters. && exit 1 shift 2 ;; --samples_file) @@ -1100,10 +1024,10 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_SAMPLES_FILE=$(ViashRemoveFlags "$1") shift 1 ;; - --S) - [ -n "$VIASH_PAR_SAMPLES_FILE" ] && ViashError Bad arguments for option \'--S\': \'$VIASH_PAR_SAMPLES_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + -S) + [ -n "$VIASH_PAR_SAMPLES_FILE" ] && ViashError Bad arguments for option \'-S\': \'$VIASH_PAR_SAMPLES_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 VIASH_PAR_SAMPLES_FILE="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --S. Use "--help" to get more information on the parameters. && exit 1 + [ $# -lt 2 ] && ViashError Not enough arguments passed to -S. Use "--help" to get more information on the parameters. && exit 1 shift 2 ;; --targets) @@ -1117,10 +1041,10 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_TARGETS=$(ViashRemoveFlags "$1") shift 1 ;; - --t) - [ -n "$VIASH_PAR_TARGETS" ] && ViashError Bad arguments for option \'--t\': \'$VIASH_PAR_TARGETS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + -t) + [ -n "$VIASH_PAR_TARGETS" ] && ViashError Bad arguments for option \'-t\': \'$VIASH_PAR_TARGETS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 VIASH_PAR_TARGETS="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --t. Use "--help" to get more information on the parameters. && exit 1 + [ $# -lt 2 ] && ViashError Not enough arguments passed to -t. Use "--help" to get more information on the parameters. && exit 1 shift 2 ;; --targets_file) @@ -1134,21 +1058,21 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_TARGETS_FILE=$(ViashRemoveFlags "$1") shift 1 ;; - --T) - [ -n "$VIASH_PAR_TARGETS_FILE" ] && ViashError Bad arguments for option \'--T\': \'$VIASH_PAR_TARGETS_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + -T) + [ -n "$VIASH_PAR_TARGETS_FILE" ] && ViashError Bad arguments for option \'-T\': \'$VIASH_PAR_TARGETS_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 VIASH_PAR_TARGETS_FILE="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --T. Use "--help" to get more information on the parameters. && exit 1 + [ $# -lt 2 ] && ViashError Not enough arguments passed to -T. Use "--help" to get more information on the parameters. && exit 1 shift 2 ;; - --targets_overlaps) - [ -n "$VIASH_PAR_TARGETS_OVERLAPS" ] && ViashError Bad arguments for option \'--targets_overlaps\': \'$VIASH_PAR_TARGETS_OVERLAPS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_TARGETS_OVERLAPS="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --targets_overlaps. Use "--help" to get more information on the parameters. && exit 1 + --targets_overlap) + [ -n "$VIASH_PAR_TARGETS_OVERLAP" ] && ViashError Bad arguments for option \'--targets_overlap\': \'$VIASH_PAR_TARGETS_OVERLAP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_TARGETS_OVERLAP="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --targets_overlap. Use "--help" to get more information on the parameters. && exit 1 shift 2 ;; - --targets_overlaps=*) - [ -n "$VIASH_PAR_TARGETS_OVERLAPS" ] && ViashError Bad arguments for option \'--targets_overlaps=*\': \'$VIASH_PAR_TARGETS_OVERLAPS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_TARGETS_OVERLAPS=$(ViashRemoveFlags "$1") + --targets_overlap=*) + [ -n "$VIASH_PAR_TARGETS_OVERLAP" ] && ViashError Bad arguments for option \'--targets_overlap=*\': \'$VIASH_PAR_TARGETS_OVERLAP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_TARGETS_OVERLAP=$(ViashRemoveFlags "$1") shift 1 ;; --user_tstv) @@ -1162,10 +1086,10 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_USER_TSTV=$(ViashRemoveFlags "$1") shift 1 ;; - --u) - [ -n "$VIASH_PAR_USER_TSTV" ] && ViashError Bad arguments for option \'--u\': \'$VIASH_PAR_USER_TSTV\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + -u) + [ -n "$VIASH_PAR_USER_TSTV" ] && ViashError Bad arguments for option \'-u\': \'$VIASH_PAR_USER_TSTV\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 VIASH_PAR_USER_TSTV="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --u. Use "--help" to get more information on the parameters. && exit 1 + [ $# -lt 2 ] && ViashError Not enough arguments passed to -u. Use "--help" to get more information on the parameters. && exit 1 shift 2 ;; --verbose) @@ -1173,8 +1097,8 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_VERBOSE=true shift 1 ;; - --v) - [ -n "$VIASH_PAR_VERBOSE" ] && ViashError Bad arguments for option \'--v\': \'$VIASH_PAR_VERBOSE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + -v) + [ -n "$VIASH_PAR_VERBOSE" ] && ViashError Bad arguments for option \'-v\': \'$VIASH_PAR_VERBOSE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 VIASH_PAR_VERBOSE=true shift 1 ;; @@ -1288,13 +1212,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bcftools' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bcftools' 'ps' 'bash' fi # setting computational defaults @@ -1407,16 +1331,12 @@ if [ ! -z "$VIASH_PAR_INPUT" ]; then done set +f fi -if [ ! -z "$VIASH_PAR_ALLELE_FREQUENCY_BINS_FILE" ] && [ ! -e "$VIASH_PAR_ALLELE_FREQUENCY_BINS_FILE" ]; then - ViashError "Input file '$VIASH_PAR_ALLELE_FREQUENCY_BINS_FILE' does not exist." - exit 1 -fi if [ ! -z "$VIASH_PAR_EXONS" ] && [ ! -e "$VIASH_PAR_EXONS" ]; then ViashError "Input file '$VIASH_PAR_EXONS' does not exist." exit 1 fi -if [ ! -z "$VIASH_PAR_FASTA_REFERENCE" ] && [ ! -e "$VIASH_PAR_FASTA_REFERENCE" ]; then - ViashError "Input file '$VIASH_PAR_FASTA_REFERENCE' does not exist." +if [ ! -z "$VIASH_PAR_FASTA_REF" ] && [ ! -e "$VIASH_PAR_FASTA_REF" ]; then + ViashError "Input file '$VIASH_PAR_FASTA_REF' does not exist." exit 1 fi if [ ! -z "$VIASH_PAR_REGIONS_FILE" ] && [ ! -e "$VIASH_PAR_REGIONS_FILE" ]; then @@ -1441,7 +1361,7 @@ if [[ -n "$VIASH_PAR_FIRST_ALLELE_ONLY" ]]; then fi if [[ -n "$VIASH_PAR_SPLIT_BY_ID" ]]; then if ! [[ "$VIASH_PAR_SPLIT_BY_ID" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then - ViashError '--split_by_ID' has to be a boolean_true. Use "--help" to get more information on the parameters. + ViashError '--split_by_id' has to be a boolean_true. Use "--help" to get more information on the parameters. exit 1 fi fi @@ -1549,12 +1469,12 @@ if [ ! -z "$VIASH_PAR_REGIONS_OVERLAP" ]; then unset IFS fi -if [ ! -z "$VIASH_PAR_TARGETS_OVERLAPS" ]; then - VIASH_PAR_TARGETS_OVERLAPS_CHOICES=("pos;record;variant;0;1;2") +if [ ! -z "$VIASH_PAR_TARGETS_OVERLAP" ]; then + VIASH_PAR_TARGETS_OVERLAP_CHOICES=("pos;record;variant;0;1;2") IFS=';' set -f - if ! [[ ";${VIASH_PAR_TARGETS_OVERLAPS_CHOICES[*]};" =~ ";$VIASH_PAR_TARGETS_OVERLAPS;" ]]; then - ViashError '--targets_overlaps' specified value of \'$VIASH_PAR_TARGETS_OVERLAPS\' is not in the list of allowed values. Use "--help" to get more information on the parameters. + if ! [[ ";${VIASH_PAR_TARGETS_OVERLAP_CHOICES[*]};" =~ ";$VIASH_PAR_TARGETS_OVERLAP;" ]]; then + ViashError '--targets_overlap' specified value of \'$VIASH_PAR_TARGETS_OVERLAP\' is not in the list of allowed values. Use "--help" to get more information on the parameters. exit 1 fi set +f @@ -1594,17 +1514,13 @@ if [ ! -z "$VIASH_PAR_OUTPUT" ]; then VIASH_PAR_OUTPUT=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT") VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTPUT" ) fi -if [ ! -z "$VIASH_PAR_ALLELE_FREQUENCY_BINS_FILE" ]; then - VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_ALLELE_FREQUENCY_BINS_FILE")" ) - VIASH_PAR_ALLELE_FREQUENCY_BINS_FILE=$(ViashDockerAutodetectMount "$VIASH_PAR_ALLELE_FREQUENCY_BINS_FILE") -fi if [ ! -z "$VIASH_PAR_EXONS" ]; then VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_EXONS")" ) VIASH_PAR_EXONS=$(ViashDockerAutodetectMount "$VIASH_PAR_EXONS") fi -if [ ! -z "$VIASH_PAR_FASTA_REFERENCE" ]; then - VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_FASTA_REFERENCE")" ) - VIASH_PAR_FASTA_REFERENCE=$(ViashDockerAutodetectMount "$VIASH_PAR_FASTA_REFERENCE") +if [ ! -z "$VIASH_PAR_FASTA_REF" ]; then + VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_FASTA_REF")" ) + VIASH_PAR_FASTA_REF=$(ViashDockerAutodetectMount "$VIASH_PAR_FASTA_REF") fi if [ ! -z "$VIASH_PAR_REGIONS_FILE" ]; then VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_REGIONS_FILE")" ) @@ -1691,18 +1607,17 @@ cat > "\$tempscript" << 'VIASHMAIN' # The following code has been auto-generated by Viash. $( if [ ! -z ${VIASH_PAR_INPUT+x} ]; then echo "${VIASH_PAR_INPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_input='&'#" ; else echo "# par_input="; fi ) $( if [ ! -z ${VIASH_PAR_OUTPUT+x} ]; then echo "${VIASH_PAR_OUTPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_output='&'#" ; else echo "# par_output="; fi ) -$( if [ ! -z ${VIASH_PAR_ALLELE_FREQUENCY_BINS+x} ]; then echo "${VIASH_PAR_ALLELE_FREQUENCY_BINS}" | sed "s#'#'\"'\"'#g;s#.*#par_allele_frequency_bins='&'#" ; else echo "# par_allele_frequency_bins="; fi ) -$( if [ ! -z ${VIASH_PAR_ALLELE_FREQUENCY_BINS_FILE+x} ]; then echo "${VIASH_PAR_ALLELE_FREQUENCY_BINS_FILE}" | sed "s#'#'\"'\"'#g;s#.*#par_allele_frequency_bins_file='&'#" ; else echo "# par_allele_frequency_bins_file="; fi ) -$( if [ ! -z ${VIASH_PAR_ALLELE_FREQUENCY_TAG+x} ]; then echo "${VIASH_PAR_ALLELE_FREQUENCY_TAG}" | sed "s#'#'\"'\"'#g;s#.*#par_allele_frequency_tag='&'#" ; else echo "# par_allele_frequency_tag="; fi ) -$( if [ ! -z ${VIASH_PAR_FIRST_ALLELE_ONLY+x} ]; then echo "${VIASH_PAR_FIRST_ALLELE_ONLY}" | sed "s#'#'\"'\"'#g;s#.*#par_first_allele_only='&'#" ; else echo "# par_first_allele_only="; fi ) +$( if [ ! -z ${VIASH_PAR_AF_BINS+x} ]; then echo "${VIASH_PAR_AF_BINS}" | sed "s#'#'\"'\"'#g;s#.*#par_af_bins='&'#" ; else echo "# par_af_bins="; fi ) +$( if [ ! -z ${VIASH_PAR_AF_TAG+x} ]; then echo "${VIASH_PAR_AF_TAG}" | sed "s#'#'\"'\"'#g;s#.*#par_af_tag='&'#" ; else echo "# par_af_tag="; fi ) $( if [ ! -z ${VIASH_PAR_COLLAPSE+x} ]; then echo "${VIASH_PAR_COLLAPSE}" | sed "s#'#'\"'\"'#g;s#.*#par_collapse='&'#" ; else echo "# par_collapse="; fi ) $( if [ ! -z ${VIASH_PAR_DEPTH+x} ]; then echo "${VIASH_PAR_DEPTH}" | sed "s#'#'\"'\"'#g;s#.*#par_depth='&'#" ; else echo "# par_depth="; fi ) $( if [ ! -z ${VIASH_PAR_EXCLUDE+x} ]; then echo "${VIASH_PAR_EXCLUDE}" | sed "s#'#'\"'\"'#g;s#.*#par_exclude='&'#" ; else echo "# par_exclude="; fi ) $( if [ ! -z ${VIASH_PAR_EXONS+x} ]; then echo "${VIASH_PAR_EXONS}" | sed "s#'#'\"'\"'#g;s#.*#par_exons='&'#" ; else echo "# par_exons="; fi ) $( if [ ! -z ${VIASH_PAR_APPLY_FILTERS+x} ]; then echo "${VIASH_PAR_APPLY_FILTERS}" | sed "s#'#'\"'\"'#g;s#.*#par_apply_filters='&'#" ; else echo "# par_apply_filters="; fi ) -$( if [ ! -z ${VIASH_PAR_FASTA_REFERENCE+x} ]; then echo "${VIASH_PAR_FASTA_REFERENCE}" | sed "s#'#'\"'\"'#g;s#.*#par_fasta_reference='&'#" ; else echo "# par_fasta_reference="; fi ) +$( if [ ! -z ${VIASH_PAR_FASTA_REF+x} ]; then echo "${VIASH_PAR_FASTA_REF}" | sed "s#'#'\"'\"'#g;s#.*#par_fasta_ref='&'#" ; else echo "# par_fasta_ref="; fi ) +$( if [ ! -z ${VIASH_PAR_FIRST_ALLELE_ONLY+x} ]; then echo "${VIASH_PAR_FIRST_ALLELE_ONLY}" | sed "s#'#'\"'\"'#g;s#.*#par_first_allele_only='&'#" ; else echo "# par_first_allele_only="; fi ) $( if [ ! -z ${VIASH_PAR_INCLUDE+x} ]; then echo "${VIASH_PAR_INCLUDE}" | sed "s#'#'\"'\"'#g;s#.*#par_include='&'#" ; else echo "# par_include="; fi ) -$( if [ ! -z ${VIASH_PAR_SPLIT_BY_ID+x} ]; then echo "${VIASH_PAR_SPLIT_BY_ID}" | sed "s#'#'\"'\"'#g;s#.*#par_split_by_ID='&'#" ; else echo "# par_split_by_ID="; fi ) +$( if [ ! -z ${VIASH_PAR_SPLIT_BY_ID+x} ]; then echo "${VIASH_PAR_SPLIT_BY_ID}" | sed "s#'#'\"'\"'#g;s#.*#par_split_by_id='&'#" ; else echo "# par_split_by_id="; fi ) $( if [ ! -z ${VIASH_PAR_REGIONS+x} ]; then echo "${VIASH_PAR_REGIONS}" | sed "s#'#'\"'\"'#g;s#.*#par_regions='&'#" ; else echo "# par_regions="; fi ) $( if [ ! -z ${VIASH_PAR_REGIONS_FILE+x} ]; then echo "${VIASH_PAR_REGIONS_FILE}" | sed "s#'#'\"'\"'#g;s#.*#par_regions_file='&'#" ; else echo "# par_regions_file="; fi ) $( if [ ! -z ${VIASH_PAR_REGIONS_OVERLAP+x} ]; then echo "${VIASH_PAR_REGIONS_OVERLAP}" | sed "s#'#'\"'\"'#g;s#.*#par_regions_overlap='&'#" ; else echo "# par_regions_overlap="; fi ) @@ -1710,7 +1625,7 @@ $( if [ ! -z ${VIASH_PAR_SAMPLES+x} ]; then echo "${VIASH_PAR_SAMPLES}" | sed "s $( if [ ! -z ${VIASH_PAR_SAMPLES_FILE+x} ]; then echo "${VIASH_PAR_SAMPLES_FILE}" | sed "s#'#'\"'\"'#g;s#.*#par_samples_file='&'#" ; else echo "# par_samples_file="; fi ) $( if [ ! -z ${VIASH_PAR_TARGETS+x} ]; then echo "${VIASH_PAR_TARGETS}" | sed "s#'#'\"'\"'#g;s#.*#par_targets='&'#" ; else echo "# par_targets="; fi ) $( if [ ! -z ${VIASH_PAR_TARGETS_FILE+x} ]; then echo "${VIASH_PAR_TARGETS_FILE}" | sed "s#'#'\"'\"'#g;s#.*#par_targets_file='&'#" ; else echo "# par_targets_file="; fi ) -$( if [ ! -z ${VIASH_PAR_TARGETS_OVERLAPS+x} ]; then echo "${VIASH_PAR_TARGETS_OVERLAPS}" | sed "s#'#'\"'\"'#g;s#.*#par_targets_overlaps='&'#" ; else echo "# par_targets_overlaps="; fi ) +$( if [ ! -z ${VIASH_PAR_TARGETS_OVERLAP+x} ]; then echo "${VIASH_PAR_TARGETS_OVERLAP}" | sed "s#'#'\"'\"'#g;s#.*#par_targets_overlap='&'#" ; else echo "# par_targets_overlap="; fi ) $( if [ ! -z ${VIASH_PAR_USER_TSTV+x} ]; then echo "${VIASH_PAR_USER_TSTV}" | sed "s#'#'\"'\"'#g;s#.*#par_user_tstv='&'#" ; else echo "# par_user_tstv="; fi ) $( if [ ! -z ${VIASH_PAR_VERBOSE+x} ]; then echo "${VIASH_PAR_VERBOSE}" | sed "s#'#'\"'\"'#g;s#.*#par_verbose='&'#" ; else echo "# par_verbose="; fi ) $( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "${VIASH_META_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_name='&'#" ; else echo "# meta_name="; fi ) @@ -1734,56 +1649,55 @@ $( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}" ## VIASH END -# Exit on error set -eo pipefail -# Unset parameters -unset_if_false=( - par_first_allele_only - par_split_by_ID - par_verbose -) +# Unset false boolean parameters +[[ "\$par_first_allele_only" == "false" ]] && unset par_first_allele_only +[[ "\$par_split_by_id" == "false" ]] && unset par_split_by_id +[[ "\$par_verbose" == "false" ]] && unset par_verbose -for par in \${unset_if_false[@]}; do - test_val="\${!par}" - [[ "\$test_val" == "false" ]] && unset \$par -done +# Handle multiple input files (semicolon-separated) +IFS=';' read -ra input_files <<< "\$par_input" -# Create input array -IFS=";" read -ra input <<< \$par_input - -# Check the size of the input array -if [[ \${#input[@]} -gt 2 ]]; then - echo "Error: --input only takes a max of two files!" - exit 1 +# Validate input files (maximum 2 allowed) +if [[ \${#input_files[@]} -gt 2 ]]; then + echo "Error: Maximum of two input files allowed" >&2 + exit 1 fi -# Execute bcftools stats with the provided arguments -bcftools stats \\ - \${par_first_allele_only:+--1st-allele-only} \\ - \${par_split_by_ID:+--split-by-ID} \\ - \${par_verbose:+--verbose} \\ - \${par_allele_frequency_bins:+--af-bins "\${par_allele_frequency_bins}"} \\ - \${par_allele_frequency_bins_file:+--af-bins "\${par_allele_frequency_bins_file}"} \\ - \${par_allele_frequency_tag:+--af-tag "\${par_allele_frequency_tag}"} \\ - \${par_collapse:+-c "\${par_collapse}"} \\ - \${par_depth:+-d "\${par_depth}"} \\ - \${par_exclude:+-e "\${par_exclude}"} \\ - \${par_exons:+-E "\${par_exons}"} \\ - \${par_apply_filters:+-f "\${par_apply_filters}"} \\ - \${par_fasta_reference:+-F "\${par_fasta_reference}"} \\ - \${par_include:+-i "\${par_include}"} \\ - \${par_regions:+-r "\${par_regions}"} \\ - \${par_regions_file:+-R "\${par_regions_file}"} \\ - \${par_regions_overlap:+--regions-overlap "\${par_regions_overlap}"} \\ - \${par_samples:+-s "\${par_samples}"} \\ - \${par_samples_file:+-S "\${par_samples_file}"} \\ - \${par_targets:+-t "\${par_targets}"} \\ - \${par_targets_file:+-T "\${par_targets_file}"} \\ - \${par_targets_overlaps:+--targets-overlap "\${par_targets_overlaps}"} \\ - \${par_user_tstv:+-u "\${par_user_tstv}"} \\ - "\${input[@]}" \\ - > \$par_output +# Build command array +cmd_args=( + "bcftools" "stats" + \${par_af_bins:+--af-bins "\$par_af_bins"} + \${par_af_tag:+--af-tag "\$par_af_tag"} + \${par_collapse:+-c "\$par_collapse"} + \${par_depth:+-d "\$par_depth"} + \${par_exclude:+-e "\$par_exclude"} + \${par_exons:+-E "\$par_exons"} + \${par_apply_filters:+-f "\$par_apply_filters"} + \${par_fasta_ref:+-F "\$par_fasta_ref"} + \${par_first_allele_only:+--1st-allele-only} + \${par_include:+-i "\$par_include"} + \${par_split_by_id:+-I} + \${par_regions:+-r "\$par_regions"} + \${par_regions_file:+-R "\$par_regions_file"} + \${par_regions_overlap:+--regions-overlap "\$par_regions_overlap"} + \${par_samples:+-s "\$par_samples"} + \${par_samples_file:+-S "\$par_samples_file"} + \${par_targets:+-t "\$par_targets"} + \${par_targets_file:+-T "\$par_targets_file"} + \${par_targets_overlap:+--targets-overlap "\$par_targets_overlap"} + \${par_user_tstv:+-u "\$par_user_tstv"} + \${par_verbose:+-v} +) + +# Add input files +for file in "\${input_files[@]}"; do + cmd_args+=("\$file") +done + +# Execute command and redirect output +"\${cmd_args[@]}" > "\$par_output" VIASHMAIN bash "\$tempscript" & wait "\$!" @@ -1810,14 +1724,11 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then if [ ! -z "$VIASH_PAR_OUTPUT" ]; then VIASH_PAR_OUTPUT=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT") fi - if [ ! -z "$VIASH_PAR_ALLELE_FREQUENCY_BINS_FILE" ]; then - VIASH_PAR_ALLELE_FREQUENCY_BINS_FILE=$(ViashDockerStripAutomount "$VIASH_PAR_ALLELE_FREQUENCY_BINS_FILE") - fi if [ ! -z "$VIASH_PAR_EXONS" ]; then VIASH_PAR_EXONS=$(ViashDockerStripAutomount "$VIASH_PAR_EXONS") fi - if [ ! -z "$VIASH_PAR_FASTA_REFERENCE" ]; then - VIASH_PAR_FASTA_REFERENCE=$(ViashDockerStripAutomount "$VIASH_PAR_FASTA_REFERENCE") + if [ ! -z "$VIASH_PAR_FASTA_REF" ]; then + VIASH_PAR_FASTA_REF=$(ViashDockerStripAutomount "$VIASH_PAR_FASTA_REF") fi if [ ! -z "$VIASH_PAR_REGIONS_FILE" ]; then VIASH_PAR_REGIONS_FILE=$(ViashDockerStripAutomount "$VIASH_PAR_REGIONS_FILE") diff --git a/target/executable/bcl_convert/.config.vsh.yaml b/target/executable/bcl_convert/.config.vsh.yaml index b8ba93d1..8e654b84 100644 --- a/target/executable/bcl_convert/.config.vsh.yaml +++ b/target/executable/bcl_convert/.config.vsh.yaml @@ -431,7 +431,7 @@ build_info: output: "target/executable/bcl_convert" executable: "target/executable/bcl_convert/bcl_convert" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -453,138 +453,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bcl_convert/bcl_convert b/target/executable/bcl_convert/bcl_convert index c66cad61..efb8b79b 100755 --- a/target/executable/bcl_convert/bcl_convert +++ b/target/executable/bcl_convert/bcl_convert @@ -462,9 +462,9 @@ RUN echo "bcl-convert: \"$(bcl-convert -V 2>&1 >/dev/null | sed -n '/Version/ s/ LABEL org.opencontainers.image.authors="Toni Verbeiren, Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component bcl_convert" -LABEL org.opencontainers.image.created="2025-09-01T11:02:59Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:10Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml b/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml index 0e78bc5f..4a89878e 100644 --- a/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml +++ b/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml @@ -166,6 +166,7 @@ scope: target: "public" requirements: commands: + - "cwl-runner" - "ps" keywords: - "genome" @@ -279,7 +280,7 @@ build_info: output: "target/executable/bd_rhapsody/bd_rhapsody_make_reference" executable: "target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -301,138 +302,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference b/target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference index d6300b7f..208ccb8f 100755 --- a/target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference +++ b/target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference @@ -465,9 +465,9 @@ RUN VERSION=$(ls -v /var/bd_rhapsody_cwl | grep '^v' | sed 's#v##' | tail -1) RUN echo "bdgenomics/rhapsody: \"$VERSION\"" > /var/software_versions.txt LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Weiwei Schultz" LABEL org.opencontainers.image.description="Companion container for running component bd_rhapsody bd_rhapsody_make_reference" -LABEL org.opencontainers.image.created="2025-09-01T11:02:54Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:04Z" LABEL org.opencontainers.image.source="https://bitbucket.org/CRSwDev/cwl/src/master/v2.2.1/Extra_Utilities/" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -932,13 +932,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'cwl-runner' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'cwl-runner' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/.config.vsh.yaml b/target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/.config.vsh.yaml index 51c91a44..34386f62 100644 --- a/target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/.config.vsh.yaml +++ b/target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/.config.vsh.yaml @@ -996,6 +996,7 @@ scope: target: "public" requirements: commands: + - "cwl-runner" - "ps" keywords: - "rna-seq" @@ -1120,7 +1121,7 @@ build_info: output: "target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis" executable: "target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/bd_rhapsody_sequence_analysis" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -1142,138 +1143,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/bd_rhapsody_sequence_analysis b/target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/bd_rhapsody_sequence_analysis index fa39f97c..6e1145c4 100755 --- a/target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/bd_rhapsody_sequence_analysis +++ b/target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/bd_rhapsody_sequence_analysis @@ -465,9 +465,9 @@ RUN VERSION=$(ls -v /var/bd_rhapsody_cwl | grep '^v' | sed 's#v##' | tail -1) RUN echo "bdgenomics/rhapsody: \"$VERSION\"" > /var/software_versions.txt LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Weiwei Schultz" LABEL org.opencontainers.image.description="Companion container for running component bd_rhapsody bd_rhapsody_sequence_analysis" -LABEL org.opencontainers.image.created="2025-09-01T11:02:54Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:04Z" LABEL org.opencontainers.image.source="https://bitbucket.org/CRSwDev/cwl/src/master/v2.2.1" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -1992,13 +1992,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'cwl-runner' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'cwl-runner' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/bedtools/bedtools_annotate/.config.vsh.yaml b/target/executable/bedtools/bedtools_annotate/.config.vsh.yaml index f74a6f03..6be44abc 100644 --- a/target/executable/bedtools/bedtools_annotate/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_annotate/.config.vsh.yaml @@ -143,6 +143,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "Annotate" @@ -246,7 +247,7 @@ build_info: output: "target/executable/bedtools/bedtools_annotate" executable: "target/executable/bedtools/bedtools_annotate/bedtools_annotate" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -268,138 +269,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_annotate/bedtools_annotate b/target/executable/bedtools/bedtools_annotate/bedtools_annotate index c45e91e2..9b806114 100755 --- a/target/executable/bedtools/bedtools_annotate/bedtools_annotate +++ b/target/executable/bedtools/bedtools_annotate/bedtools_annotate @@ -451,9 +451,9 @@ ENTRYPOINT [] RUN bedtools --version 2>&1 | head -1 | sed 's/.*bedtools v/bedtools: /' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_annotate" -LABEL org.opencontainers.image.created="2025-09-01T11:02:47Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:16Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -898,13 +898,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/bedtools/bedtools_bamtobed/.config.vsh.yaml b/target/executable/bedtools/bedtools_bamtobed/.config.vsh.yaml index d74e973d..23865468 100644 --- a/target/executable/bedtools/bedtools_bamtobed/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_bamtobed/.config.vsh.yaml @@ -163,6 +163,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "Converts" @@ -265,7 +266,7 @@ build_info: output: "target/executable/bedtools/bedtools_bamtobed" executable: "target/executable/bedtools/bedtools_bamtobed/bedtools_bamtobed" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -287,138 +288,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_bamtobed/bedtools_bamtobed b/target/executable/bedtools/bedtools_bamtobed/bedtools_bamtobed index 2df5b6d7..506cfe1f 100755 --- a/target/executable/bedtools/bedtools_bamtobed/bedtools_bamtobed +++ b/target/executable/bedtools/bedtools_bamtobed/bedtools_bamtobed @@ -452,9 +452,9 @@ ENTRYPOINT [] RUN bedtools --version 2>&1 | head -1 | sed 's/.*bedtools v/bedtools: /' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bamtobed" -LABEL org.opencontainers.image.created="2025-09-01T11:02:54Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:11Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -925,13 +925,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml b/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml index 75d0def8..556f2bb3 100644 --- a/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml @@ -110,6 +110,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "Conversion" @@ -210,7 +211,7 @@ build_info: output: "target/executable/bedtools/bedtools_bamtofastq" executable: "target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -232,138 +233,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq b/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq index 0bd1f683..30de09a3 100755 --- a/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq +++ b/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq @@ -452,9 +452,9 @@ ENTRYPOINT [] RUN bedtools --version 2>&1 | head -1 | sed 's/.*bedtools v/bedtools: /' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bamtofastq" -LABEL org.opencontainers.image.created="2025-09-01T11:02:49Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:12Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -830,13 +830,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml b/target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml index 81b94efb..87a387cc 100644 --- a/target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml @@ -98,6 +98,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "Converts" @@ -198,7 +199,7 @@ build_info: output: "target/executable/bedtools/bedtools_bed12tobed6" executable: "target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -220,138 +221,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6 b/target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6 index ccad972a..ff488257 100755 --- a/target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6 +++ b/target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6 @@ -452,9 +452,9 @@ ENTRYPOINT [] RUN bedtools --version 2>&1 | head -1 | sed 's/.*bedtools v/bedtools: /' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bed12tobed6" -LABEL org.opencontainers.image.created="2025-09-01T11:02:53Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:09Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -811,13 +811,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/bedtools/bedtools_bedpetobam/.config.vsh.yaml b/target/executable/bedtools/bedtools_bedpetobam/.config.vsh.yaml index 3d24e4c7..e6b399ed 100644 --- a/target/executable/bedtools/bedtools_bedpetobam/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_bedpetobam/.config.vsh.yaml @@ -115,6 +115,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -218,7 +219,7 @@ build_info: output: "target/executable/bedtools/bedtools_bedpetobam" executable: "target/executable/bedtools/bedtools_bedpetobam/bedtools_bedpetobam" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -240,138 +241,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_bedpetobam/bedtools_bedpetobam b/target/executable/bedtools/bedtools_bedpetobam/bedtools_bedpetobam index 786c07a2..b02d6eca 100755 --- a/target/executable/bedtools/bedtools_bedpetobam/bedtools_bedpetobam +++ b/target/executable/bedtools/bedtools_bedpetobam/bedtools_bedpetobam @@ -452,9 +452,9 @@ RUN bedtools --version 2>&1 | head -1 | sed 's/.*bedtools v/bedtools: /' > /var/ LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bedpetobam" -LABEL org.opencontainers.image.created="2025-09-01T11:02:49Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:17Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -845,13 +845,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml b/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml index 8e3da893..220d620c 100644 --- a/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml @@ -132,6 +132,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "Converts" @@ -234,7 +235,7 @@ build_info: output: "target/executable/bedtools/bedtools_bedtobam" executable: "target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -256,138 +257,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam b/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam index 15588655..2f5c358e 100755 --- a/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam +++ b/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam @@ -452,9 +452,9 @@ ENTRYPOINT [] RUN bedtools --version 2>&1 | head -1 | sed 's/.*bedtools v/bedtools: /' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bedtobam" -LABEL org.opencontainers.image.created="2025-09-01T11:02:54Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:17Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -874,13 +874,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/bedtools/bedtools_closest/.config.vsh.yaml b/target/executable/bedtools/bedtools_closest/.config.vsh.yaml index 59ffa5b5..71b475d8 100644 --- a/target/executable/bedtools/bedtools_closest/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_closest/.config.vsh.yaml @@ -236,6 +236,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "Closest" @@ -340,7 +341,7 @@ build_info: output: "target/executable/bedtools/bedtools_closest" executable: "target/executable/bedtools/bedtools_closest/bedtools_closest" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -362,138 +363,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_closest/bedtools_closest b/target/executable/bedtools/bedtools_closest/bedtools_closest index 3059ec3a..1e2f46ae 100755 --- a/target/executable/bedtools/bedtools_closest/bedtools_closest +++ b/target/executable/bedtools/bedtools_closest/bedtools_closest @@ -451,9 +451,9 @@ ENTRYPOINT [] RUN bedtools --version 2>&1 | head -1 | sed 's/.*bedtools v/bedtools: /' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_closest" -LABEL org.opencontainers.image.created="2025-09-01T11:02:53Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:14Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -1055,13 +1055,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/bedtools/bedtools_cluster/.config.vsh.yaml b/target/executable/bedtools/bedtools_cluster/.config.vsh.yaml index b3234031..e208cdc4 100644 --- a/target/executable/bedtools/bedtools_cluster/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_cluster/.config.vsh.yaml @@ -104,6 +104,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -207,7 +208,7 @@ build_info: output: "target/executable/bedtools/bedtools_cluster" executable: "target/executable/bedtools/bedtools_cluster/bedtools_cluster" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -229,138 +230,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_cluster/bedtools_cluster b/target/executable/bedtools/bedtools_cluster/bedtools_cluster index b952226f..b94d98d4 100755 --- a/target/executable/bedtools/bedtools_cluster/bedtools_cluster +++ b/target/executable/bedtools/bedtools_cluster/bedtools_cluster @@ -452,9 +452,9 @@ RUN bedtools --version 2>&1 | head -1 | sed 's/.*bedtools v/bedtools: /' > /var/ LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_cluster" -LABEL org.opencontainers.image.created="2025-09-01T11:02:56Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:09Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -832,13 +832,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/bedtools/bedtools_complement/.config.vsh.yaml b/target/executable/bedtools/bedtools_complement/.config.vsh.yaml index e03c7c2b..d402c675 100644 --- a/target/executable/bedtools/bedtools_complement/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_complement/.config.vsh.yaml @@ -105,6 +105,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -208,7 +209,7 @@ build_info: output: "target/executable/bedtools/bedtools_complement" executable: "target/executable/bedtools/bedtools_complement/bedtools_complement" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -230,138 +231,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_complement/bedtools_complement b/target/executable/bedtools/bedtools_complement/bedtools_complement index ebb48b2e..d68e267c 100755 --- a/target/executable/bedtools/bedtools_complement/bedtools_complement +++ b/target/executable/bedtools/bedtools_complement/bedtools_complement @@ -452,9 +452,9 @@ RUN bedtools --version 2>&1 | head -1 | sed 's/.*bedtools v/bedtools: /' > /var/ LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_complement" -LABEL org.opencontainers.image.created="2025-09-01T11:02:52Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:14Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -834,13 +834,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/bedtools/bedtools_coverage/.config.vsh.yaml b/target/executable/bedtools/bedtools_coverage/.config.vsh.yaml index bc040753..528dfe66 100644 --- a/target/executable/bedtools/bedtools_coverage/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_coverage/.config.vsh.yaml @@ -257,6 +257,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -361,7 +362,7 @@ build_info: output: "target/executable/bedtools/bedtools_coverage" executable: "target/executable/bedtools/bedtools_coverage/bedtools_coverage" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -383,138 +384,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_coverage/bedtools_coverage b/target/executable/bedtools/bedtools_coverage/bedtools_coverage index 52d07f6a..1f7b5c84 100755 --- a/target/executable/bedtools/bedtools_coverage/bedtools_coverage +++ b/target/executable/bedtools/bedtools_coverage/bedtools_coverage @@ -452,9 +452,9 @@ RUN bedtools --version 2>&1 | head -1 | sed 's/.*bedtools v/bedtools: /' > /var/ LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_coverage" -LABEL org.opencontainers.image.created="2025-09-01T11:02:47Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:13Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -1095,13 +1095,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/bedtools/bedtools_expand/.config.vsh.yaml b/target/executable/bedtools/bedtools_expand/.config.vsh.yaml index d5a0e9b4..76623ce5 100644 --- a/target/executable/bedtools/bedtools_expand/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_expand/.config.vsh.yaml @@ -90,6 +90,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -193,7 +194,7 @@ build_info: output: "target/executable/bedtools/bedtools_expand" executable: "target/executable/bedtools/bedtools_expand/bedtools_expand" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -215,138 +216,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_expand/bedtools_expand b/target/executable/bedtools/bedtools_expand/bedtools_expand index d8179786..624679f2 100755 --- a/target/executable/bedtools/bedtools_expand/bedtools_expand +++ b/target/executable/bedtools/bedtools_expand/bedtools_expand @@ -452,9 +452,9 @@ RUN bedtools --version 2>&1 | head -1 | sed 's/.*bedtools v/bedtools: /' > /var/ LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_expand" -LABEL org.opencontainers.image.created="2025-09-01T11:02:56Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:13Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -812,13 +812,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/bedtools/bedtools_fisher/.config.vsh.yaml b/target/executable/bedtools/bedtools_fisher/.config.vsh.yaml index 8534e1dc..76ea86b7 100644 --- a/target/executable/bedtools/bedtools_fisher/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_fisher/.config.vsh.yaml @@ -238,6 +238,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -342,7 +343,7 @@ build_info: output: "target/executable/bedtools/bedtools_fisher" executable: "target/executable/bedtools/bedtools_fisher/bedtools_fisher" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -364,138 +365,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_fisher/bedtools_fisher b/target/executable/bedtools/bedtools_fisher/bedtools_fisher index 19194f48..ac31d0e8 100755 --- a/target/executable/bedtools/bedtools_fisher/bedtools_fisher +++ b/target/executable/bedtools/bedtools_fisher/bedtools_fisher @@ -452,9 +452,9 @@ RUN bedtools --version 2>&1 | head -1 | sed 's/.*bedtools v/bedtools: /' > /var/ LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_fisher" -LABEL org.opencontainers.image.created="2025-09-01T11:02:57Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:10Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -1074,13 +1074,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/bedtools/bedtools_flank/.config.vsh.yaml b/target/executable/bedtools/bedtools_flank/.config.vsh.yaml index 9b147771..b3675b9f 100644 --- a/target/executable/bedtools/bedtools_flank/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_flank/.config.vsh.yaml @@ -169,6 +169,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -273,7 +274,7 @@ build_info: output: "target/executable/bedtools/bedtools_flank" executable: "target/executable/bedtools/bedtools_flank/bedtools_flank" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -295,138 +296,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_flank/bedtools_flank b/target/executable/bedtools/bedtools_flank/bedtools_flank index 223c7d09..2d9cafa8 100755 --- a/target/executable/bedtools/bedtools_flank/bedtools_flank +++ b/target/executable/bedtools/bedtools_flank/bedtools_flank @@ -452,9 +452,9 @@ RUN bedtools --version 2>&1 | head -1 | sed 's/.*bedtools v/bedtools: /' > /var/ LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_flank" -LABEL org.opencontainers.image.created="2025-09-01T11:02:48Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:10Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -938,13 +938,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/bedtools/bedtools_genomecov/.config.vsh.yaml b/target/executable/bedtools/bedtools_genomecov/.config.vsh.yaml index 83f333f0..06177fdc 100644 --- a/target/executable/bedtools/bedtools_genomecov/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_genomecov/.config.vsh.yaml @@ -260,6 +260,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genome coverage" @@ -365,7 +366,7 @@ build_info: output: "target/executable/bedtools/bedtools_genomecov" executable: "target/executable/bedtools/bedtools_genomecov/bedtools_genomecov" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -387,138 +388,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_genomecov/bedtools_genomecov b/target/executable/bedtools/bedtools_genomecov/bedtools_genomecov index 3c6673d0..49ae84cb 100755 --- a/target/executable/bedtools/bedtools_genomecov/bedtools_genomecov +++ b/target/executable/bedtools/bedtools_genomecov/bedtools_genomecov @@ -452,9 +452,9 @@ ENTRYPOINT [] RUN bedtools --version 2>&1 | head -1 | sed 's/.*bedtools v/bedtools: /' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_genomecov" -LABEL org.opencontainers.image.created="2025-09-01T11:02:51Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:19Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -1110,13 +1110,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml b/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml index fedef932..c7c6707c 100644 --- a/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml @@ -160,6 +160,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "sequencing" @@ -262,7 +263,7 @@ build_info: output: "target/executable/bedtools/bedtools_getfasta" executable: "target/executable/bedtools/bedtools_getfasta/bedtools_getfasta" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -284,138 +285,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta b/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta index c8c50955..2003d361 100755 --- a/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta +++ b/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta @@ -452,9 +452,9 @@ ENTRYPOINT [] RUN bedtools --version 2>&1 | head -1 | sed 's/.*bedtools v/bedtools: /' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Dries Schaumont, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_getfasta" -LABEL org.opencontainers.image.created="2025-09-01T11:02:52Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:12Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -924,13 +924,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml b/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml index f5efe816..4305b659 100644 --- a/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml @@ -184,6 +184,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "groupby" @@ -284,7 +285,7 @@ build_info: output: "target/executable/bedtools/bedtools_groupby" executable: "target/executable/bedtools/bedtools_groupby/bedtools_groupby" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -306,138 +307,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_groupby/bedtools_groupby b/target/executable/bedtools/bedtools_groupby/bedtools_groupby index 77638887..10bb514e 100755 --- a/target/executable/bedtools/bedtools_groupby/bedtools_groupby +++ b/target/executable/bedtools/bedtools_groupby/bedtools_groupby @@ -452,9 +452,9 @@ ENTRYPOINT [] RUN bedtools --version 2>&1 | head -1 | sed 's/.*bedtools v/bedtools: /' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_groupby" -LABEL org.opencontainers.image.created="2025-09-01T11:02:50Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:19Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -982,13 +982,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/bedtools/bedtools_igv/.config.vsh.yaml b/target/executable/bedtools/bedtools_igv/.config.vsh.yaml index 25e1210c..573242ea 100644 --- a/target/executable/bedtools/bedtools_igv/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_igv/.config.vsh.yaml @@ -186,6 +186,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -290,7 +291,7 @@ build_info: output: "target/executable/bedtools/bedtools_igv" executable: "target/executable/bedtools/bedtools_igv/bedtools_igv" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -312,138 +313,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_igv/bedtools_igv b/target/executable/bedtools/bedtools_igv/bedtools_igv index dd49091a..63b466b9 100755 --- a/target/executable/bedtools/bedtools_igv/bedtools_igv +++ b/target/executable/bedtools/bedtools_igv/bedtools_igv @@ -452,9 +452,9 @@ RUN bedtools --version 2>&1 | head -1 | sed 's/.*bedtools v/bedtools: /' > /var/ LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_igv" -LABEL org.opencontainers.image.created="2025-09-01T11:02:53Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:12Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -957,13 +957,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml b/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml index 7097414d..130a6769 100644 --- a/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml @@ -313,6 +313,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "feature intersection" @@ -416,7 +417,7 @@ build_info: output: "target/executable/bedtools/bedtools_intersect" executable: "target/executable/bedtools/bedtools_intersect/bedtools_intersect" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -438,138 +439,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_intersect/bedtools_intersect b/target/executable/bedtools/bedtools_intersect/bedtools_intersect index fb93872f..33159cd1 100755 --- a/target/executable/bedtools/bedtools_intersect/bedtools_intersect +++ b/target/executable/bedtools/bedtools_intersect/bedtools_intersect @@ -453,9 +453,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_intersect" -LABEL org.opencontainers.image.created="2025-09-01T11:02:57Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:11Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -1211,13 +1211,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/bedtools/bedtools_jaccard/.config.vsh.yaml b/target/executable/bedtools/bedtools_jaccard/.config.vsh.yaml index c8627562..a1ffcb95 100644 --- a/target/executable/bedtools/bedtools_jaccard/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_jaccard/.config.vsh.yaml @@ -235,6 +235,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -340,7 +341,7 @@ build_info: output: "target/executable/bedtools/bedtools_jaccard" executable: "target/executable/bedtools/bedtools_jaccard/bedtools_jaccard" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -362,138 +363,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_jaccard/bedtools_jaccard b/target/executable/bedtools/bedtools_jaccard/bedtools_jaccard index 1fe33b5b..7c364756 100755 --- a/target/executable/bedtools/bedtools_jaccard/bedtools_jaccard +++ b/target/executable/bedtools/bedtools_jaccard/bedtools_jaccard @@ -452,9 +452,9 @@ RUN bedtools --version 2>&1 | head -1 | sed 's/.*bedtools v/bedtools: /' > /var/ LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_jaccard" -LABEL org.opencontainers.image.created="2025-09-01T11:02:46Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:10Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -1062,13 +1062,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/bedtools/bedtools_links/.config.vsh.yaml b/target/executable/bedtools/bedtools_links/.config.vsh.yaml index f2322c66..8e809809 100644 --- a/target/executable/bedtools/bedtools_links/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_links/.config.vsh.yaml @@ -132,6 +132,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "HTML" @@ -236,7 +237,7 @@ build_info: output: "target/executable/bedtools/bedtools_links" executable: "target/executable/bedtools/bedtools_links/bedtools_links" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -258,138 +259,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_links/bedtools_links b/target/executable/bedtools/bedtools_links/bedtools_links index d4b5879a..3663b759 100755 --- a/target/executable/bedtools/bedtools_links/bedtools_links +++ b/target/executable/bedtools/bedtools_links/bedtools_links @@ -452,9 +452,9 @@ ENTRYPOINT [] RUN bedtools --version 2>&1 | head -1 | sed 's/.*bedtools v/bedtools: /' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_links" -LABEL org.opencontainers.image.created="2025-09-01T11:02:49Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:18Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -874,13 +874,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/bedtools/bedtools_makewindows/.config.vsh.yaml b/target/executable/bedtools/bedtools_makewindows/.config.vsh.yaml index 88ee065d..11f6391c 100644 --- a/target/executable/bedtools/bedtools_makewindows/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_makewindows/.config.vsh.yaml @@ -173,6 +173,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -278,7 +279,7 @@ build_info: output: "target/executable/bedtools/bedtools_makewindows" executable: "target/executable/bedtools/bedtools_makewindows/bedtools_makewindows" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -300,138 +301,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_makewindows/bedtools_makewindows b/target/executable/bedtools/bedtools_makewindows/bedtools_makewindows index fb638192..61442e3d 100755 --- a/target/executable/bedtools/bedtools_makewindows/bedtools_makewindows +++ b/target/executable/bedtools/bedtools_makewindows/bedtools_makewindows @@ -452,9 +452,9 @@ RUN bedtools --version 2>&1 | head -1 | sed 's/.*bedtools v/bedtools: /' > /var/ LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_makewindows" -LABEL org.opencontainers.image.created="2025-09-01T11:02:48Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:17Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -942,13 +942,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/bedtools/bedtools_map/.config.vsh.yaml b/target/executable/bedtools/bedtools_map/.config.vsh.yaml index 4774e370..bff8385f 100644 --- a/target/executable/bedtools/bedtools_map/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_map/.config.vsh.yaml @@ -298,6 +298,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -403,7 +404,7 @@ build_info: output: "target/executable/bedtools/bedtools_map" executable: "target/executable/bedtools/bedtools_map/bedtools_map" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -425,138 +426,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_map/bedtools_map b/target/executable/bedtools/bedtools_map/bedtools_map index dda4d04e..68fe002a 100755 --- a/target/executable/bedtools/bedtools_map/bedtools_map +++ b/target/executable/bedtools/bedtools_map/bedtools_map @@ -452,9 +452,9 @@ RUN bedtools --version 2>&1 | head -1 | sed 's/.*bedtools v/bedtools: /' > /var/ LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_map" -LABEL org.opencontainers.image.created="2025-09-01T11:02:46Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:19Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -1171,13 +1171,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/bedtools/bedtools_maskfasta/.config.vsh.yaml b/target/executable/bedtools/bedtools_maskfasta/.config.vsh.yaml index 69f16c31..bdaa24ec 100644 --- a/target/executable/bedtools/bedtools_maskfasta/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_maskfasta/.config.vsh.yaml @@ -137,6 +137,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -239,7 +240,7 @@ build_info: output: "target/executable/bedtools/bedtools_maskfasta" executable: "target/executable/bedtools/bedtools_maskfasta/bedtools_maskfasta" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -261,138 +262,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_maskfasta/bedtools_maskfasta b/target/executable/bedtools/bedtools_maskfasta/bedtools_maskfasta index 7e8d77a9..3ee9e208 100755 --- a/target/executable/bedtools/bedtools_maskfasta/bedtools_maskfasta +++ b/target/executable/bedtools/bedtools_maskfasta/bedtools_maskfasta @@ -452,9 +452,9 @@ RUN bedtools --version 2>&1 | head -1 | sed 's/.*bedtools v/bedtools: /' > /var/ LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_maskfasta" -LABEL org.opencontainers.image.created="2025-09-01T11:02:50Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:13Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -891,13 +891,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/bedtools/bedtools_merge/.config.vsh.yaml b/target/executable/bedtools/bedtools_merge/.config.vsh.yaml index 399d1e8a..082f6fc7 100644 --- a/target/executable/bedtools/bedtools_merge/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_merge/.config.vsh.yaml @@ -224,6 +224,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "Merge" @@ -327,7 +328,7 @@ build_info: output: "target/executable/bedtools/bedtools_merge" executable: "target/executable/bedtools/bedtools_merge/bedtools_merge" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -349,138 +350,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_merge/bedtools_merge b/target/executable/bedtools/bedtools_merge/bedtools_merge index 0255fcc3..e7da0609 100755 --- a/target/executable/bedtools/bedtools_merge/bedtools_merge +++ b/target/executable/bedtools/bedtools_merge/bedtools_merge @@ -452,9 +452,9 @@ ENTRYPOINT [] RUN bedtools --version 2>&1 | head -1 | sed 's/.*bedtools v/bedtools: /' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_merge" -LABEL org.opencontainers.image.created="2025-09-01T11:02:49Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:18Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -1022,13 +1022,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/bedtools/bedtools_multicov/.config.vsh.yaml b/target/executable/bedtools/bedtools_multicov/.config.vsh.yaml index 8965c4af..7351c151 100644 --- a/target/executable/bedtools/bedtools_multicov/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_multicov/.config.vsh.yaml @@ -210,6 +210,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -314,7 +315,7 @@ build_info: output: "target/executable/bedtools/bedtools_multicov" executable: "target/executable/bedtools/bedtools_multicov/bedtools_multicov" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -336,138 +337,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_multicov/bedtools_multicov b/target/executable/bedtools/bedtools_multicov/bedtools_multicov index 7d876e17..1e2d5f93 100755 --- a/target/executable/bedtools/bedtools_multicov/bedtools_multicov +++ b/target/executable/bedtools/bedtools_multicov/bedtools_multicov @@ -452,9 +452,9 @@ RUN bedtools --version 2>&1 | head -1 | sed 's/.*bedtools v/bedtools: /' > /var/ LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_multicov" -LABEL org.opencontainers.image.created="2025-09-01T11:02:51Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:18Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -1017,13 +1017,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/bedtools/bedtools_multiinter/.config.vsh.yaml b/target/executable/bedtools/bedtools_multiinter/.config.vsh.yaml index 93490cb2..79176b27 100644 --- a/target/executable/bedtools/bedtools_multiinter/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_multiinter/.config.vsh.yaml @@ -155,6 +155,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -260,7 +261,7 @@ build_info: output: "target/executable/bedtools/bedtools_multiinter" executable: "target/executable/bedtools/bedtools_multiinter/bedtools_multiinter" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -282,138 +283,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_multiinter/bedtools_multiinter b/target/executable/bedtools/bedtools_multiinter/bedtools_multiinter index 0f71b7a7..b8dc3744 100755 --- a/target/executable/bedtools/bedtools_multiinter/bedtools_multiinter +++ b/target/executable/bedtools/bedtools_multiinter/bedtools_multiinter @@ -452,9 +452,9 @@ RUN bedtools --version 2>&1 | head -1 | sed 's/.*bedtools v/bedtools: /' > /var/ LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_multiinter" -LABEL org.opencontainers.image.created="2025-09-01T11:02:56Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:08Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -922,13 +922,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/bedtools/bedtools_overlap/.config.vsh.yaml b/target/executable/bedtools/bedtools_overlap/.config.vsh.yaml index ac68af9a..9ccd4f0c 100644 --- a/target/executable/bedtools/bedtools_overlap/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_overlap/.config.vsh.yaml @@ -102,6 +102,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -205,7 +206,7 @@ build_info: output: "target/executable/bedtools/bedtools_overlap" executable: "target/executable/bedtools/bedtools_overlap/bedtools_overlap" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -227,138 +228,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_overlap/bedtools_overlap b/target/executable/bedtools/bedtools_overlap/bedtools_overlap index d4704eda..58f559b1 100755 --- a/target/executable/bedtools/bedtools_overlap/bedtools_overlap +++ b/target/executable/bedtools/bedtools_overlap/bedtools_overlap @@ -452,9 +452,9 @@ RUN bedtools --version 2>&1 | head -1 | sed 's/.*bedtools v/bedtools: /' > /var/ LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_overlap" -LABEL org.opencontainers.image.created="2025-09-01T11:02:51Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:15Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -826,13 +826,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/bedtools/bedtools_pairtobed/.config.vsh.yaml b/target/executable/bedtools/bedtools_pairtobed/.config.vsh.yaml index 6b93f61e..0113aa53 100644 --- a/target/executable/bedtools/bedtools_pairtobed/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_pairtobed/.config.vsh.yaml @@ -225,6 +225,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -329,7 +330,7 @@ build_info: output: "target/executable/bedtools/bedtools_pairtobed" executable: "target/executable/bedtools/bedtools_pairtobed/bedtools_pairtobed" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -351,138 +352,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_pairtobed/bedtools_pairtobed b/target/executable/bedtools/bedtools_pairtobed/bedtools_pairtobed index 2945e0e8..596e899d 100755 --- a/target/executable/bedtools/bedtools_pairtobed/bedtools_pairtobed +++ b/target/executable/bedtools/bedtools_pairtobed/bedtools_pairtobed @@ -452,9 +452,9 @@ RUN bedtools --version 2>&1 | head -1 | sed 's/.*bedtools v/bedtools: /' > /var/ LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_pairtobed" -LABEL org.opencontainers.image.created="2025-09-01T11:02:50Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:14Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -1003,13 +1003,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/bedtools/bedtools_pairtopair/.config.vsh.yaml b/target/executable/bedtools/bedtools_pairtopair/.config.vsh.yaml index 4e17d5c2..2aa3d14d 100644 --- a/target/executable/bedtools/bedtools_pairtopair/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_pairtopair/.config.vsh.yaml @@ -184,6 +184,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -287,7 +288,7 @@ build_info: output: "target/executable/bedtools/bedtools_pairtopair" executable: "target/executable/bedtools/bedtools_pairtopair/bedtools_pairtopair" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -309,138 +310,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_pairtopair/bedtools_pairtopair b/target/executable/bedtools/bedtools_pairtopair/bedtools_pairtopair index 2c34ef78..6aa8b28e 100755 --- a/target/executable/bedtools/bedtools_pairtopair/bedtools_pairtopair +++ b/target/executable/bedtools/bedtools_pairtopair/bedtools_pairtopair @@ -452,9 +452,9 @@ RUN bedtools --version 2>&1 | head -1 | sed 's/.*bedtools v/bedtools: /' > /var/ LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_pairtopair" -LABEL org.opencontainers.image.created="2025-09-01T11:02:56Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:15Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -952,13 +952,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/bedtools/bedtools_random/.config.vsh.yaml b/target/executable/bedtools/bedtools_random/.config.vsh.yaml index e87f2c78..ecf5e2a1 100644 --- a/target/executable/bedtools/bedtools_random/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_random/.config.vsh.yaml @@ -135,6 +135,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -239,7 +240,7 @@ build_info: output: "target/executable/bedtools/bedtools_random" executable: "target/executable/bedtools/bedtools_random/bedtools_random" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -261,138 +262,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_random/bedtools_random b/target/executable/bedtools/bedtools_random/bedtools_random index 717b0e09..6b882a48 100755 --- a/target/executable/bedtools/bedtools_random/bedtools_random +++ b/target/executable/bedtools/bedtools_random/bedtools_random @@ -452,9 +452,9 @@ RUN bedtools --version 2>&1 | head -1 | sed 's/.*bedtools v/bedtools: /' > /var/ LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_random" -LABEL org.opencontainers.image.created="2025-09-01T11:02:52Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:14Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -881,13 +881,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/bedtools/bedtools_reldist/.config.vsh.yaml b/target/executable/bedtools/bedtools_reldist/.config.vsh.yaml index 872aa7be..4016838f 100644 --- a/target/executable/bedtools/bedtools_reldist/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_reldist/.config.vsh.yaml @@ -116,6 +116,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -220,7 +221,7 @@ build_info: output: "target/executable/bedtools/bedtools_reldist" executable: "target/executable/bedtools/bedtools_reldist/bedtools_reldist" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -242,138 +243,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_reldist/bedtools_reldist b/target/executable/bedtools/bedtools_reldist/bedtools_reldist index b8293575..6759879d 100755 --- a/target/executable/bedtools/bedtools_reldist/bedtools_reldist +++ b/target/executable/bedtools/bedtools_reldist/bedtools_reldist @@ -452,9 +452,9 @@ RUN bedtools --version 2>&1 | head -1 | sed 's/.*bedtools v/bedtools: /' > /var/ LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_reldist" -LABEL org.opencontainers.image.created="2025-09-01T11:02:51Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:10Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -851,13 +851,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/bedtools/bedtools_sample/.config.vsh.yaml b/target/executable/bedtools/bedtools_sample/.config.vsh.yaml index 6d240727..575d2696 100644 --- a/target/executable/bedtools/bedtools_sample/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_sample/.config.vsh.yaml @@ -189,6 +189,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -292,7 +293,7 @@ build_info: output: "target/executable/bedtools/bedtools_sample" executable: "target/executable/bedtools/bedtools_sample/bedtools_sample" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -314,138 +315,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_sample/bedtools_sample b/target/executable/bedtools/bedtools_sample/bedtools_sample index 3e5b2215..849a4306 100755 --- a/target/executable/bedtools/bedtools_sample/bedtools_sample +++ b/target/executable/bedtools/bedtools_sample/bedtools_sample @@ -452,9 +452,9 @@ RUN bedtools --version 2>&1 | head -1 | sed 's/.*bedtools v/bedtools: /' > /var/ LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_sample" -LABEL org.opencontainers.image.created="2025-09-01T11:02:55Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:17Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -973,13 +973,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/bedtools/bedtools_shift/.config.vsh.yaml b/target/executable/bedtools/bedtools_shift/.config.vsh.yaml index 285e3cd9..5bc90cc9 100644 --- a/target/executable/bedtools/bedtools_shift/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_shift/.config.vsh.yaml @@ -169,6 +169,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -272,7 +273,7 @@ build_info: output: "target/executable/bedtools/bedtools_shift" executable: "target/executable/bedtools/bedtools_shift/bedtools_shift" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -294,138 +295,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_shift/bedtools_shift b/target/executable/bedtools/bedtools_shift/bedtools_shift index c97e12cd..a31e0ca2 100755 --- a/target/executable/bedtools/bedtools_shift/bedtools_shift +++ b/target/executable/bedtools/bedtools_shift/bedtools_shift @@ -452,9 +452,9 @@ RUN bedtools --version 2>&1 | head -1 | sed 's/.*bedtools v/bedtools: /' > /var/ LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_shift" -LABEL org.opencontainers.image.created="2025-09-01T11:02:54Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:12Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -945,13 +945,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/bedtools/bedtools_shuffle/.config.vsh.yaml b/target/executable/bedtools/bedtools_shuffle/.config.vsh.yaml index d3122b25..1bf32e65 100644 --- a/target/executable/bedtools/bedtools_shuffle/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_shuffle/.config.vsh.yaml @@ -243,6 +243,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -347,7 +348,7 @@ build_info: output: "target/executable/bedtools/bedtools_shuffle" executable: "target/executable/bedtools/bedtools_shuffle/bedtools_shuffle" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -369,138 +370,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_shuffle/bedtools_shuffle b/target/executable/bedtools/bedtools_shuffle/bedtools_shuffle index b0b0c394..68603d57 100755 --- a/target/executable/bedtools/bedtools_shuffle/bedtools_shuffle +++ b/target/executable/bedtools/bedtools_shuffle/bedtools_shuffle @@ -452,9 +452,9 @@ RUN bedtools --version 2>&1 | head -1 | sed 's/.*bedtools v/bedtools: /' > /var/ LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_shuffle" -LABEL org.opencontainers.image.created="2025-09-01T11:02:55Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:16Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -1061,13 +1061,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/bedtools/bedtools_slop/.config.vsh.yaml b/target/executable/bedtools/bedtools_slop/.config.vsh.yaml index d971c2cd..92b7a471 100644 --- a/target/executable/bedtools/bedtools_slop/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_slop/.config.vsh.yaml @@ -183,6 +183,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -287,7 +288,7 @@ build_info: output: "target/executable/bedtools/bedtools_slop" executable: "target/executable/bedtools/bedtools_slop/bedtools_slop" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -309,138 +310,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_slop/bedtools_slop b/target/executable/bedtools/bedtools_slop/bedtools_slop index b813ea5d..f49abb3d 100755 --- a/target/executable/bedtools/bedtools_slop/bedtools_slop +++ b/target/executable/bedtools/bedtools_slop/bedtools_slop @@ -452,9 +452,9 @@ RUN bedtools --version 2>&1 | head -1 | sed 's/.*bedtools v/bedtools: /' > /var/ LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_slop" -LABEL org.opencontainers.image.created="2025-09-01T11:02:55Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:16Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -966,13 +966,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/bedtools/bedtools_sort/.config.vsh.yaml b/target/executable/bedtools/bedtools_sort/.config.vsh.yaml index f9c1fc80..a0967d85 100644 --- a/target/executable/bedtools/bedtools_sort/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_sort/.config.vsh.yaml @@ -172,6 +172,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "Sort" @@ -275,7 +276,7 @@ build_info: output: "target/executable/bedtools/bedtools_sort" executable: "target/executable/bedtools/bedtools_sort/bedtools_sort" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -297,138 +298,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_sort/bedtools_sort b/target/executable/bedtools/bedtools_sort/bedtools_sort index 86a74980..80d46200 100755 --- a/target/executable/bedtools/bedtools_sort/bedtools_sort +++ b/target/executable/bedtools/bedtools_sort/bedtools_sort @@ -452,9 +452,9 @@ ENTRYPOINT [] RUN bedtools --version 2>&1 | head -1 | sed 's/.*bedtools v/bedtools: /' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_sort" -LABEL org.opencontainers.image.created="2025-09-01T11:02:55Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:19Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -922,13 +922,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/bedtools/bedtools_spacing/.config.vsh.yaml b/target/executable/bedtools/bedtools_spacing/.config.vsh.yaml index 1adfbd76..d644ad95 100644 --- a/target/executable/bedtools/bedtools_spacing/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_spacing/.config.vsh.yaml @@ -134,6 +134,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -238,7 +239,7 @@ build_info: output: "target/executable/bedtools/bedtools_spacing" executable: "target/executable/bedtools/bedtools_spacing/bedtools_spacing" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -260,138 +261,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_spacing/bedtools_spacing b/target/executable/bedtools/bedtools_spacing/bedtools_spacing index 0d85179e..74cb6bd5 100755 --- a/target/executable/bedtools/bedtools_spacing/bedtools_spacing +++ b/target/executable/bedtools/bedtools_spacing/bedtools_spacing @@ -452,9 +452,9 @@ RUN bedtools --version 2>&1 | head -1 | sed 's/.*bedtools v/bedtools: /' > /var/ LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_spacing" -LABEL org.opencontainers.image.created="2025-09-01T11:02:48Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:16Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -888,13 +888,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/bedtools/bedtools_split/.config.vsh.yaml b/target/executable/bedtools/bedtools_split/.config.vsh.yaml index 71eec667..bad22e40 100644 --- a/target/executable/bedtools/bedtools_split/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_split/.config.vsh.yaml @@ -138,6 +138,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -242,7 +243,7 @@ build_info: output: "target/executable/bedtools/bedtools_split" executable: "target/executable/bedtools/bedtools_split/bedtools_split" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -264,138 +265,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_split/bedtools_split b/target/executable/bedtools/bedtools_split/bedtools_split index 3927ec4a..c58a9721 100755 --- a/target/executable/bedtools/bedtools_split/bedtools_split +++ b/target/executable/bedtools/bedtools_split/bedtools_split @@ -452,9 +452,9 @@ RUN bedtools --version 2>&1 | head -1 | sed 's/.*bedtools v/bedtools: /' > /var/ LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_split" -LABEL org.opencontainers.image.created="2025-09-01T11:02:47Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:09Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -888,13 +888,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/bedtools/bedtools_subtract/.config.vsh.yaml b/target/executable/bedtools/bedtools_subtract/.config.vsh.yaml index d68d9e9f..c55ae8df 100644 --- a/target/executable/bedtools/bedtools_subtract/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_subtract/.config.vsh.yaml @@ -318,6 +318,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -422,7 +423,7 @@ build_info: output: "target/executable/bedtools/bedtools_subtract" executable: "target/executable/bedtools/bedtools_subtract/bedtools_subtract" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -444,138 +445,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_subtract/bedtools_subtract b/target/executable/bedtools/bedtools_subtract/bedtools_subtract index 95d0486a..4030c2cc 100755 --- a/target/executable/bedtools/bedtools_subtract/bedtools_subtract +++ b/target/executable/bedtools/bedtools_subtract/bedtools_subtract @@ -452,9 +452,9 @@ RUN bedtools --version 2>&1 | head -1 | sed 's/.*bedtools v/bedtools: /' > /var/ LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_subtract" -LABEL org.opencontainers.image.created="2025-09-01T11:02:57Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:13Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -1195,13 +1195,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/bedtools/bedtools_summary/.config.vsh.yaml b/target/executable/bedtools/bedtools_summary/.config.vsh.yaml index 7b28fe70..9a969916 100644 --- a/target/executable/bedtools/bedtools_summary/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_summary/.config.vsh.yaml @@ -106,6 +106,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -210,7 +211,7 @@ build_info: output: "target/executable/bedtools/bedtools_summary" executable: "target/executable/bedtools/bedtools_summary/bedtools_summary" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -232,138 +233,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_summary/bedtools_summary b/target/executable/bedtools/bedtools_summary/bedtools_summary index 9f03287d..00c531b3 100755 --- a/target/executable/bedtools/bedtools_summary/bedtools_summary +++ b/target/executable/bedtools/bedtools_summary/bedtools_summary @@ -452,9 +452,9 @@ RUN bedtools --version 2>&1 | head -1 | sed 's/.*bedtools v/bedtools: /' > /var/ LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_summary" -LABEL org.opencontainers.image.created="2025-09-01T11:02:53Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:11Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -834,13 +834,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/bedtools/bedtools_tag/.config.vsh.yaml b/target/executable/bedtools/bedtools_tag/.config.vsh.yaml index 6831d048..8b02770b 100644 --- a/target/executable/bedtools/bedtools_tag/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_tag/.config.vsh.yaml @@ -215,6 +215,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -319,7 +320,7 @@ build_info: output: "target/executable/bedtools/bedtools_tag" executable: "target/executable/bedtools/bedtools_tag/bedtools_tag" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -341,138 +342,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_tag/bedtools_tag b/target/executable/bedtools/bedtools_tag/bedtools_tag index cff02625..762f6a2a 100755 --- a/target/executable/bedtools/bedtools_tag/bedtools_tag +++ b/target/executable/bedtools/bedtools_tag/bedtools_tag @@ -452,9 +452,9 @@ RUN bedtools --version 2>&1 | head -1 | sed 's/.*bedtools v/bedtools: /' > /var/ LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_tag" -LABEL org.opencontainers.image.created="2025-09-01T11:02:54Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:11Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -1018,13 +1018,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/bedtools/bedtools_unionbedg/.config.vsh.yaml b/target/executable/bedtools/bedtools_unionbedg/.config.vsh.yaml index 0ff0f4c5..f54258ff 100644 --- a/target/executable/bedtools/bedtools_unionbedg/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_unionbedg/.config.vsh.yaml @@ -97,6 +97,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -200,7 +201,7 @@ build_info: output: "target/executable/bedtools/bedtools_unionbedg" executable: "target/executable/bedtools/bedtools_unionbedg/bedtools_unionbedg" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -222,138 +223,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_unionbedg/bedtools_unionbedg b/target/executable/bedtools/bedtools_unionbedg/bedtools_unionbedg index 5e605296..ab15356a 100755 --- a/target/executable/bedtools/bedtools_unionbedg/bedtools_unionbedg +++ b/target/executable/bedtools/bedtools_unionbedg/bedtools_unionbedg @@ -452,9 +452,9 @@ RUN bedtools --version 2>&1 | head -1 | sed 's/.*bedtools v/bedtools: /' > /var/ LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_unionbedg" -LABEL org.opencontainers.image.created="2025-09-01T11:02:50Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:18Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -830,13 +830,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/bedtools/bedtools_window/.config.vsh.yaml b/target/executable/bedtools/bedtools_window/.config.vsh.yaml index 0bf69b76..2d33c287 100644 --- a/target/executable/bedtools/bedtools_window/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_window/.config.vsh.yaml @@ -261,6 +261,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -365,7 +366,7 @@ build_info: output: "target/executable/bedtools/bedtools_window" executable: "target/executable/bedtools/bedtools_window/bedtools_window" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -387,138 +388,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_window/bedtools_window b/target/executable/bedtools/bedtools_window/bedtools_window index 8bf34933..ec757fae 100755 --- a/target/executable/bedtools/bedtools_window/bedtools_window +++ b/target/executable/bedtools/bedtools_window/bedtools_window @@ -451,9 +451,9 @@ ENTRYPOINT [] RUN bedtools --version 2>&1 | head -1 | sed 's/.*bedtools v/bedtools: /' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_window" -LABEL org.opencontainers.image.created="2025-09-01T11:02:48Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:15Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -1093,13 +1093,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bedtools' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/bowtie2/bowtie2_align/.config.vsh.yaml b/target/executable/bowtie2/bowtie2_align/.config.vsh.yaml index f347faa9..9e834030 100644 --- a/target/executable/bowtie2/bowtie2_align/.config.vsh.yaml +++ b/target/executable/bowtie2/bowtie2_align/.config.vsh.yaml @@ -744,6 +744,7 @@ scope: target: "public" requirements: commands: + - "bowtie2" - "ps" keywords: - "Alignment" @@ -843,7 +844,7 @@ build_info: output: "target/executable/bowtie2/bowtie2_align" executable: "target/executable/bowtie2/bowtie2_align/bowtie2_align" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -865,138 +866,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bowtie2/bowtie2_align/bowtie2_align b/target/executable/bowtie2/bowtie2_align/bowtie2_align index ae2dcdcf..29f7b30a 100755 --- a/target/executable/bowtie2/bowtie2_align/bowtie2_align +++ b/target/executable/bowtie2/bowtie2_align/bowtie2_align @@ -452,9 +452,9 @@ RUN bowtie2 --version 2>&1 | head -1 | sed 's/.*version /bowtie2: /' > /var/soft LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component bowtie2 bowtie2_align" -LABEL org.opencontainers.image.created="2025-09-01T11:02:49Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:13Z" LABEL org.opencontainers.image.source="https://github.com/BenLangmead/bowtie2" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -1878,13 +1878,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bowtie2' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bowtie2' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/bowtie2/bowtie2_build/.config.vsh.yaml b/target/executable/bowtie2/bowtie2_build/.config.vsh.yaml index 4836c0f5..b89bbbd6 100644 --- a/target/executable/bowtie2/bowtie2_build/.config.vsh.yaml +++ b/target/executable/bowtie2/bowtie2_build/.config.vsh.yaml @@ -206,6 +206,7 @@ scope: target: "public" requirements: commands: + - "bowtie2-build" - "ps" keywords: - "Alignment" @@ -306,7 +307,7 @@ build_info: output: "target/executable/bowtie2/bowtie2_build" executable: "target/executable/bowtie2/bowtie2_build/bowtie2_build" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -328,138 +329,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bowtie2/bowtie2_build/bowtie2_build b/target/executable/bowtie2/bowtie2_build/bowtie2_build index baff1b5c..a4bc24f9 100755 --- a/target/executable/bowtie2/bowtie2_build/bowtie2_build +++ b/target/executable/bowtie2/bowtie2_build/bowtie2_build @@ -452,9 +452,9 @@ RUN bowtie2-build --version 2>&1 | head -1 | sed 's/.*version /bowtie2-build: /' LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component bowtie2 bowtie2_build" -LABEL org.opencontainers.image.created="2025-09-01T11:02:49Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:12Z" LABEL org.opencontainers.image.source="https://github.com/BenLangmead/bowtie2" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -1001,13 +1001,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bowtie2-build' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bowtie2-build' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/bowtie2/bowtie2_inspect/.config.vsh.yaml b/target/executable/bowtie2/bowtie2_inspect/.config.vsh.yaml index 4cce0644..e345314c 100644 --- a/target/executable/bowtie2/bowtie2_inspect/.config.vsh.yaml +++ b/target/executable/bowtie2/bowtie2_inspect/.config.vsh.yaml @@ -117,6 +117,7 @@ scope: target: "public" requirements: commands: + - "bowtie2-inspect" - "ps" keywords: - "Alignment" @@ -218,7 +219,7 @@ build_info: output: "target/executable/bowtie2/bowtie2_inspect" executable: "target/executable/bowtie2/bowtie2_inspect/bowtie2_inspect" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -240,138 +241,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bowtie2/bowtie2_inspect/bowtie2_inspect b/target/executable/bowtie2/bowtie2_inspect/bowtie2_inspect index b9a65f8c..2de20baf 100755 --- a/target/executable/bowtie2/bowtie2_inspect/bowtie2_inspect +++ b/target/executable/bowtie2/bowtie2_inspect/bowtie2_inspect @@ -452,9 +452,9 @@ RUN bowtie2-inspect --help 2>&1 | head -1 | sed 's/.*version /bowtie2-inspect: / LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component bowtie2 bowtie2_inspect" -LABEL org.opencontainers.image.created="2025-09-01T11:02:49Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:13Z" LABEL org.opencontainers.image.source="https://github.com/BenLangmead/bowtie2" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -855,13 +855,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bowtie2-inspect' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bowtie2-inspect' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/busco/busco_download_datasets/.config.vsh.yaml b/target/executable/busco/busco_download_datasets/.config.vsh.yaml index 2ef164a8..386f7705 100644 --- a/target/executable/busco/busco_download_datasets/.config.vsh.yaml +++ b/target/executable/busco/busco_download_datasets/.config.vsh.yaml @@ -161,7 +161,7 @@ build_info: output: "target/executable/busco/busco_download_datasets" executable: "target/executable/busco/busco_download_datasets/busco_download_datasets" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -183,138 +183,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/busco/busco_download_datasets/busco_download_datasets b/target/executable/busco/busco_download_datasets/busco_download_datasets index 8127ba2a..fb6afbfb 100755 --- a/target/executable/busco/busco_download_datasets/busco_download_datasets +++ b/target/executable/busco/busco_download_datasets/busco_download_datasets @@ -452,9 +452,9 @@ RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_version LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component busco busco_download_datasets" -LABEL org.opencontainers.image.created="2025-09-01T11:02:59Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:20Z" LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/busco/busco_list_datasets/.config.vsh.yaml b/target/executable/busco/busco_list_datasets/.config.vsh.yaml index cca2005d..7ef219be 100644 --- a/target/executable/busco/busco_list_datasets/.config.vsh.yaml +++ b/target/executable/busco/busco_list_datasets/.config.vsh.yaml @@ -148,7 +148,7 @@ build_info: output: "target/executable/busco/busco_list_datasets" executable: "target/executable/busco/busco_list_datasets/busco_list_datasets" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -170,138 +170,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/busco/busco_list_datasets/busco_list_datasets b/target/executable/busco/busco_list_datasets/busco_list_datasets index 3986cc07..e462fd2d 100755 --- a/target/executable/busco/busco_list_datasets/busco_list_datasets +++ b/target/executable/busco/busco_list_datasets/busco_list_datasets @@ -452,9 +452,9 @@ RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_version LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component busco busco_list_datasets" -LABEL org.opencontainers.image.created="2025-09-01T11:02:59Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:04Z" LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/busco/busco_run/.config.vsh.yaml b/target/executable/busco/busco_run/.config.vsh.yaml index 2cdaa42f..b3fac354 100644 --- a/target/executable/busco/busco_run/.config.vsh.yaml +++ b/target/executable/busco/busco_run/.config.vsh.yaml @@ -426,7 +426,7 @@ build_info: output: "target/executable/busco/busco_run" executable: "target/executable/busco/busco_run/busco_run" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -448,138 +448,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/busco/busco_run/busco_run b/target/executable/busco/busco_run/busco_run index 8ad90f1d..ffbea2cc 100755 --- a/target/executable/busco/busco_run/busco_run +++ b/target/executable/busco/busco_run/busco_run @@ -452,9 +452,9 @@ RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_version LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component busco busco_run" -LABEL org.opencontainers.image.created="2025-09-01T11:02:59Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:20Z" LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bwa/bwa_aln/.config.vsh.yaml b/target/executable/bwa/bwa_aln/.config.vsh.yaml index 39238a32..3f745b1a 100644 --- a/target/executable/bwa/bwa_aln/.config.vsh.yaml +++ b/target/executable/bwa/bwa_aln/.config.vsh.yaml @@ -326,6 +326,7 @@ scope: target: "public" requirements: commands: + - "bwa" - "ps" keywords: - "alignment" @@ -425,7 +426,7 @@ build_info: output: "target/executable/bwa/bwa_aln" executable: "target/executable/bwa/bwa_aln/bwa_aln" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -447,138 +448,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bwa/bwa_aln/bwa_aln b/target/executable/bwa/bwa_aln/bwa_aln index 14ca3d48..a444d7d2 100755 --- a/target/executable/bwa/bwa_aln/bwa_aln +++ b/target/executable/bwa/bwa_aln/bwa_aln @@ -453,9 +453,9 @@ RUN bwa 2>&1 | grep "Version:" | sed 's/Version: /bwa: /' > /var/software_versio LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Toni Verbeiren" LABEL org.opencontainers.image.description="Companion container for running component bwa bwa_aln" -LABEL org.opencontainers.image.created="2025-09-01T11:03:01Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:05Z" LABEL org.opencontainers.image.source="https://github.com/lh3/bwa" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -1218,13 +1218,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bwa' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bwa' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/bwa/bwa_index/.config.vsh.yaml b/target/executable/bwa/bwa_index/.config.vsh.yaml index edc8e86b..0b1ed5e5 100644 --- a/target/executable/bwa/bwa_index/.config.vsh.yaml +++ b/target/executable/bwa/bwa_index/.config.vsh.yaml @@ -122,6 +122,7 @@ scope: target: "public" requirements: commands: + - "bwa" - "ps" keywords: - "alignment" @@ -220,7 +221,7 @@ build_info: output: "target/executable/bwa/bwa_index" executable: "target/executable/bwa/bwa_index/bwa_index" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -242,138 +243,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bwa/bwa_index/bwa_index b/target/executable/bwa/bwa_index/bwa_index index 9d392160..f0666f08 100755 --- a/target/executable/bwa/bwa_index/bwa_index +++ b/target/executable/bwa/bwa_index/bwa_index @@ -453,9 +453,9 @@ RUN bwa 2>&1 | grep "Version:" | sed 's/Version: /bwa: /' > /var/software_versio LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Toni Verbeiren" LABEL org.opencontainers.image.description="Companion container for running component bwa bwa_index" -LABEL org.opencontainers.image.created="2025-09-01T11:03:00Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:04Z" LABEL org.opencontainers.image.source="https://github.com/lh3/bwa" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -853,13 +853,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bwa' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bwa' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/bwa/bwa_mem/.config.vsh.yaml b/target/executable/bwa/bwa_mem/.config.vsh.yaml index e8e031fa..f6e18298 100644 --- a/target/executable/bwa/bwa_mem/.config.vsh.yaml +++ b/target/executable/bwa/bwa_mem/.config.vsh.yaml @@ -488,6 +488,7 @@ scope: target: "public" requirements: commands: + - "bwa" - "ps" keywords: - "alignment" @@ -586,7 +587,7 @@ build_info: output: "target/executable/bwa/bwa_mem" executable: "target/executable/bwa/bwa_mem/bwa_mem" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -608,138 +609,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bwa/bwa_mem/bwa_mem b/target/executable/bwa/bwa_mem/bwa_mem index a887430c..64ea9a10 100755 --- a/target/executable/bwa/bwa_mem/bwa_mem +++ b/target/executable/bwa/bwa_mem/bwa_mem @@ -453,9 +453,9 @@ RUN bwa 2>&1 | grep "Version:" | sed 's/Version: /bwa: /' > /var/software_versio LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Toni Verbeiren" LABEL org.opencontainers.image.description="Companion container for running component bwa bwa_mem" -LABEL org.opencontainers.image.created="2025-09-01T11:03:00Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:04Z" LABEL org.opencontainers.image.source="https://github.com/lh3/bwa" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -1508,13 +1508,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bwa' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bwa' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/bwa/bwa_sampe/.config.vsh.yaml b/target/executable/bwa/bwa_sampe/.config.vsh.yaml index 5a29eea2..0d500b6f 100644 --- a/target/executable/bwa/bwa_sampe/.config.vsh.yaml +++ b/target/executable/bwa/bwa_sampe/.config.vsh.yaml @@ -227,6 +227,7 @@ scope: target: "public" requirements: commands: + - "bwa" - "ps" keywords: - "alignment" @@ -326,7 +327,7 @@ build_info: output: "target/executable/bwa/bwa_sampe" executable: "target/executable/bwa/bwa_sampe/bwa_sampe" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -348,138 +349,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bwa/bwa_sampe/bwa_sampe b/target/executable/bwa/bwa_sampe/bwa_sampe index c79379ed..60f39048 100755 --- a/target/executable/bwa/bwa_sampe/bwa_sampe +++ b/target/executable/bwa/bwa_sampe/bwa_sampe @@ -453,9 +453,9 @@ RUN bwa 2>&1 | grep "Version:" | sed 's/Version: /bwa: /' > /var/software_versio LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Toni Verbeiren" LABEL org.opencontainers.image.description="Companion container for running component bwa bwa_sampe" -LABEL org.opencontainers.image.created="2025-09-01T11:03:01Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:05Z" LABEL org.opencontainers.image.source="https://github.com/lh3/bwa" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -1017,13 +1017,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bwa' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bwa' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/bwa/bwa_samse/.config.vsh.yaml b/target/executable/bwa/bwa_samse/.config.vsh.yaml index f0891199..8d9c273f 100644 --- a/target/executable/bwa/bwa_samse/.config.vsh.yaml +++ b/target/executable/bwa/bwa_samse/.config.vsh.yaml @@ -132,6 +132,7 @@ scope: target: "public" requirements: commands: + - "bwa" - "ps" keywords: - "alignment" @@ -231,7 +232,7 @@ build_info: output: "target/executable/bwa/bwa_samse" executable: "target/executable/bwa/bwa_samse/bwa_samse" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -253,138 +254,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bwa/bwa_samse/bwa_samse b/target/executable/bwa/bwa_samse/bwa_samse index b0375644..25838454 100755 --- a/target/executable/bwa/bwa_samse/bwa_samse +++ b/target/executable/bwa/bwa_samse/bwa_samse @@ -453,9 +453,9 @@ RUN bwa 2>&1 | grep "Version:" | sed 's/Version: /bwa: /' > /var/software_versio LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Toni Verbeiren" LABEL org.opencontainers.image.description="Companion container for running component bwa bwa_samse" -LABEL org.opencontainers.image.created="2025-09-01T11:03:01Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:05Z" LABEL org.opencontainers.image.source="https://github.com/lh3/bwa" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -854,13 +854,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bwa' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bwa' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/cellranger/cellranger_count/.config.vsh.yaml b/target/executable/cellranger/cellranger_count/.config.vsh.yaml index d471157b..43e47bff 100644 --- a/target/executable/cellranger/cellranger_count/.config.vsh.yaml +++ b/target/executable/cellranger/cellranger_count/.config.vsh.yaml @@ -266,6 +266,7 @@ scope: target: "public" requirements: commands: + - "cellranger" - "ps" keywords: - "cellranger" @@ -373,7 +374,7 @@ build_info: output: "target/executable/cellranger/cellranger_count" executable: "target/executable/cellranger/cellranger_count/cellranger_count" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -395,138 +396,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/cellranger/cellranger_count/cellranger_count b/target/executable/cellranger/cellranger_count/cellranger_count index a46e802a..add1d10c 100755 --- a/target/executable/cellranger/cellranger_count/cellranger_count +++ b/target/executable/cellranger/cellranger_count/cellranger_count @@ -456,9 +456,9 @@ RUN cellranger --version | sed 's/ cellranger-/: /' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component cellranger cellranger_count" -LABEL org.opencontainers.image.created="2025-09-01T11:02:58Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:09Z" LABEL org.opencontainers.image.source="https://github.com/10XGenomics/cellranger/blob/main/bin/sc_rna/count" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -1096,13 +1096,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'cellranger' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'cellranger' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/cellranger/cellranger_mkref/.config.vsh.yaml b/target/executable/cellranger/cellranger_mkref/.config.vsh.yaml index cc91c37b..f1b4ab14 100644 --- a/target/executable/cellranger/cellranger_mkref/.config.vsh.yaml +++ b/target/executable/cellranger/cellranger_mkref/.config.vsh.yaml @@ -75,6 +75,10 @@ scope: target: "public" requirements: commands: + - "cellranger" + - "pigz" + - "unpigz" + - "tar" - "ps" keywords: - "cellranger" @@ -193,7 +197,7 @@ build_info: output: "target/executable/cellranger/cellranger_mkref" executable: "target/executable/cellranger/cellranger_mkref/cellranger_mkref" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -215,138 +219,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/cellranger/cellranger_mkref/cellranger_mkref b/target/executable/cellranger/cellranger_mkref/cellranger_mkref index a2b823c6..f023e49c 100755 --- a/target/executable/cellranger/cellranger_mkref/cellranger_mkref +++ b/target/executable/cellranger/cellranger_mkref/cellranger_mkref @@ -454,9 +454,9 @@ RUN apt-get update && \ LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component cellranger cellranger_mkref" -LABEL org.opencontainers.image.created="2025-09-01T11:02:58Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:09Z" LABEL org.opencontainers.image.source="https://github.com/10XGenomics/cellranger/blob/main/lib/python/cellranger/reference_builder.py" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -803,13 +803,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'cellranger' 'pigz' 'unpigz' 'tar' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'cellranger' 'pigz' 'unpigz' 'tar' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/cutadapt/.config.vsh.yaml b/target/executable/cutadapt/.config.vsh.yaml index 6575f719..481026f6 100644 --- a/target/executable/cutadapt/.config.vsh.yaml +++ b/target/executable/cutadapt/.config.vsh.yaml @@ -743,7 +743,7 @@ build_info: output: "target/executable/cutadapt" executable: "target/executable/cutadapt/cutadapt" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -765,138 +765,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/cutadapt/cutadapt b/target/executable/cutadapt/cutadapt index 4de17e9c..0dfa789d 100755 --- a/target/executable/cutadapt/cutadapt +++ b/target/executable/cutadapt/cutadapt @@ -455,9 +455,9 @@ RUN cutadapt --version | sed 's/\(.*\)/cutadapt: "\1"/' > /var/software_versions LABEL org.opencontainers.image.authors="Toni Verbeiren" LABEL org.opencontainers.image.description="Companion container for running component cutadapt" -LABEL org.opencontainers.image.created="2025-09-01T11:02:45Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:10Z" LABEL org.opencontainers.image.source="https://github.com/marcelm/cutadapt" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/falco/.config.vsh.yaml b/target/executable/falco/.config.vsh.yaml index e8b25c4c..d735f000 100644 --- a/target/executable/falco/.config.vsh.yaml +++ b/target/executable/falco/.config.vsh.yaml @@ -42,7 +42,7 @@ argument_groups: description: "Specifies a non-default file which contains \nthe list of contaminants\ \ to screen \noverrepresented sequences against. The file \nmust contain sets\ \ of named contaminants in \nthe form name[tab]sequence. Lines prefixed \nwith\ - \ a hash will be ignored. Default: \nhttps://github.com/smithlabcode/falco/blob/v1.2.2/Configuration/contaminant_list.txt\n" + \ a hash will be ignored. Default: \nhttps://github.com/smithlabcode/falco/blob/v1.2.5/Configuration/contaminant_list.txt\n" info: null must_exist: true create_parent: true @@ -55,7 +55,7 @@ argument_groups: description: "Specifies a non-default file which contains \nthe list of adapter\ \ sequences which will be \nexplicity searched against the library. The \nfile\ \ must contain sets of named adapters in \nthe form name[tab]sequence. Lines\ - \ prefixed \nwith a hash will be ignored. Default:\nhttps://github.com/smithlabcode/falco/blob/v1.2.2/Configuration/adapter_list.txt\n" + \ prefixed \nwith a hash will be ignored. Default:\nhttps://github.com/smithlabcode/falco/blob/v1.2.5/Configuration/adapter_list.txt\n" info: null must_exist: true create_parent: true @@ -69,7 +69,7 @@ argument_groups: \ which will be used to \ndetermine the warn/error limits for the \nvarious\ \ modules. This file can also be used \nto selectively remove some modules from\ \ the \noutput all together. The format needs to \nmirror the default limits.txt\ - \ file found in \nthe Configuration folder. Default: \nhttps://github.com/smithlabcode/falco/blob/v1.2.2/Configuration/limits.txt\n" + \ file found in \nthe Configuration folder. Default: \nhttps://github.com/smithlabcode/falco/blob/v1.2.5/Configuration/limits.txt\n" info: null must_exist: true create_parent: true @@ -108,6 +108,12 @@ argument_groups: \ be \ntested by swapping A/T and C/G\n" info: null direction: "input" + - type: "boolean_true" + name: "--allow_empty_input" + description: "Allow empty input files and generate empty output files without\ + \ an error state.\n" + info: null + direction: "input" - name: "Output arguments" arguments: - type: "file" @@ -201,6 +207,8 @@ test_resources: - type: "bash_script" path: "test.sh" is_executable: true +- type: "file" + path: "test_helpers.sh" info: null status: "enabled" scope: @@ -208,6 +216,7 @@ scope: target: "public" requirements: commands: + - "falco" - "ps" keywords: - "qc" @@ -288,24 +297,11 @@ runners: engines: - type: "docker" id: "docker" - image: "debian:trixie-slim" + image: "quay.io/biocontainers/falco:1.2.5--h077b44d_0" target_registry: "images.viash-hub.com" target_tag: "main" namespace_separator: "/" setup: - - type: "apt" - packages: - - "wget" - - "build-essential" - - "g++" - - "zlib1g-dev" - - "procps" - interactive: false - - type: "docker" - run: - - "wget https://github.com/smithlabcode/falco/releases/download/v1.2.2/falco-1.2.2.tar.gz\ - \ -O /tmp/falco.tar.gz && \\\ncd /tmp && \\\ntar xvf falco.tar.gz && \\\ncd\ - \ falco-1.2.2 && \\\n./configure && \\\nmake all && \\\nmake install\n" - type: "docker" run: - "echo \"falco: \\\"$(falco -v | sed -n 's/^falco //p')\\\"\" > /var/software_versions.txt\n" @@ -320,7 +316,7 @@ build_info: output: "target/executable/falco" executable: "target/executable/falco/falco" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -342,138 +338,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/falco/falco b/target/executable/falco/falco index ec0cb4b6..add01bee 100755 --- a/target/executable/falco/falco +++ b/target/executable/falco/falco @@ -446,27 +446,15 @@ function ViashDockerfile { if [[ "$engine_id" == "docker" ]]; then cat << 'VIASHDOCKER' -FROM debian:trixie-slim +FROM quay.io/biocontainers/falco:1.2.5--h077b44d_0 ENTRYPOINT [] -RUN apt-get update && \ - DEBIAN_FRONTEND=noninteractive apt-get install -y wget build-essential g++ zlib1g-dev procps && \ - rm -rf /var/lib/apt/lists/* - -RUN wget https://github.com/smithlabcode/falco/releases/download/v1.2.2/falco-1.2.2.tar.gz -O /tmp/falco.tar.gz && \ -cd /tmp && \ -tar xvf falco.tar.gz && \ -cd falco-1.2.2 && \ -./configure && \ -make all && \ -make install - RUN echo "falco: \"$(falco -v | sed -n 's/^falco //p')\"" > /var/software_versions.txt LABEL org.opencontainers.image.authors="Toni Verbeiren" LABEL org.opencontainers.image.description="Companion container for running component falco" -LABEL org.opencontainers.image.created="2025-09-01T11:02:56Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:12Z" LABEL org.opencontainers.image.source="https://github.com/smithlabcode/falco" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -612,7 +600,7 @@ function ViashHelp { echo " the form name[tab]sequence. Lines prefixed" echo " with a hash will be ignored. Default:" echo " " - echo "https://github.com/smithlabcode/falco/blob/v1.2.2/Configuration/contaminant_list.txt" + echo "https://github.com/smithlabcode/falco/blob/v1.2.5/Configuration/contaminant_list.txt" echo "" echo " --adapters" echo " type: file, file must exist" @@ -623,7 +611,7 @@ function ViashHelp { echo " the form name[tab]sequence. Lines prefixed" echo " with a hash will be ignored. Default:" echo " " - echo "https://github.com/smithlabcode/falco/blob/v1.2.2/Configuration/adapter_list.txt" + echo "https://github.com/smithlabcode/falco/blob/v1.2.5/Configuration/adapter_list.txt" echo "" echo " --limits" echo " type: file, file must exist" @@ -636,7 +624,7 @@ function ViashHelp { echo " mirror the default limits.txt file found in" echo " the Configuration folder. Default:" echo " " - echo "https://github.com/smithlabcode/falco/blob/v1.2.2/Configuration/limits.txt" + echo "https://github.com/smithlabcode/falco/blob/v1.2.5/Configuration/limits.txt" echo "" echo " -s, --subsample" echo " type: integer" @@ -659,6 +647,11 @@ function ViashHelp { echo " reverse-complement. All modules will be" echo " tested by swapping A/T and C/G" echo "" + echo " --allow_empty_input" + echo " type: boolean_true" + echo " Allow empty input files and generate empty output files without an error" + echo " state." + echo "" echo "Output arguments:" echo " -o, --outdir" echo " type: file, required parameter, output, file must exist" @@ -849,6 +842,11 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_REVERSE_COMPLEMENT=true shift 1 ;; + --allow_empty_input) + [ -n "$VIASH_PAR_ALLOW_EMPTY_INPUT" ] && ViashError Bad arguments for option \'--allow_empty_input\': \'$VIASH_PAR_ALLOW_EMPTY_INPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_ALLOW_EMPTY_INPUT=true + shift 1 + ;; --outdir) [ -n "$VIASH_PAR_OUTDIR" ] && ViashError Bad arguments for option \'--outdir\': \'$VIASH_PAR_OUTDIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 VIASH_PAR_OUTDIR="$2" @@ -1044,13 +1042,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'falco' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'falco' 'ps' 'bash' fi # setting computational defaults @@ -1149,6 +1147,9 @@ fi if [ -z ${VIASH_PAR_REVERSE_COMPLEMENT+x} ]; then VIASH_PAR_REVERSE_COMPLEMENT="false" fi +if [ -z ${VIASH_PAR_ALLOW_EMPTY_INPUT+x} ]; then + VIASH_PAR_ALLOW_EMPTY_INPUT="false" +fi # check whether required files exist if [ ! -z "$VIASH_PAR_INPUT" ]; then @@ -1201,6 +1202,12 @@ if [[ -n "$VIASH_PAR_REVERSE_COMPLEMENT" ]]; then exit 1 fi fi +if [[ -n "$VIASH_PAR_ALLOW_EMPTY_INPUT" ]]; then + if ! [[ "$VIASH_PAR_ALLOW_EMPTY_INPUT" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then + ViashError '--allow_empty_input' has to be a boolean_true. Use "--help" to get more information on the parameters. + exit 1 + fi +fi if [[ -n "$VIASH_META_CPUS" ]]; then if ! [[ "$VIASH_META_CPUS" =~ ^[-+]?[0-9]+$ ]]; then ViashError 'cpus' has to be an integer. Use "--help" to get more information on the parameters. @@ -1433,6 +1440,7 @@ $( if [ ! -z ${VIASH_PAR_LIMITS+x} ]; then echo "${VIASH_PAR_LIMITS}" | sed "s#' $( if [ ! -z ${VIASH_PAR_SUBSAMPLE+x} ]; then echo "${VIASH_PAR_SUBSAMPLE}" | sed "s#'#'\"'\"'#g;s#.*#par_subsample='&'#" ; else echo "# par_subsample="; fi ) $( if [ ! -z ${VIASH_PAR_BISULFITE+x} ]; then echo "${VIASH_PAR_BISULFITE}" | sed "s#'#'\"'\"'#g;s#.*#par_bisulfite='&'#" ; else echo "# par_bisulfite="; fi ) $( if [ ! -z ${VIASH_PAR_REVERSE_COMPLEMENT+x} ]; then echo "${VIASH_PAR_REVERSE_COMPLEMENT}" | sed "s#'#'\"'\"'#g;s#.*#par_reverse_complement='&'#" ; else echo "# par_reverse_complement="; fi ) +$( if [ ! -z ${VIASH_PAR_ALLOW_EMPTY_INPUT+x} ]; then echo "${VIASH_PAR_ALLOW_EMPTY_INPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_allow_empty_input='&'#" ; else echo "# par_allow_empty_input="; fi ) $( if [ ! -z ${VIASH_PAR_OUTDIR+x} ]; then echo "${VIASH_PAR_OUTDIR}" | sed "s#'#'\"'\"'#g;s#.*#par_outdir='&'#" ; else echo "# par_outdir="; fi ) $( if [ ! -z ${VIASH_PAR_FORMAT+x} ]; then echo "${VIASH_PAR_FORMAT}" | sed "s#'#'\"'\"'#g;s#.*#par_format='&'#" ; else echo "# par_format="; fi ) $( if [ ! -z ${VIASH_PAR_DATA_FILENAME+x} ]; then echo "${VIASH_PAR_DATA_FILENAME}" | sed "s#'#'\"'\"'#g;s#.*#par_data_filename='&'#" ; else echo "# par_data_filename="; fi ) @@ -1465,6 +1473,8 @@ set -eo pipefail [[ "\$par_nogroup" == "false" ]] && unset par_nogroup [[ "\$par_bisulfite" == "false" ]] && unset par_bisulfite [[ "\$par_reverse_complement" == "false" ]] && unset par_reverse_complement +[[ "\$par_allow_empty_input" == "false" ]] && unset par_allow_empty_input + IFS=";" read -ra input <<< \$par_input @@ -1475,6 +1485,7 @@ IFS=";" read -ra input <<< \$par_input \${par_limits:+--limits "\$par_limits"} \\ \${par_subsample:+-subsample \$par_subsample} \\ \${par_bisulfite:+-bisulfite} \\ + \${par_allow_empty_input:+-allow-empty-input} \\ \${par_reverse_complement:+-reverse-complement} \\ \${par_outdir:+--outdir "\$par_outdir"} \\ \${par_format:+--format "\$par_format"} \\ diff --git a/target/executable/fastp/.config.vsh.yaml b/target/executable/fastp/.config.vsh.yaml index 87a2e597..926475a6 100644 --- a/target/executable/fastp/.config.vsh.yaml +++ b/target/executable/fastp/.config.vsh.yaml @@ -1086,7 +1086,7 @@ build_info: output: "target/executable/fastp" executable: "target/executable/fastp/fastp" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -1108,138 +1108,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/fastp/fastp b/target/executable/fastp/fastp index 6f439411..168e754e 100755 --- a/target/executable/fastp/fastp +++ b/target/executable/fastp/fastp @@ -452,9 +452,9 @@ RUN fastp --version 2>&1 | sed 's# #: "#;s#$#"#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component fastp" -LABEL org.opencontainers.image.created="2025-09-01T11:02:50Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:09Z" LABEL org.opencontainers.image.source="https://github.com/OpenGene/fastp" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/fastqc/.config.vsh.yaml b/target/executable/fastqc/.config.vsh.yaml index e3cb28db..c07d3a1e 100644 --- a/target/executable/fastqc/.config.vsh.yaml +++ b/target/executable/fastqc/.config.vsh.yaml @@ -351,7 +351,7 @@ build_info: output: "target/executable/fastqc" executable: "target/executable/fastqc/fastqc" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -373,138 +373,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/fastqc/fastqc b/target/executable/fastqc/fastqc index 642a8406..a08cd429 100755 --- a/target/executable/fastqc/fastqc +++ b/target/executable/fastqc/fastqc @@ -452,9 +452,9 @@ RUN echo "fastqc: $(fastqc --version | sed -n 's/^FastQC //p')" > /var/software_ LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component fastqc" -LABEL org.opencontainers.image.created="2025-09-01T11:02:48Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:04Z" LABEL org.opencontainers.image.source="https://github.com/s-andrews/FastQC" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/featurecounts/.config.vsh.yaml b/target/executable/featurecounts/.config.vsh.yaml index 649777ba..5d5bacb7 100644 --- a/target/executable/featurecounts/.config.vsh.yaml +++ b/target/executable/featurecounts/.config.vsh.yaml @@ -543,6 +543,7 @@ scope: target: "public" requirements: commands: + - "featureCounts" - "ps" keywords: - "Read counting" @@ -643,7 +644,7 @@ build_info: output: "target/executable/featurecounts" executable: "target/executable/featurecounts/featurecounts" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -665,138 +666,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/featurecounts/featurecounts b/target/executable/featurecounts/featurecounts index 38482740..aadcc0db 100755 --- a/target/executable/featurecounts/featurecounts +++ b/target/executable/featurecounts/featurecounts @@ -452,9 +452,9 @@ RUN featureCounts -v 2>&1 | sed 's/featureCounts v\([0-9.]*\)/featureCounts: \1/ LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa" LABEL org.opencontainers.image.description="Companion container for running component featurecounts" -LABEL org.opencontainers.image.created="2025-09-01T11:02:58Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:15Z" LABEL org.opencontainers.image.source="https://github.com/ShiLab-Bioinformatics/subread" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -1545,13 +1545,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'featureCounts' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'featureCounts' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/fq/fq_filter/.config.vsh.yaml b/target/executable/fq/fq_filter/.config.vsh.yaml index f8ff3697..a6784bf1 100644 --- a/target/executable/fq/fq_filter/.config.vsh.yaml +++ b/target/executable/fq/fq_filter/.config.vsh.yaml @@ -81,6 +81,7 @@ scope: target: "public" requirements: commands: + - "fq" - "ps" keywords: - "fastq" @@ -178,7 +179,7 @@ build_info: output: "target/executable/fq/fq_filter" executable: "target/executable/fq/fq_filter/fq_filter" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -200,138 +201,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/fq/fq_filter/fq_filter b/target/executable/fq/fq_filter/fq_filter index 748a15f7..cd3f6e9c 100755 --- a/target/executable/fq/fq_filter/fq_filter +++ b/target/executable/fq/fq_filter/fq_filter @@ -452,9 +452,9 @@ RUN fq -V | sed 's#fq \([0-9.]*\) .*#fq: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component fq fq_filter" -LABEL org.opencontainers.image.created="2025-09-01T11:02:47Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:12Z" LABEL org.opencontainers.image.source="https://github.com/stjude-rust-labs/fq" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -801,13 +801,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'fq' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'fq' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/fq/fq_generate/.config.vsh.yaml b/target/executable/fq/fq_generate/.config.vsh.yaml index 30c97eb3..18859f32 100644 --- a/target/executable/fq/fq_generate/.config.vsh.yaml +++ b/target/executable/fq/fq_generate/.config.vsh.yaml @@ -104,6 +104,7 @@ scope: target: "public" requirements: commands: + - "fq" - "ps" keywords: - "FASTQ" @@ -202,7 +203,7 @@ build_info: output: "target/executable/fq/fq_generate" executable: "target/executable/fq/fq_generate/fq_generate" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -224,138 +225,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/fq/fq_generate/fq_generate b/target/executable/fq/fq_generate/fq_generate index 2e32316d..3e3980d4 100755 --- a/target/executable/fq/fq_generate/fq_generate +++ b/target/executable/fq/fq_generate/fq_generate @@ -452,9 +452,9 @@ RUN fq --version | sed 's/^/fq: /' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component fq fq_generate" -LABEL org.opencontainers.image.created="2025-09-01T11:02:47Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:11Z" LABEL org.opencontainers.image.source="https://github.com/stjude-rust-labs/fq" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -832,13 +832,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'fq' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'fq' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/fq/fq_lint/.config.vsh.yaml b/target/executable/fq/fq_lint/.config.vsh.yaml index 8339a833..420f4b86 100644 --- a/target/executable/fq/fq_lint/.config.vsh.yaml +++ b/target/executable/fq/fq_lint/.config.vsh.yaml @@ -131,6 +131,7 @@ scope: target: "public" requirements: commands: + - "fq" - "ps" keywords: - "fastq" @@ -229,7 +230,7 @@ build_info: output: "target/executable/fq/fq_lint" executable: "target/executable/fq/fq_lint/fq_lint" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -251,138 +252,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/fq/fq_lint/fq_lint b/target/executable/fq/fq_lint/fq_lint index 6ace49ff..2b4529e9 100755 --- a/target/executable/fq/fq_lint/fq_lint +++ b/target/executable/fq/fq_lint/fq_lint @@ -453,9 +453,9 @@ RUN fq -V | sed 's#fq \([0-9.]*\) .*#fq: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component fq fq_lint" -LABEL org.opencontainers.image.created="2025-09-01T11:02:47Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:12Z" LABEL org.opencontainers.image.source="https://github.com/stjude-rust-labs/fq" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -862,13 +862,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'fq' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'fq' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/fq/fq_subsample/.config.vsh.yaml b/target/executable/fq/fq_subsample/.config.vsh.yaml index fe3607da..4eea4102 100644 --- a/target/executable/fq/fq_subsample/.config.vsh.yaml +++ b/target/executable/fq/fq_subsample/.config.vsh.yaml @@ -117,6 +117,7 @@ scope: target: "public" requirements: commands: + - "fq" - "ps" keywords: - "fastq" @@ -214,7 +215,7 @@ build_info: output: "target/executable/fq/fq_subsample" executable: "target/executable/fq/fq_subsample/fq_subsample" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -236,138 +237,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/fq/fq_subsample/fq_subsample b/target/executable/fq/fq_subsample/fq_subsample index af2dce49..00651964 100755 --- a/target/executable/fq/fq_subsample/fq_subsample +++ b/target/executable/fq/fq_subsample/fq_subsample @@ -453,9 +453,9 @@ RUN fq -V | sed 's#fq \([0-9.]*\) .*#fq: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component fq fq_subsample" -LABEL org.opencontainers.image.created="2025-09-01T11:02:47Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:11Z" LABEL org.opencontainers.image.source="https://github.com/stjude-rust-labs/fq" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -848,13 +848,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'fq' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'fq' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/gffread/.config.vsh.yaml b/target/executable/gffread/.config.vsh.yaml index 66e95d65..45cea616 100644 --- a/target/executable/gffread/.config.vsh.yaml +++ b/target/executable/gffread/.config.vsh.yaml @@ -683,7 +683,7 @@ build_info: output: "target/executable/gffread" executable: "target/executable/gffread/gffread" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -705,138 +705,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/gffread/gffread b/target/executable/gffread/gffread index f9d4be20..50c3739d 100755 --- a/target/executable/gffread/gffread +++ b/target/executable/gffread/gffread @@ -452,9 +452,9 @@ RUN echo "gffread: \"$(gffread --version 2>&1)\"" > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component gffread" -LABEL org.opencontainers.image.created="2025-09-01T11:02:46Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:07Z" LABEL org.opencontainers.image.source="https://github.com/gpertea/gffread" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/kallisto/kallisto_index/.config.vsh.yaml b/target/executable/kallisto/kallisto_index/.config.vsh.yaml index 63668494..6a699ae4 100644 --- a/target/executable/kallisto/kallisto_index/.config.vsh.yaml +++ b/target/executable/kallisto/kallisto_index/.config.vsh.yaml @@ -221,7 +221,7 @@ build_info: output: "target/executable/kallisto/kallisto_index" executable: "target/executable/kallisto/kallisto_index/kallisto_index" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -243,138 +243,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/kallisto/kallisto_index/kallisto_index b/target/executable/kallisto/kallisto_index/kallisto_index index 24338fee..e2bad28f 100755 --- a/target/executable/kallisto/kallisto_index/kallisto_index +++ b/target/executable/kallisto/kallisto_index/kallisto_index @@ -452,9 +452,9 @@ tar -xzf kallisto_linux-v0.50.1.tar.gz && \ mv kallisto/kallisto /usr/local/bin/ LABEL org.opencontainers.image.description="Companion container for running component kallisto kallisto_index" -LABEL org.opencontainers.image.created="2025-09-01T11:02:50Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:07Z" LABEL org.opencontainers.image.source="https://github.com/pachterlab/kallisto" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/kallisto/kallisto_quant/.config.vsh.yaml b/target/executable/kallisto/kallisto_quant/.config.vsh.yaml index 57f42ef7..224b7bde 100644 --- a/target/executable/kallisto/kallisto_quant/.config.vsh.yaml +++ b/target/executable/kallisto/kallisto_quant/.config.vsh.yaml @@ -249,7 +249,7 @@ build_info: output: "target/executable/kallisto/kallisto_quant" executable: "target/executable/kallisto/kallisto_quant/kallisto_quant" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -271,138 +271,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/kallisto/kallisto_quant/kallisto_quant b/target/executable/kallisto/kallisto_quant/kallisto_quant index 9f77a1c0..0fa22637 100755 --- a/target/executable/kallisto/kallisto_quant/kallisto_quant +++ b/target/executable/kallisto/kallisto_quant/kallisto_quant @@ -454,9 +454,9 @@ mv kallisto/kallisto /usr/local/bin/ RUN echo "kallisto: $(kallisto version | sed 's/kallisto, version //')" > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component kallisto kallisto_quant" -LABEL org.opencontainers.image.created="2025-09-01T11:02:50Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:07Z" LABEL org.opencontainers.image.source="https://github.com/pachterlab/kallisto" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/lofreq/lofreq_call/.config.vsh.yaml b/target/executable/lofreq/lofreq_call/.config.vsh.yaml index c560f3e1..26c8a1e3 100644 --- a/target/executable/lofreq/lofreq_call/.config.vsh.yaml +++ b/target/executable/lofreq/lofreq_call/.config.vsh.yaml @@ -400,6 +400,7 @@ scope: target: "public" requirements: commands: + - "lofreq" - "ps" keywords: - "variant calling" @@ -502,7 +503,7 @@ build_info: output: "target/executable/lofreq/lofreq_call" executable: "target/executable/lofreq/lofreq_call/lofreq_call" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -524,138 +525,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/lofreq/lofreq_call/lofreq_call b/target/executable/lofreq/lofreq_call/lofreq_call index 5b046c4c..52e0d4b5 100755 --- a/target/executable/lofreq/lofreq_call/lofreq_call +++ b/target/executable/lofreq/lofreq_call/lofreq_call @@ -453,9 +453,9 @@ echo "lofreq: $version" > /var/software_versions.txt LABEL org.opencontainers.image.authors="Kai Waldrant" LABEL org.opencontainers.image.description="Companion container for running component lofreq lofreq_call" -LABEL org.opencontainers.image.created="2025-09-01T11:02:46Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:20Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -1367,13 +1367,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'lofreq' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'lofreq' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml b/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml index 908adbcd..cc5760b3 100644 --- a/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml +++ b/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml @@ -106,6 +106,7 @@ scope: target: "public" requirements: commands: + - "lofreq" - "ps" keywords: - "bam" @@ -210,7 +211,7 @@ build_info: output: "target/executable/lofreq/lofreq_indelqual" executable: "target/executable/lofreq/lofreq_indelqual/lofreq_indelqual" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -232,138 +233,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual b/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual index c31fa197..fef0f96b 100755 --- a/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual +++ b/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual @@ -453,9 +453,9 @@ echo "lofreq: $version" > /var/software_versions.txt LABEL org.opencontainers.image.authors="Kai Waldrant" LABEL org.opencontainers.image.description="Companion container for running component lofreq lofreq_indelqual" -LABEL org.opencontainers.image.created="2025-09-01T11:02:46Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:20Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -851,13 +851,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'lofreq' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'lofreq' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/multiqc/.config.vsh.yaml b/target/executable/multiqc/.config.vsh.yaml index 0a93c986..f46a3d61 100644 --- a/target/executable/multiqc/.config.vsh.yaml +++ b/target/executable/multiqc/.config.vsh.yaml @@ -459,7 +459,7 @@ build_info: output: "target/executable/multiqc" executable: "target/executable/multiqc/multiqc" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -481,138 +481,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/multiqc/multiqc b/target/executable/multiqc/multiqc index a09eea82..d680101a 100755 --- a/target/executable/multiqc/multiqc +++ b/target/executable/multiqc/multiqc @@ -452,9 +452,9 @@ RUN multiqc --version | sed 's/multiqc, version\s\(.*\)/multiqc: "\1"/' > /var/s LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component multiqc" -LABEL org.opencontainers.image.created="2025-09-01T11:02:49Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:20Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/nanoplot/.config.vsh.yaml b/target/executable/nanoplot/.config.vsh.yaml index e006b903..2749da99 100644 --- a/target/executable/nanoplot/.config.vsh.yaml +++ b/target/executable/nanoplot/.config.vsh.yaml @@ -495,7 +495,7 @@ build_info: output: "target/executable/nanoplot" executable: "target/executable/nanoplot/nanoplot" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -517,138 +517,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/nanoplot/nanoplot b/target/executable/nanoplot/nanoplot index c22bbe46..30127990 100755 --- a/target/executable/nanoplot/nanoplot +++ b/target/executable/nanoplot/nanoplot @@ -449,9 +449,9 @@ RUN version=$(NanoPlot --version) && \ echo "$version" > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component nanoplot" -LABEL org.opencontainers.image.created="2025-09-01T11:03:01Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:10Z" LABEL org.opencontainers.image.source="https://github.com/wdecoster/NanoPlot" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/pear/.config.vsh.yaml b/target/executable/pear/.config.vsh.yaml index 6e3deda4..6bf51b52 100644 --- a/target/executable/pear/.config.vsh.yaml +++ b/target/executable/pear/.config.vsh.yaml @@ -292,6 +292,8 @@ scope: target: "public" requirements: commands: + - "pear" + - "gzip" - "ps" keywords: - "pair-end" @@ -393,7 +395,7 @@ build_info: output: "target/executable/pear" executable: "target/executable/pear/pear" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -415,138 +417,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/pear/pear b/target/executable/pear/pear index 63df8df4..5f32476f 100755 --- a/target/executable/pear/pear +++ b/target/executable/pear/pear @@ -453,9 +453,9 @@ echo "pear: $version" > /var/software_versions.txt LABEL org.opencontainers.image.authors="Kai Waldrant" LABEL org.opencontainers.image.description="Companion container for running component pear" -LABEL org.opencontainers.image.created="2025-09-01T11:02:57Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:09Z" LABEL org.opencontainers.image.source="https://github.com/tseemann/PEAR" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -1160,13 +1160,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'pear' 'gzip' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'pear' 'gzip' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml b/target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml index f840488d..4f682dd4 100644 --- a/target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml +++ b/target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml @@ -267,7 +267,7 @@ build_info: output: "target/executable/qualimap/qualimap_rnaseq" executable: "target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -289,138 +289,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq b/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq index bb7ff7ad..325b832a 100755 --- a/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq +++ b/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq @@ -452,9 +452,9 @@ RUN echo QualiMap: $(qualimap 2>&1 | grep QualiMap | sed 's/^.*QualiMap//') > /v LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component qualimap qualimap_rnaseq" -LABEL org.opencontainers.image.created="2025-09-01T11:02:58Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:08Z" LABEL org.opencontainers.image.source="https://bitbucket.org/kokonech/qualimap/commits/branch/master" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml b/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml index 461f212b..0361021a 100644 --- a/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml +++ b/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml @@ -855,7 +855,7 @@ build_info: output: "target/executable/rsem/rsem_calculate_expression" executable: "target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -877,138 +877,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression b/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression index 1c541037..78786caf 100755 --- a/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression +++ b/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression @@ -470,9 +470,9 @@ echo "bowtie: `bowtie --version | grep -oP 'bowtie-align-s version \K\d+\.\d+\.\ echo "HISAT2: `hisat2 --version | grep -oP 'hisat2-align-s version \K\d+\.\d+\.\d+'`" >> /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_calculate_expression" -LABEL org.opencontainers.image.created="2025-09-01T11:02:46Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:17Z" LABEL org.opencontainers.image.source="https://github.com/deweylab/RSEM" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/rsem/rsem_prepare_reference/.config.vsh.yaml b/target/executable/rsem/rsem_prepare_reference/.config.vsh.yaml index f419f5a5..efda1493 100644 --- a/target/executable/rsem/rsem_prepare_reference/.config.vsh.yaml +++ b/target/executable/rsem/rsem_prepare_reference/.config.vsh.yaml @@ -268,6 +268,7 @@ scope: target: "public" requirements: commands: + - "rsem-prepare-reference" - "ps" keywords: - "Transcriptome" @@ -414,7 +415,7 @@ build_info: output: "target/executable/rsem/rsem_prepare_reference" executable: "target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -436,138 +437,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference b/target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference index 017e6dad..c230e171 100755 --- a/target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference +++ b/target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference @@ -494,9 +494,9 @@ echo "HISAT2: `hisat2 --version | grep -oP 'hisat2-align-s version \K\d+\.\d+\.\ LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa" LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_prepare_reference" -LABEL org.opencontainers.image.created="2025-09-01T11:02:46Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:17Z" LABEL org.opencontainers.image.source="https://github.com/deweylab/RSEM" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -1140,13 +1140,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'rsem-prepare-reference' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'rsem-prepare-reference' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml b/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml index 9066c8b8..5c743a47 100644 --- a/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml @@ -173,7 +173,7 @@ build_info: output: "target/executable/rseqc/rseqc_bamstat" executable: "target/executable/rseqc/rseqc_bamstat/rseqc_bamstat" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -195,138 +195,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat b/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat index 8f461299..b47be733 100755 --- a/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat +++ b/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat @@ -455,9 +455,9 @@ RUN echo "RSeQC bam_stat.py: $(bam_stat.py --version | cut -d' ' -f2-)" > /var/s LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_bamstat" -LABEL org.opencontainers.image.created="2025-09-01T11:03:01Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:15Z" LABEL org.opencontainers.image.source="https://github.com/MonashBioinformaticsPlatform/RSeQC" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml b/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml index be607e2c..0c7379eb 100644 --- a/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml @@ -199,7 +199,7 @@ build_info: output: "target/executable/rseqc/rseqc_inferexperiment" executable: "target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -221,138 +221,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment b/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment index d6a5ae17..ba9391b8 100755 --- a/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment +++ b/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment @@ -455,9 +455,9 @@ RUN echo "RSeQC - infer_experiment.py: $(infer_experiment.py --version | cut -d' LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_inferexperiment" -LABEL org.opencontainers.image.created="2025-09-01T11:03:02Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:14Z" LABEL org.opencontainers.image.source="https://github.com/MonashBioinformaticsPlatform/RSeQC" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_inner_distance/.config.vsh.yaml b/target/executable/rseqc/rseqc_inner_distance/.config.vsh.yaml index 65bf157a..6808b3e0 100644 --- a/target/executable/rseqc/rseqc_inner_distance/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_inner_distance/.config.vsh.yaml @@ -292,7 +292,7 @@ build_info: output: "target/executable/rseqc/rseqc_inner_distance" executable: "target/executable/rseqc/rseqc_inner_distance/rseqc_inner_distance" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -314,138 +314,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/rseqc/rseqc_inner_distance/rseqc_inner_distance b/target/executable/rseqc/rseqc_inner_distance/rseqc_inner_distance index 88c7fbb9..5520810f 100755 --- a/target/executable/rseqc/rseqc_inner_distance/rseqc_inner_distance +++ b/target/executable/rseqc/rseqc_inner_distance/rseqc_inner_distance @@ -459,9 +459,9 @@ RUN echo "RSeQC - inner_distance.py: $(inner_distance.py --version | cut -d' ' - LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_inner_distance" -LABEL org.opencontainers.image.created="2025-09-01T11:02:45Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:14Z" LABEL org.opencontainers.image.source="https://github.com/MonashBioinformaticsPlatform/RSeQC" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/salmon/salmon_index/.config.vsh.yaml b/target/executable/salmon/salmon_index/.config.vsh.yaml index 20790e9a..81a1e7c6 100644 --- a/target/executable/salmon/salmon_index/.config.vsh.yaml +++ b/target/executable/salmon/salmon_index/.config.vsh.yaml @@ -176,6 +176,7 @@ scope: target: "public" requirements: commands: + - "salmon" - "ps" keywords: - "Transcriptome" @@ -275,7 +276,7 @@ build_info: output: "target/executable/salmon/salmon_index" executable: "target/executable/salmon/salmon_index/salmon_index" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -297,138 +298,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/salmon/salmon_index/salmon_index b/target/executable/salmon/salmon_index/salmon_index index eb15754a..c7bdcd79 100755 --- a/target/executable/salmon/salmon_index/salmon_index +++ b/target/executable/salmon/salmon_index/salmon_index @@ -452,9 +452,9 @@ RUN salmon index -v 2>&1 | sed 's/salmon \([0-9.]*\)/salmon: \1/' > /var/softwar LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa" LABEL org.opencontainers.image.description="Companion container for running component salmon salmon_index" -LABEL org.opencontainers.image.created="2025-09-01T11:02:54Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:15Z" LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -967,13 +967,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'salmon' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'salmon' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/salmon/salmon_quant/.config.vsh.yaml b/target/executable/salmon/salmon_quant/.config.vsh.yaml index 3584b2fd..cc432755 100644 --- a/target/executable/salmon/salmon_quant/.config.vsh.yaml +++ b/target/executable/salmon/salmon_quant/.config.vsh.yaml @@ -1072,6 +1072,7 @@ scope: target: "public" requirements: commands: + - "salmon" - "ps" keywords: - "Transcriptome" @@ -1171,7 +1172,7 @@ build_info: output: "target/executable/salmon/salmon_quant" executable: "target/executable/salmon/salmon_quant/salmon_quant" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -1193,138 +1194,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/salmon/salmon_quant/salmon_quant b/target/executable/salmon/salmon_quant/salmon_quant index bf7530c6..e447ccaa 100755 --- a/target/executable/salmon/salmon_quant/salmon_quant +++ b/target/executable/salmon/salmon_quant/salmon_quant @@ -452,9 +452,9 @@ RUN salmon index -v 2>&1 | sed 's/salmon \([0-9.]*\)/salmon: \1/' > /var/softwar LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa" LABEL org.opencontainers.image.description="Companion container for running component salmon salmon_quant" -LABEL org.opencontainers.image.created="2025-09-01T11:02:54Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:15Z" LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -2322,13 +2322,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'salmon' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'salmon' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/samtools/samtools_collate/.config.vsh.yaml b/target/executable/samtools/samtools_collate/.config.vsh.yaml index e8ac0910..e39af7f4 100644 --- a/target/executable/samtools/samtools_collate/.config.vsh.yaml +++ b/target/executable/samtools/samtools_collate/.config.vsh.yaml @@ -262,7 +262,7 @@ build_info: output: "target/executable/samtools/samtools_collate" executable: "target/executable/samtools/samtools_collate/samtools_collate" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -284,138 +284,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/samtools/samtools_collate/samtools_collate b/target/executable/samtools/samtools_collate/samtools_collate index 2220767f..6ebf9f99 100755 --- a/target/executable/samtools/samtools_collate/samtools_collate +++ b/target/executable/samtools/samtools_collate/samtools_collate @@ -453,9 +453,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_collate" -LABEL org.opencontainers.image.created="2025-09-01T11:02:58Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:17Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/samtools/samtools_faidx/.config.vsh.yaml b/target/executable/samtools/samtools_faidx/.config.vsh.yaml index 362411bb..bf4cf4da 100644 --- a/target/executable/samtools/samtools_faidx/.config.vsh.yaml +++ b/target/executable/samtools/samtools_faidx/.config.vsh.yaml @@ -241,7 +241,7 @@ build_info: output: "target/executable/samtools/samtools_faidx" executable: "target/executable/samtools/samtools_faidx/samtools_faidx" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -263,138 +263,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/samtools/samtools_faidx/samtools_faidx b/target/executable/samtools/samtools_faidx/samtools_faidx index cb655ea2..5faecd00 100755 --- a/target/executable/samtools/samtools_faidx/samtools_faidx +++ b/target/executable/samtools/samtools_faidx/samtools_faidx @@ -453,9 +453,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_faidx" -LABEL org.opencontainers.image.created="2025-09-01T11:03:00Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:19Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/samtools/samtools_fasta/.config.vsh.yaml b/target/executable/samtools/samtools_fasta/.config.vsh.yaml index 621f6fed..76e462f8 100644 --- a/target/executable/samtools/samtools_fasta/.config.vsh.yaml +++ b/target/executable/samtools/samtools_fasta/.config.vsh.yaml @@ -431,7 +431,7 @@ build_info: output: "target/executable/samtools/samtools_fasta" executable: "target/executable/samtools/samtools_fasta/samtools_fasta" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -453,138 +453,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/samtools/samtools_fasta/samtools_fasta b/target/executable/samtools/samtools_fasta/samtools_fasta index 70d9f687..705ac85f 100755 --- a/target/executable/samtools/samtools_fasta/samtools_fasta +++ b/target/executable/samtools/samtools_fasta/samtools_fasta @@ -453,9 +453,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_fasta" -LABEL org.opencontainers.image.created="2025-09-01T11:02:59Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:17Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/samtools/samtools_fastq/.config.vsh.yaml b/target/executable/samtools/samtools_fastq/.config.vsh.yaml index ccc6f33e..d2935353 100644 --- a/target/executable/samtools/samtools_fastq/.config.vsh.yaml +++ b/target/executable/samtools/samtools_fastq/.config.vsh.yaml @@ -431,7 +431,7 @@ build_info: output: "target/executable/samtools/samtools_fastq" executable: "target/executable/samtools/samtools_fastq/samtools_fastq" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -453,138 +453,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/samtools/samtools_fastq/samtools_fastq b/target/executable/samtools/samtools_fastq/samtools_fastq index 5b219cf0..b714a098 100755 --- a/target/executable/samtools/samtools_fastq/samtools_fastq +++ b/target/executable/samtools/samtools_fastq/samtools_fastq @@ -453,9 +453,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_fastq" -LABEL org.opencontainers.image.created="2025-09-01T11:02:59Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:19Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/samtools/samtools_flagstat/.config.vsh.yaml b/target/executable/samtools/samtools_flagstat/.config.vsh.yaml index 2eba88d3..5dd2dcfc 100644 --- a/target/executable/samtools/samtools_flagstat/.config.vsh.yaml +++ b/target/executable/samtools/samtools_flagstat/.config.vsh.yaml @@ -171,7 +171,7 @@ build_info: output: "target/executable/samtools/samtools_flagstat" executable: "target/executable/samtools/samtools_flagstat/samtools_flagstat" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -193,138 +193,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/samtools/samtools_flagstat/samtools_flagstat b/target/executable/samtools/samtools_flagstat/samtools_flagstat index ca4afc6e..39af9c19 100755 --- a/target/executable/samtools/samtools_flagstat/samtools_flagstat +++ b/target/executable/samtools/samtools_flagstat/samtools_flagstat @@ -453,9 +453,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_flagstat" -LABEL org.opencontainers.image.created="2025-09-01T11:02:59Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:18Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/samtools/samtools_idxstats/.config.vsh.yaml b/target/executable/samtools/samtools_idxstats/.config.vsh.yaml index 58f40f9a..eb86b673 100644 --- a/target/executable/samtools/samtools_idxstats/.config.vsh.yaml +++ b/target/executable/samtools/samtools_idxstats/.config.vsh.yaml @@ -181,7 +181,7 @@ build_info: output: "target/executable/samtools/samtools_idxstats" executable: "target/executable/samtools/samtools_idxstats/samtools_idxstats" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -203,138 +203,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/samtools/samtools_idxstats/samtools_idxstats b/target/executable/samtools/samtools_idxstats/samtools_idxstats index 6f424ce8..77f76960 100755 --- a/target/executable/samtools/samtools_idxstats/samtools_idxstats +++ b/target/executable/samtools/samtools_idxstats/samtools_idxstats @@ -453,9 +453,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_idxstats" -LABEL org.opencontainers.image.created="2025-09-01T11:03:01Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:19Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/samtools/samtools_index/.config.vsh.yaml b/target/executable/samtools/samtools_index/.config.vsh.yaml index 71af9f40..97a80103 100644 --- a/target/executable/samtools/samtools_index/.config.vsh.yaml +++ b/target/executable/samtools/samtools_index/.config.vsh.yaml @@ -187,7 +187,7 @@ build_info: output: "target/executable/samtools/samtools_index" executable: "target/executable/samtools/samtools_index/samtools_index" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -209,138 +209,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/samtools/samtools_index/samtools_index b/target/executable/samtools/samtools_index/samtools_index index fa34d530..c7c5f69c 100755 --- a/target/executable/samtools/samtools_index/samtools_index +++ b/target/executable/samtools/samtools_index/samtools_index @@ -453,9 +453,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_index" -LABEL org.opencontainers.image.created="2025-09-01T11:03:00Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:18Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/samtools/samtools_sort/.config.vsh.yaml b/target/executable/samtools/samtools_sort/.config.vsh.yaml index 1e2535e7..6b6354d2 100644 --- a/target/executable/samtools/samtools_sort/.config.vsh.yaml +++ b/target/executable/samtools/samtools_sort/.config.vsh.yaml @@ -330,7 +330,7 @@ build_info: output: "target/executable/samtools/samtools_sort" executable: "target/executable/samtools/samtools_sort/samtools_sort" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -352,138 +352,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/samtools/samtools_sort/samtools_sort b/target/executable/samtools/samtools_sort/samtools_sort index 997e9b96..3d98bd8e 100755 --- a/target/executable/samtools/samtools_sort/samtools_sort +++ b/target/executable/samtools/samtools_sort/samtools_sort @@ -453,9 +453,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_sort" -LABEL org.opencontainers.image.created="2025-09-01T11:03:01Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:18Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/samtools/samtools_stats/.config.vsh.yaml b/target/executable/samtools/samtools_stats/.config.vsh.yaml index 5d4c942a..569f0853 100644 --- a/target/executable/samtools/samtools_stats/.config.vsh.yaml +++ b/target/executable/samtools/samtools_stats/.config.vsh.yaml @@ -399,7 +399,7 @@ build_info: output: "target/executable/samtools/samtools_stats" executable: "target/executable/samtools/samtools_stats/samtools_stats" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -421,138 +421,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/samtools/samtools_stats/samtools_stats b/target/executable/samtools/samtools_stats/samtools_stats index 8609ddd9..fba564f5 100755 --- a/target/executable/samtools/samtools_stats/samtools_stats +++ b/target/executable/samtools/samtools_stats/samtools_stats @@ -453,9 +453,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_stats" -LABEL org.opencontainers.image.created="2025-09-01T11:03:00Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:18Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/samtools/samtools_view/.config.vsh.yaml b/target/executable/samtools/samtools_view/.config.vsh.yaml index 0a360494..e6953203 100644 --- a/target/executable/samtools/samtools_view/.config.vsh.yaml +++ b/target/executable/samtools/samtools_view/.config.vsh.yaml @@ -663,7 +663,7 @@ build_info: output: "target/executable/samtools/samtools_view" executable: "target/executable/samtools/samtools_view/samtools_view" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -685,138 +685,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/samtools/samtools_view/samtools_view b/target/executable/samtools/samtools_view/samtools_view index 0b877e22..8a71f453 100755 --- a/target/executable/samtools/samtools_view/samtools_view +++ b/target/executable/samtools/samtools_view/samtools_view @@ -453,9 +453,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_view" -LABEL org.opencontainers.image.created="2025-09-01T11:03:00Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:19Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/seqtk/seqtk_sample/.config.vsh.yaml b/target/executable/seqtk/seqtk_sample/.config.vsh.yaml index 5e259ef3..5707f572 100644 --- a/target/executable/seqtk/seqtk_sample/.config.vsh.yaml +++ b/target/executable/seqtk/seqtk_sample/.config.vsh.yaml @@ -176,7 +176,7 @@ build_info: output: "target/executable/seqtk/seqtk_sample" executable: "target/executable/seqtk/seqtk_sample/seqtk_sample" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -198,138 +198,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/seqtk/seqtk_sample/seqtk_sample b/target/executable/seqtk/seqtk_sample/seqtk_sample index 07b42d8e..8518751d 100755 --- a/target/executable/seqtk/seqtk_sample/seqtk_sample +++ b/target/executable/seqtk/seqtk_sample/seqtk_sample @@ -450,9 +450,9 @@ FROM quay.io/biocontainers/seqtk:1.4--he4a0461_2 ENTRYPOINT [] LABEL org.opencontainers.image.authors="Jakub Majercik" LABEL org.opencontainers.image.description="Companion container for running component seqtk seqtk_sample" -LABEL org.opencontainers.image.created="2025-09-01T11:02:57Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:16Z" LABEL org.opencontainers.image.source="https://github.com/lh3/seqtk/tree/v1.4" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/seqtk/seqtk_subseq/.config.vsh.yaml b/target/executable/seqtk/seqtk_subseq/.config.vsh.yaml index 1a44a15a..fda8bb0f 100644 --- a/target/executable/seqtk/seqtk_subseq/.config.vsh.yaml +++ b/target/executable/seqtk/seqtk_subseq/.config.vsh.yaml @@ -195,7 +195,7 @@ build_info: output: "target/executable/seqtk/seqtk_subseq" executable: "target/executable/seqtk/seqtk_subseq/seqtk_subseq" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -217,138 +217,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/seqtk/seqtk_subseq/seqtk_subseq b/target/executable/seqtk/seqtk_subseq/seqtk_subseq index 49648f2f..330f2642 100755 --- a/target/executable/seqtk/seqtk_subseq/seqtk_subseq +++ b/target/executable/seqtk/seqtk_subseq/seqtk_subseq @@ -452,9 +452,9 @@ RUN echo $(echo $(seqtk 2>&1) | sed -n 's/.*\(Version: [^ ]*\).*/\1/p') > /var/s LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component seqtk seqtk_subseq" -LABEL org.opencontainers.image.created="2025-09-01T11:02:56Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:16Z" LABEL org.opencontainers.image.source="https://github.com/lh3/seqtk/tree/v1.4" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/sgdemux/.config.vsh.yaml b/target/executable/sgdemux/.config.vsh.yaml index ac583e55..74ae2f79 100644 --- a/target/executable/sgdemux/.config.vsh.yaml +++ b/target/executable/sgdemux/.config.vsh.yaml @@ -333,6 +333,7 @@ scope: target: "public" requirements: commands: + - "sgdemux" - "ps" keywords: - "demultiplex" @@ -432,7 +433,7 @@ build_info: output: "target/executable/sgdemux" executable: "target/executable/sgdemux/sgdemux" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -454,138 +455,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/sgdemux/sgdemux b/target/executable/sgdemux/sgdemux index 6c678155..889032fa 100755 --- a/target/executable/sgdemux/sgdemux +++ b/target/executable/sgdemux/sgdemux @@ -457,9 +457,9 @@ echo "sgdemux: $(sgdemux --version | cut -d' ' -f2)" > /var/software_versions.tx LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component sgdemux" -LABEL org.opencontainers.image.created="2025-09-01T11:03:00Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:08Z" LABEL org.opencontainers.image.source="https://github.com/Singular-Genomics/singular-demux" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -1276,13 +1276,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'sgdemux' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'sgdemux' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/snpeff/.config.vsh.yaml b/target/executable/snpeff/snpeff_ann/.config.vsh.yaml similarity index 84% rename from target/executable/snpeff/.config.vsh.yaml rename to target/executable/snpeff/snpeff_ann/.config.vsh.yaml index 38b8a551..2e3879d6 100644 --- a/target/executable/snpeff/.config.vsh.yaml +++ b/target/executable/snpeff/snpeff_ann/.config.vsh.yaml @@ -1,4 +1,5 @@ -name: "snpeff" +name: "snpeff_ann" +namespace: "snpeff" version: "main" argument_groups: - name: "Inputs" @@ -20,7 +21,7 @@ argument_groups: description: "Reference genome version." info: null example: - - "GRCh37.75" + - "GRCh38.86" required: true direction: "input" multiple: false @@ -512,6 +513,8 @@ resources: - type: "bash_script" path: "script.sh" is_executable: true +- type: "file" + path: "config.patch" description: "Genetic variant annotation, and functional effect prediction toolbox.\ \ \nIt annotates and predicts the effects of genetic variants on genes and \nproteins\ \ (such as amino acid changes).\n" @@ -611,11 +614,21 @@ runners: engines: - type: "docker" id: "docker" - image: "quay.io/staphb/snpeff:5.2a" + image: "quay.io/staphb/snpeff:5.2f" target_registry: "images.viash-hub.com" target_tag: "main" namespace_separator: "/" setup: + - type: "docker" + copy: + - "config.patch /opt/config.patch" + - type: "apt" + packages: + - "git" + interactive: false + - type: "docker" + run: + - "bash -c \"pushd /snpEff && git apply /opt/config.patch && popd\"\n" - type: "docker" run: - "version=$(snpEff -version) && \\\nversion_trimmed=$(echo \"$version\" | awk\ @@ -625,13 +638,13 @@ engines: - type: "native" id: "native" build_info: - config: "src/snpeff/config.vsh.yaml" + config: "src/snpeff/snpeff_ann/config.vsh.yaml" runner: "executable" engine: "docker|native" - output: "target/executable/snpeff" - executable: "target/executable/snpeff/snpeff" + output: "target/executable/snpeff/snpeff_ann" + executable: "target/executable/snpeff/snpeff_ann/snpeff_ann" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -653,138 +666,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/snpeff/snpeff_ann/config.patch b/target/executable/snpeff/snpeff_ann/config.patch new file mode 100644 index 00000000..1f2970f2 --- /dev/null +++ b/target/executable/snpeff/snpeff_ann/config.patch @@ -0,0 +1,40 @@ +diff --git a/snpEff.config b/snpEff.config +index 3aa2710f..c5ff6926 100644 +--- a/snpEff.config ++++ b/snpEff.config +@@ -24,22 +24,29 @@ data.dir = ./data/ + # Database repository: A URL to the server where you can download databases (command: 'snpEff download dbName') + #--- + +-# Old SourceForge databases +-# database.repository = http://downloads.sourceforge.net/project/snpeff/databases ++# AstraZeneca S3 bucket (ODSP: Oncology Data Science & AI) ++database.repository = https://snpeff.odsp.astrazeneca.com/databases + +-# Secondary Azure blob storage using SAS-Token (Shared Access Signature) ++# Deprecated (2025-08): Azure blob storage (primary) ++#database.repository = https://snpeff.blob.core.windows.net/databases/ ++ ++# Deprecated (2025-08): Azure blob storage (secondary) using SAS-Token (Shared Access Signature) + #database.repository = "https://datasetsnpeff.blob.core.windows.net/dataset" + #database.repositoryKey = "?sv=2019-10-10&st=2020-09-01T00%3A00%3A00Z&se=2050-09-01T00%3A00%3A00Z&si=prod&sr=c&sig=isafOa9tGnYBAvsXFUMDGMTbsG2z%2FShaihzp7JE5dHw%3D" + +-# Primary Azure blob storage +-database.repository = https://snpeff.blob.core.windows.net/databases/ ++# Deprecated (2018-03): SourceForge databases ++#database.repository = http://downloads.sourceforge.net/project/snpeff/databases + + #--- + # Latest version numbers. Check here if there is an update. + #--- +-#versions.url = https://pcingola.github.io/SnpEff/versions.txt ++ ++# Deprecated (2025): Azure versions.txt + versions.url = https://snpeff.blob.core.windows.net/databases/versions.txt + ++# Deprecated (2018): GitHub vertsions.txt ++#versions.url = https://pcingola.github.io/SnpEff/versions.txt ++ + #------------------------------------------------------------------------------- + # Third party databases + #------------------------------------------------------------------------------- diff --git a/target/executable/snpeff/snpeff b/target/executable/snpeff/snpeff_ann/snpeff_ann similarity index 99% rename from target/executable/snpeff/snpeff rename to target/executable/snpeff/snpeff_ann/snpeff_ann index 18d107d9..c309792f 100755 --- a/target/executable/snpeff/snpeff +++ b/target/executable/snpeff/snpeff_ann/snpeff_ann @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# snpeff main +# snpeff_ann main # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -162,8 +162,8 @@ VIASH_META_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}` VIASH_TARGET_DIR=`ViashFindTargetDir $VIASH_META_RESOURCES_DIR` # define meta fields -VIASH_META_NAME="snpeff" -VIASH_META_FUNCTIONALITY_NAME="snpeff" +VIASH_META_NAME="snpeff_ann" +VIASH_META_FUNCTIONALITY_NAME="snpeff_ann" VIASH_META_EXECUTABLE="$VIASH_META_RESOURCES_DIR/$VIASH_META_NAME" VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml" VIASH_META_TEMP_DIR="$VIASH_TEMP" @@ -443,16 +443,23 @@ function ViashDockerfile { if [[ "$engine_id" == "docker" ]]; then cat << 'VIASHDOCKER' -FROM quay.io/staphb/snpeff:5.2a +FROM quay.io/staphb/snpeff:5.2f ENTRYPOINT [] +COPY config.patch /opt/config.patch +RUN apt-get update && \ + DEBIAN_FRONTEND=noninteractive apt-get install -y git && \ + rm -rf /var/lib/apt/lists/* + +RUN bash -c "pushd /snpEff && git apply /opt/config.patch && popd" + RUN version=$(snpEff -version) && \ version_trimmed=$(echo "$version" | awk '{print $1, $2}') && \ echo "$version_trimmed" > /var/software_versions.txt -LABEL org.opencontainers.image.description="Companion container for running component snpeff" -LABEL org.opencontainers.image.created="2025-09-01T11:02:58Z" +LABEL org.opencontainers.image.description="Companion container for running component snpeff snpeff_ann" +LABEL org.opencontainers.image.created="2025-10-03T08:11:07Z" LABEL org.opencontainers.image.source="https://github.com/pcingola/SnpEff" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -570,7 +577,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "snpeff main" + echo "snpeff_ann main" echo "" echo "Genetic variant annotation, and functional effect prediction toolbox." echo "It annotates and predicts the effects of genetic variants on genes and" @@ -584,7 +591,7 @@ function ViashHelp { echo "" echo " --genome_version" echo " type: string, required parameter" - echo " example: GRCh37.75" + echo " example: GRCh38.86" echo " Reference genome version." echo "" echo "Outputs:" @@ -921,7 +928,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "snpeff main" + echo "snpeff_ann main" exit ;; --input) @@ -1575,7 +1582,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/snpeff:main' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/snpeff/snpeff_ann:main' fi # print dockerfile @@ -2353,7 +2360,7 @@ fi ViashDebug "Running command: $(echo $VIASH_CMD)" cat << VIASHEOF | eval $VIASH_CMD set -e -tempscript=\$(mktemp "$VIASH_META_TEMP_DIR/viash-run-snpeff-XXXXXX").sh +tempscript=\$(mktemp "$VIASH_META_TEMP_DIR/viash-run-snpeff_ann-XXXXXX").sh function clean_up { rm "\$tempscript" } @@ -2510,7 +2517,7 @@ done # Run SnpEff -snpEff \\ +snpEff ann \\ \${par_chr:+-chr "\$par_chr"} \\ \${par_classic:+-classic} \\ \${par_csv_stats:+-csvStats "\$par_csv_stats"} \\ diff --git a/target/executable/sortmerna/.config.vsh.yaml b/target/executable/sortmerna/.config.vsh.yaml index 64c7f4e2..34ab1b3a 100644 --- a/target/executable/sortmerna/.config.vsh.yaml +++ b/target/executable/sortmerna/.config.vsh.yaml @@ -597,7 +597,7 @@ build_info: output: "target/executable/sortmerna" executable: "target/executable/sortmerna/sortmerna" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -619,138 +619,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/sortmerna/sortmerna b/target/executable/sortmerna/sortmerna index 5a2a005b..b71e6777 100755 --- a/target/executable/sortmerna/sortmerna +++ b/target/executable/sortmerna/sortmerna @@ -448,9 +448,9 @@ ENTRYPOINT [] RUN echo SortMeRNA: `sortmerna --version | sed -n 's/.*version \([0-9]\+\.[0-9]\+\.[0-9]\+\).*/\1/p'` LABEL org.opencontainers.image.description="Companion container for running component sortmerna" -LABEL org.opencontainers.image.created="2025-09-01T11:03:00Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:08Z" LABEL org.opencontainers.image.source="https://github.com/sortmerna/sortmerna" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/star/star_align_reads/.config.vsh.yaml b/target/executable/star/star_align_reads/.config.vsh.yaml index 8cc0b996..67f9878a 100644 --- a/target/executable/star/star_align_reads/.config.vsh.yaml +++ b/target/executable/star/star_align_reads/.config.vsh.yaml @@ -2545,6 +2545,11 @@ scope: target: "public" requirements: commands: + - "STAR" + - "python" + - "ps" + - "zcat" + - "bzcat" - "ps" keywords: - "align" @@ -2666,7 +2671,7 @@ build_info: output: "target/executable/star/star_align_reads" executable: "target/executable/star/star_align_reads/star_align_reads" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -2688,138 +2693,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/star/star_align_reads/star_align_reads b/target/executable/star/star_align_reads/star_align_reads index 6eba70d5..275b73d0 100755 --- a/target/executable/star/star_align_reads/star_align_reads +++ b/target/executable/star/star_align_reads/star_align_reads @@ -475,9 +475,9 @@ RUN STAR --version | sed 's#\(.*\)#star: "\1"#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component star star_align_reads" -LABEL org.opencontainers.image.created="2025-09-01T11:02:57Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:05Z" LABEL org.opencontainers.image.source="https://github.com/alexdobin/STAR" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -4590,13 +4590,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'STAR' 'python' 'ps' 'zcat' 'bzcat' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'STAR' 'python' 'ps' 'zcat' 'bzcat' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/star/star_genome_generate/.config.vsh.yaml b/target/executable/star/star_genome_generate/.config.vsh.yaml index 78efd30d..04b76256 100644 --- a/target/executable/star/star_genome_generate/.config.vsh.yaml +++ b/target/executable/star/star_genome_generate/.config.vsh.yaml @@ -221,6 +221,7 @@ scope: target: "public" requirements: commands: + - "STAR" - "ps" keywords: - "genome" @@ -331,7 +332,7 @@ build_info: output: "target/executable/star/star_genome_generate" executable: "target/executable/star/star_genome_generate/star_genome_generate" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -353,138 +354,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/star/star_genome_generate/star_genome_generate b/target/executable/star/star_genome_generate/star_genome_generate index 554c1585..a1baf320 100755 --- a/target/executable/star/star_genome_generate/star_genome_generate +++ b/target/executable/star/star_genome_generate/star_genome_generate @@ -467,9 +467,9 @@ RUN STAR --version | sed 's#\(.*\)#star: "\1"#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa" LABEL org.opencontainers.image.description="Companion container for running component star star_genome_generate" -LABEL org.opencontainers.image.created="2025-09-01T11:02:57Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:05Z" LABEL org.opencontainers.image.source="https://github.com/alexdobin/STAR" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -1060,13 +1060,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'STAR' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'STAR' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/trimgalore/.config.vsh.yaml b/target/executable/trimgalore/.config.vsh.yaml index 278fadf1..578faca4 100644 --- a/target/executable/trimgalore/.config.vsh.yaml +++ b/target/executable/trimgalore/.config.vsh.yaml @@ -668,6 +668,7 @@ scope: target: "public" requirements: commands: + - "trim_galore" - "ps" keywords: - "trimming" @@ -768,7 +769,7 @@ build_info: output: "target/executable/trimgalore" executable: "target/executable/trimgalore/trimgalore" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -790,138 +791,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/trimgalore/trimgalore b/target/executable/trimgalore/trimgalore index 2f30cb58..14fc040c 100755 --- a/target/executable/trimgalore/trimgalore +++ b/target/executable/trimgalore/trimgalore @@ -452,9 +452,9 @@ RUN echo "TrimGalore: `trim_galore --version | sed -n 's/.*version\s\+\([0-9]\+\ LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa" LABEL org.opencontainers.image.description="Companion container for running component trimgalore" -LABEL org.opencontainers.image.created="2025-09-01T11:02:57Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:16Z" LABEL org.opencontainers.image.source="https://github.com/FelixKrueger/TrimGalore" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -1692,13 +1692,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # build docker image elif [ "$VIASH_MODE" == "setup" ]; then ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'trim_galore' 'ps' 'bash' exit 0 fi # check if docker image exists ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild - ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'trim_galore' 'ps' 'bash' fi # setting computational defaults diff --git a/target/executable/umi_tools/umi_tools_dedup/.config.vsh.yaml b/target/executable/umi_tools/umi_tools_dedup/.config.vsh.yaml index 7edd3ca6..682013ce 100644 --- a/target/executable/umi_tools/umi_tools_dedup/.config.vsh.yaml +++ b/target/executable/umi_tools/umi_tools_dedup/.config.vsh.yaml @@ -609,7 +609,7 @@ build_info: output: "target/executable/umi_tools/umi_tools_dedup" executable: "target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -631,138 +631,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup b/target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup index c227d3d8..26c1f37b 100755 --- a/target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup +++ b/target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup @@ -452,9 +452,9 @@ RUN umi_tools -v | sed 's/ version//g' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component umi_tools umi_tools_dedup" -LABEL org.opencontainers.image.created="2025-09-01T11:02:48Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:13Z" LABEL org.opencontainers.image.source="https://github.com/CGATOxford/UMI-tools" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/umi_tools/umi_tools_extract/.config.vsh.yaml b/target/executable/umi_tools/umi_tools_extract/.config.vsh.yaml index cee6c3f7..f0682a8f 100644 --- a/target/executable/umi_tools/umi_tools_extract/.config.vsh.yaml +++ b/target/executable/umi_tools/umi_tools_extract/.config.vsh.yaml @@ -437,7 +437,7 @@ build_info: output: "target/executable/umi_tools/umi_tools_extract" executable: "target/executable/umi_tools/umi_tools_extract/umi_tools_extract" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -459,138 +459,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/umi_tools/umi_tools_extract/umi_tools_extract b/target/executable/umi_tools/umi_tools_extract/umi_tools_extract index be3b8477..bea9341d 100755 --- a/target/executable/umi_tools/umi_tools_extract/umi_tools_extract +++ b/target/executable/umi_tools/umi_tools_extract/umi_tools_extract @@ -448,9 +448,9 @@ ENTRYPOINT [] RUN umi_tools -v | sed 's/ version//g' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component umi_tools umi_tools_extract" -LABEL org.opencontainers.image.created="2025-09-01T11:02:48Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:14Z" LABEL org.opencontainers.image.source="https://github.com/CGATOxford/UMI-tools" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/umi_tools/umi_tools_prepareforrsem/.config.vsh.yaml b/target/executable/umi_tools/umi_tools_prepareforrsem/.config.vsh.yaml index 12b5b35c..8c37688e 100644 --- a/target/executable/umi_tools/umi_tools_prepareforrsem/.config.vsh.yaml +++ b/target/executable/umi_tools/umi_tools_prepareforrsem/.config.vsh.yaml @@ -259,7 +259,7 @@ build_info: output: "target/executable/umi_tools/umi_tools_prepareforrsem" executable: "target/executable/umi_tools/umi_tools_prepareforrsem/umi_tools_prepareforrsem" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -281,138 +281,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/umi_tools/umi_tools_prepareforrsem/umi_tools_prepareforrsem b/target/executable/umi_tools/umi_tools_prepareforrsem/umi_tools_prepareforrsem index 99105983..072d7d40 100755 --- a/target/executable/umi_tools/umi_tools_prepareforrsem/umi_tools_prepareforrsem +++ b/target/executable/umi_tools/umi_tools_prepareforrsem/umi_tools_prepareforrsem @@ -448,9 +448,9 @@ ENTRYPOINT [] RUN umi_tools -v | sed 's/ version//g' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component umi_tools umi_tools_prepareforrsem" -LABEL org.opencontainers.image.created="2025-09-01T11:02:48Z" +LABEL org.opencontainers.image.created="2025-10-03T08:11:14Z" LABEL org.opencontainers.image.source="https://github.com/CGATOxford/UMI-tools" -LABEL org.opencontainers.image.revision="7158daa5f609274a6d98fd196a7e84e302717216" +LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/nextflow/agat/agat_convert_bed2gff/.config.vsh.yaml b/target/nextflow/agat/agat_convert_bed2gff/.config.vsh.yaml index 3cb7ce95..23875096 100644 --- a/target/nextflow/agat/agat_convert_bed2gff/.config.vsh.yaml +++ b/target/nextflow/agat/agat_convert_bed2gff/.config.vsh.yaml @@ -133,6 +133,7 @@ scope: target: "public" requirements: commands: + - "agat_convert_bed2gff.pl" - "ps" keywords: - "gene annotations" @@ -233,7 +234,7 @@ build_info: output: "target/nextflow/agat/agat_convert_bed2gff" executable: "target/nextflow/agat/agat_convert_bed2gff/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -255,138 +256,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/agat/agat_convert_bed2gff/main.nf b/target/nextflow/agat/agat_convert_bed2gff/main.nf index 4396bba7..69382d36 100644 --- a/target/nextflow/agat/agat_convert_bed2gff/main.nf +++ b/target/nextflow/agat/agat_convert_bed2gff/main.nf @@ -3193,6 +3193,7 @@ meta = [ }, "requirements" : { "commands" : [ + "agat_convert_bed2gff.pl", "ps" ] }, @@ -3314,7 +3315,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/agat_convert_bed2gff", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3326,225 +3327,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/agat/agat_convert_embl2gff/.config.vsh.yaml b/target/nextflow/agat/agat_convert_embl2gff/.config.vsh.yaml index eb951465..8dd49364 100644 --- a/target/nextflow/agat/agat_convert_embl2gff/.config.vsh.yaml +++ b/target/nextflow/agat/agat_convert_embl2gff/.config.vsh.yaml @@ -123,6 +123,7 @@ scope: target: "public" requirements: commands: + - "agat_convert_embl2gff.pl" - "ps" keywords: - "gene annotations" @@ -223,7 +224,7 @@ build_info: output: "target/nextflow/agat/agat_convert_embl2gff" executable: "target/nextflow/agat/agat_convert_embl2gff/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -245,138 +246,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/agat/agat_convert_embl2gff/main.nf b/target/nextflow/agat/agat_convert_embl2gff/main.nf index d6be8ce5..3a2553be 100644 --- a/target/nextflow/agat/agat_convert_embl2gff/main.nf +++ b/target/nextflow/agat/agat_convert_embl2gff/main.nf @@ -3186,6 +3186,7 @@ meta = [ }, "requirements" : { "commands" : [ + "agat_convert_embl2gff.pl", "ps" ] }, @@ -3307,7 +3308,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/agat_convert_embl2gff", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3319,225 +3320,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/agat/agat_convert_genscan2gff/.config.vsh.yaml b/target/nextflow/agat/agat_convert_genscan2gff/.config.vsh.yaml index 3dfaf285..387e1ac3 100644 --- a/target/nextflow/agat/agat_convert_genscan2gff/.config.vsh.yaml +++ b/target/nextflow/agat/agat_convert_genscan2gff/.config.vsh.yaml @@ -127,6 +127,7 @@ scope: target: "public" requirements: commands: + - "agat_convert_genscan2gff.pl" - "ps" keywords: - "gene annotations" @@ -228,7 +229,7 @@ build_info: output: "target/nextflow/agat/agat_convert_genscan2gff" executable: "target/nextflow/agat/agat_convert_genscan2gff/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -250,138 +251,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/agat/agat_convert_genscan2gff/main.nf b/target/nextflow/agat/agat_convert_genscan2gff/main.nf index cfbc8c57..cfaf2fbb 100644 --- a/target/nextflow/agat/agat_convert_genscan2gff/main.nf +++ b/target/nextflow/agat/agat_convert_genscan2gff/main.nf @@ -3187,6 +3187,7 @@ meta = [ }, "requirements" : { "commands" : [ + "agat_convert_genscan2gff.pl", "ps" ] }, @@ -3309,7 +3310,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/agat_convert_genscan2gff", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3321,225 +3322,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/agat/agat_convert_mfannot2gff/.config.vsh.yaml b/target/nextflow/agat/agat_convert_mfannot2gff/.config.vsh.yaml index f459b2b4..4ab53ae8 100644 --- a/target/nextflow/agat/agat_convert_mfannot2gff/.config.vsh.yaml +++ b/target/nextflow/agat/agat_convert_mfannot2gff/.config.vsh.yaml @@ -83,6 +83,7 @@ scope: target: "public" requirements: commands: + - "agat_convert_mfannot2gff.pl" - "ps" keywords: - "gene annotations" @@ -184,7 +185,7 @@ build_info: output: "target/nextflow/agat/agat_convert_mfannot2gff" executable: "target/nextflow/agat/agat_convert_mfannot2gff/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -206,138 +207,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/agat/agat_convert_mfannot2gff/main.nf b/target/nextflow/agat/agat_convert_mfannot2gff/main.nf index 25c6c454..b6611e6a 100644 --- a/target/nextflow/agat/agat_convert_mfannot2gff/main.nf +++ b/target/nextflow/agat/agat_convert_mfannot2gff/main.nf @@ -3147,6 +3147,7 @@ meta = [ }, "requirements" : { "commands" : [ + "agat_convert_mfannot2gff.pl", "ps" ] }, @@ -3269,7 +3270,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/agat_convert_mfannot2gff", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3281,225 +3282,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml b/target/nextflow/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml index 485eeb13..de10e2b3 100644 --- a/target/nextflow/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml +++ b/target/nextflow/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml @@ -126,6 +126,7 @@ scope: target: "public" requirements: commands: + - "agat_convert_sp_gff2gtf.pl" - "ps" keywords: - "gene annotations" @@ -226,7 +227,7 @@ build_info: output: "target/nextflow/agat/agat_convert_sp_gff2gtf" executable: "target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -248,138 +249,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf b/target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf index daad18fa..52c1a60e 100644 --- a/target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf +++ b/target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf @@ -3169,6 +3169,7 @@ meta = [ }, "requirements" : { "commands" : [ + "agat_convert_sp_gff2gtf.pl", "ps" ] }, @@ -3290,7 +3291,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/agat_convert_sp_gff2gtf", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3302,225 +3303,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml b/target/nextflow/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml index 87c49901..7251ae6e 100644 --- a/target/nextflow/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml +++ b/target/nextflow/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml @@ -86,6 +86,7 @@ scope: target: "public" requirements: commands: + - "agat_convert_sp_gff2tsv.pl" - "ps" keywords: - "gene annotations" @@ -186,7 +187,7 @@ build_info: output: "target/nextflow/agat/agat_convert_sp_gff2tsv" executable: "target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -208,138 +209,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf b/target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf index fc639f3e..96ceb8a4 100644 --- a/target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf +++ b/target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf @@ -3147,6 +3147,7 @@ meta = [ }, "requirements" : { "commands" : [ + "agat_convert_sp_gff2tsv.pl", "ps" ] }, @@ -3268,7 +3269,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/agat_convert_sp_gff2tsv", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3280,225 +3281,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml b/target/nextflow/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml index d06ded8c..fad27035 100644 --- a/target/nextflow/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml +++ b/target/nextflow/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml @@ -93,6 +93,7 @@ scope: target: "public" requirements: commands: + - "agat_convert_sp_gxf2gxf.pl" - "ps" keywords: - "gene annotations" @@ -193,7 +194,7 @@ build_info: output: "target/nextflow/agat/agat_convert_sp_gxf2gxf" executable: "target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -215,138 +216,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf b/target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf index da8d4e04..f1f458eb 100644 --- a/target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf +++ b/target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf @@ -3147,6 +3147,7 @@ meta = [ }, "requirements" : { "commands" : [ + "agat_convert_sp_gxf2gxf.pl", "ps" ] }, @@ -3268,7 +3269,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/agat_convert_sp_gxf2gxf", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3280,225 +3281,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/agat/agat_sp_add_introns/.config.vsh.yaml b/target/nextflow/agat/agat_sp_add_introns/.config.vsh.yaml index 3a6e54d7..f4eff9c7 100644 --- a/target/nextflow/agat/agat_sp_add_introns/.config.vsh.yaml +++ b/target/nextflow/agat/agat_sp_add_introns/.config.vsh.yaml @@ -84,6 +84,7 @@ scope: target: "public" requirements: commands: + - "agat_sp_add_introns.pl" - "ps" keywords: - "gene annotations" @@ -184,7 +185,7 @@ build_info: output: "target/nextflow/agat/agat_sp_add_introns" executable: "target/nextflow/agat/agat_sp_add_introns/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -206,138 +207,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/agat/agat_sp_add_introns/main.nf b/target/nextflow/agat/agat_sp_add_introns/main.nf index 357e2bf8..1809b34e 100644 --- a/target/nextflow/agat/agat_sp_add_introns/main.nf +++ b/target/nextflow/agat/agat_sp_add_introns/main.nf @@ -3150,6 +3150,7 @@ meta = [ }, "requirements" : { "commands" : [ + "agat_sp_add_introns.pl", "ps" ] }, @@ -3271,7 +3272,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/agat_sp_add_introns", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3283,225 +3284,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/agat/agat_sp_filter_feature_from_kill_list/.config.vsh.yaml b/target/nextflow/agat/agat_sp_filter_feature_from_kill_list/.config.vsh.yaml index 37e55571..e779d4cf 100644 --- a/target/nextflow/agat/agat_sp_filter_feature_from_kill_list/.config.vsh.yaml +++ b/target/nextflow/agat/agat_sp_filter_feature_from_kill_list/.config.vsh.yaml @@ -133,6 +133,7 @@ scope: target: "public" requirements: commands: + - "agat_sp_filter_feature_from_kill_list.pl" - "ps" keywords: - "gene annotations" @@ -234,7 +235,7 @@ build_info: output: "target/nextflow/agat/agat_sp_filter_feature_from_kill_list" executable: "target/nextflow/agat/agat_sp_filter_feature_from_kill_list/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -256,138 +257,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/agat/agat_sp_filter_feature_from_kill_list/main.nf b/target/nextflow/agat/agat_sp_filter_feature_from_kill_list/main.nf index d778578d..df3805b8 100644 --- a/target/nextflow/agat/agat_sp_filter_feature_from_kill_list/main.nf +++ b/target/nextflow/agat/agat_sp_filter_feature_from_kill_list/main.nf @@ -3196,6 +3196,7 @@ meta = [ }, "requirements" : { "commands" : [ + "agat_sp_filter_feature_from_kill_list.pl", "ps" ] }, @@ -3318,7 +3319,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/agat_sp_filter_feature_from_kill_list", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3330,225 +3331,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/agat/agat_sp_merge_annotations/.config.vsh.yaml b/target/nextflow/agat/agat_sp_merge_annotations/.config.vsh.yaml index 955c6d46..162fe036 100644 --- a/target/nextflow/agat/agat_sp_merge_annotations/.config.vsh.yaml +++ b/target/nextflow/agat/agat_sp_merge_annotations/.config.vsh.yaml @@ -81,6 +81,7 @@ scope: target: "public" requirements: commands: + - "agat_sp_merge_annotations.pl" - "ps" keywords: - "gene annotations" @@ -182,7 +183,7 @@ build_info: output: "target/nextflow/agat/agat_sp_merge_annotations" executable: "target/nextflow/agat/agat_sp_merge_annotations/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -204,138 +205,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/agat/agat_sp_merge_annotations/main.nf b/target/nextflow/agat/agat_sp_merge_annotations/main.nf index 3e88d2d6..e43bbdf8 100644 --- a/target/nextflow/agat/agat_sp_merge_annotations/main.nf +++ b/target/nextflow/agat/agat_sp_merge_annotations/main.nf @@ -3146,6 +3146,7 @@ meta = [ }, "requirements" : { "commands" : [ + "agat_sp_merge_annotations.pl", "ps" ] }, @@ -3268,7 +3269,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/agat_sp_merge_annotations", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3280,225 +3281,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/agat/agat_sp_statistics/.config.vsh.yaml b/target/nextflow/agat/agat_sp_statistics/.config.vsh.yaml index 6c130f2d..c1a59989 100644 --- a/target/nextflow/agat/agat_sp_statistics/.config.vsh.yaml +++ b/target/nextflow/agat/agat_sp_statistics/.config.vsh.yaml @@ -128,6 +128,7 @@ scope: target: "public" requirements: commands: + - "agat_sp_statistics.pl" - "ps" keywords: - "gene annotations" @@ -229,7 +230,7 @@ build_info: output: "target/nextflow/agat/agat_sp_statistics" executable: "target/nextflow/agat/agat_sp_statistics/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -251,138 +252,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/agat/agat_sp_statistics/main.nf b/target/nextflow/agat/agat_sp_statistics/main.nf index 36bc1436..c9459514 100644 --- a/target/nextflow/agat/agat_sp_statistics/main.nf +++ b/target/nextflow/agat/agat_sp_statistics/main.nf @@ -3196,6 +3196,7 @@ meta = [ }, "requirements" : { "commands" : [ + "agat_sp_statistics.pl", "ps" ] }, @@ -3318,7 +3319,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/agat_sp_statistics", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3330,225 +3331,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/agat/agat_sq_stat_basic/.config.vsh.yaml b/target/nextflow/agat/agat_sq_stat_basic/.config.vsh.yaml index d21b81d3..1bf54a6c 100644 --- a/target/nextflow/agat/agat_sq_stat_basic/.config.vsh.yaml +++ b/target/nextflow/agat/agat_sq_stat_basic/.config.vsh.yaml @@ -124,6 +124,7 @@ scope: target: "public" requirements: commands: + - "agat_sq_stat_basic.pl" - "ps" keywords: - "gene annotations" @@ -225,7 +226,7 @@ build_info: output: "target/nextflow/agat/agat_sq_stat_basic" executable: "target/nextflow/agat/agat_sq_stat_basic/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -247,138 +248,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/agat/agat_sq_stat_basic/main.nf b/target/nextflow/agat/agat_sq_stat_basic/main.nf index 59016778..1f34bc0d 100644 --- a/target/nextflow/agat/agat_sq_stat_basic/main.nf +++ b/target/nextflow/agat/agat_sq_stat_basic/main.nf @@ -3182,6 +3182,7 @@ meta = [ }, "requirements" : { "commands" : [ + "agat_sq_stat_basic.pl", "ps" ] }, @@ -3304,7 +3305,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/agat_sq_stat_basic", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3316,225 +3317,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/arriba/.config.vsh.yaml b/target/nextflow/arriba/.config.vsh.yaml index fc7dc5b4..ba48ab6b 100644 --- a/target/nextflow/arriba/.config.vsh.yaml +++ b/target/nextflow/arriba/.config.vsh.yaml @@ -26,7 +26,10 @@ argument_groups: alternatives: - "-x" description: "File in SAM/BAM/CRAM format with main alignments as generated by\ - \ STAR\n(Aligned.out.sam). Arriba extracts candidate reads from this file.\n" + \ STAR\n(Aligned.out.sam). **Important**: The BAM file must be generated by\ + \ STAR with \nchimeric alignment parameters, specifically `--chimOutType WithinBAM\ + \ HardClip`. \nArriba extracts candidate reads from this file, including both\ + \ normal and \nchimeric alignments.\n" info: null example: - "Aligned.out.bam" @@ -594,33 +597,50 @@ resources: - type: "bash_script" path: "script.sh" is_executable: true -description: "Detect gene fusions from RNA-Seq data" +description: "Arriba is a command-line tool for the detection of gene fusions from\ + \ RNA-Seq data. It was developed for the use in a clinical research setting. Therefore,\ + \ short runtimes and high sensitivity were important design criteria.\n\nArriba\ + \ is based on the STAR RNA-Seq aligner and post-processes the alignments (output\ + \ from STAR) to:\n\n1. detect split reads and discordant mates, which are indicative\ + \ of structural rearrangements,\n2. find reads supporting gene fusions (i.e., reads\ + \ spanning the breakpoints of gene fusions),\n3. perform various filtering steps\ + \ to remove false positives, and\n4. output the final predictions in a standardized\ + \ format.\n\nIn contrast to many other fusion detection tools, Arriba does not require\ + \ to reduce the STAR parameter `--alignIntronMax` (maximum intron size). Reducing\ + \ this parameter impairs detection of long introns and may affect expression quantification.\ + \ Arriba reliably filters translocation-based false positives even when large maximum\ + \ intron sizes are used.\n\n**Important**: Arriba requires BAM files that were aligned\ + \ with STAR using specific chimeric alignment parameters, particularly `--chimOutType\ + \ WithinBAM HardClip`. See the [official workflow documentation](https://github.com/suhrig/arriba/blob/master/run_arriba.sh)\ + \ for the complete set of recommended STAR parameters.\n" test_resources: - type: "bash_script" path: "test.sh" is_executable: true - type: "file" - path: "test_data" + path: "test_helpers.sh" info: null status: "enabled" scope: image: "public" target: "public" requirements: - cpus: 1 commands: + - "arriba" - "ps" keywords: - "Gene fusion" - "RNA-Seq" +- "Structural variants" +- "Chimeric alignments" license: "MIT" references: doi: - "10.1101/gr.257246.119" links: repository: "https://github.com/suhrig/arriba" - homepage: "https://arriba.readthedocs.io/en/latest/" - documentation: "https://arriba.readthedocs.io/en/latest/" + homepage: "https://arriba.readthedocs.io/" + documentation: "https://arriba.readthedocs.io/" runners: - type: "executable" id: "executable" @@ -689,15 +709,15 @@ runners: engines: - type: "docker" id: "docker" - image: "quay.io/biocontainers/arriba:2.4.0--h0033a41_2" + image: "quay.io/biocontainers/arriba:2.5.0--h87b9561_1" target_registry: "images.viash-hub.com" target_tag: "main" namespace_separator: "/" setup: - type: "docker" run: - - "arriba -h | grep 'Version:' 2>&1 | sed 's/Version:\\s\\(.*\\)/arriba: \"\\\ - 1\"/' > /var/software_versions.txt\n" + - "arriba -h 2>&1 | head -5 | grep 'Version:' | sed 's/Version:\\s\\(.*\\)/arriba:\ + \ \"\\1\"/' > /var/software_versions.txt\n" entrypoint: [] cmd: null - type: "native" @@ -709,7 +729,7 @@ build_info: output: "target/nextflow/arriba" executable: "target/nextflow/arriba/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -731,138 +751,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/arriba/main.nf b/target/nextflow/arriba/main.nf index eb5bdb04..3430e72a 100644 --- a/target/nextflow/arriba/main.nf +++ b/target/nextflow/arriba/main.nf @@ -3074,7 +3074,7 @@ meta = [ "alternatives" : [ "-x" ], - "description" : "File in SAM/BAM/CRAM format with main alignments as generated by STAR\n(Aligned.out.sam). Arriba extracts candidate reads from this file.\n", + "description" : "File in SAM/BAM/CRAM format with main alignments as generated by STAR\n(Aligned.out.sam). **Important**: The BAM file must be generated by STAR with \nchimeric alignment parameters, specifically `--chimOutType WithinBAM HardClip`. \nArriba extracts candidate reads from this file, including both normal and \nchimeric alignments.\n", "example" : [ "Aligned.out.bam" ], @@ -3682,7 +3682,7 @@ meta = [ "is_executable" : true } ], - "description" : "Detect gene fusions from RNA-Seq data", + "description" : "Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data. It was developed for the use in a clinical research setting. Therefore, short runtimes and high sensitivity were important design criteria.\n\nArriba is based on the STAR RNA-Seq aligner and post-processes the alignments (output from STAR) to:\n\n1. detect split reads and discordant mates, which are indicative of structural rearrangements,\n2. find reads supporting gene fusions (i.e., reads spanning the breakpoints of gene fusions),\n3. perform various filtering steps to remove false positives, and\n4. output the final predictions in a standardized format.\n\nIn contrast to many other fusion detection tools, Arriba does not require to reduce the STAR parameter `--alignIntronMax` (maximum intron size). Reducing this parameter impairs detection of long introns and may affect expression quantification. Arriba reliably filters translocation-based false positives even when large maximum intron sizes are used.\n\n**Important**: Arriba requires BAM files that were aligned with STAR using specific chimeric alignment parameters, particularly `--chimOutType WithinBAM HardClip`. See the [official workflow documentation](https://github.com/suhrig/arriba/blob/master/run_arriba.sh) for the complete set of recommended STAR parameters.\n", "test_resources" : [ { "type" : "bash_script", @@ -3691,7 +3691,7 @@ meta = [ }, { "type" : "file", - "path" : "test_data" + "path" : "/src/_utils/test_helpers.sh" } ], "status" : "enabled", @@ -3700,14 +3700,16 @@ meta = [ "target" : "public" }, "requirements" : { - "cpus" : 1, "commands" : [ + "arriba", "ps" ] }, "keywords" : [ "Gene fusion", - "RNA-Seq" + "RNA-Seq", + "Structural variants", + "Chimeric alignments" ], "license" : "MIT", "references" : { @@ -3717,8 +3719,8 @@ meta = [ }, "links" : { "repository" : "https://github.com/suhrig/arriba", - "homepage" : "https://arriba.readthedocs.io/en/latest/", - "documentation" : "https://arriba.readthedocs.io/en/latest/" + "homepage" : "https://arriba.readthedocs.io/", + "documentation" : "https://arriba.readthedocs.io/" }, "runners" : [ { @@ -3798,7 +3800,7 @@ meta = [ { "type" : "docker", "id" : "docker", - "image" : "quay.io/biocontainers/arriba:2.4.0--h0033a41_2", + "image" : "quay.io/biocontainers/arriba:2.5.0--h87b9561_1", "target_registry" : "images.viash-hub.com", "target_tag" : "main", "namespace_separator" : "/", @@ -3806,7 +3808,7 @@ meta = [ { "type" : "docker", "run" : [ - "arriba -h | grep 'Version:' 2>&1 | sed 's/Version:\\\\s\\\\(.*\\\\)/arriba: \\"\\\\1\\"/' > /var/software_versions.txt\n" + "arriba -h 2>&1 | head -5 | grep 'Version:' | sed 's/Version:\\\\s\\\\(.*\\\\)/arriba: \\"\\\\1\\"/' > /var/software_versions.txt\n" ] } ] @@ -3822,7 +3824,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/arriba", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3834,225 +3836,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", @@ -4139,55 +3927,80 @@ $( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}" ## VIASH END -# unset flags +set -eo pipefail + +# unset boolean flags that are "false" [[ "\\$par_skip_duplicate_marking" == "false" ]] && unset par_skip_duplicate_marking [[ "\\$par_extra_information" == "false" ]] && unset par_extra_information [[ "\\$par_fill_gaps" == "false" ]] && unset par_fill_gaps -# replace ';' with ',' -par_interesting_contigs=\\$(echo \\$par_interesting_contigs | tr ';' ',') -par_viral_contigs=\\$(echo \\$par_viral_contigs | tr ';' ',') -par_disable_filters=\\$(echo \\$par_disable_filters | tr ';' ',') +# process multi-value parameters: replace ';' with ',' for arriba compatibility +if [[ -n "\\${par_interesting_contigs:-}" ]]; then + par_interesting_contigs=\\$(echo "\\$par_interesting_contigs" | tr ';' ',') +fi +if [[ -n "\\${par_viral_contigs:-}" ]]; then + par_viral_contigs=\\$(echo "\\$par_viral_contigs" | tr ';' ',') +fi +if [[ -n "\\${par_disable_filters:-}" ]]; then + par_disable_filters=\\$(echo "\\$par_disable_filters" | tr ';' ',') +fi -# run arriba -arriba \\\\ - -x "\\$par_bam" \\\\ - -a "\\$par_genome" \\\\ - -g "\\$par_gene_annotation" \\\\ - -o "\\$par_fusions" \\\\ - \\${par_known_fusions:+-k "\\${par_known_fusions}"} \\\\ - \\${par_blacklist:+-b "\\${par_blacklist}"} \\\\ - \\${par_structural_variants:+-d "\\${par_structural_variants}"} \\\\ - \\${par_tags:+-t "\\${par_tags}"} \\\\ - \\${par_protein_domains:+-p "\\${par_protein_domains}"} \\\\ - \\${par_fusions_discarded:+-O "\\${par_fusions_discarded}"} \\\\ - \\${par_max_genomic_breakpoint_distance:+-D "\\${par_max_genomic_breakpoint_distance}"} \\\\ - \\${par_strandedness:+-s "\\${par_strandedness}"} \\\\ - \\${par_interesting_contigs:+-i "\\${par_interesting_contigs}"} \\\\ - \\${par_viral_contigs:+-v "\\${par_viral_contigs}"} \\\\ - \\${par_disable_filters:+-f "\\${par_disable_filters}"} \\\\ - \\${par_max_e_value:+-E "\\${par_max_e_value}"} \\\\ - \\${par_min_supporting_reads:+-S "\\${par_min_supporting_reads}"} \\\\ - \\${par_max_mismappers:+-m "\\${par_max_mismappers}"} \\\\ - \\${par_max_homolog_identity:+-L "\\${par_max_homolog_identity}"} \\\\ - \\${par_homopolymer_length:+-H "\\${par_homopolymer_length}"} \\\\ - \\${par_read_through_distance:+-R "\\${par_read_through_distance}"} \\\\ - \\${par_min_anchor_length:+-A "\\${par_min_anchor_length}"} \\\\ - \\${par_many_spliced_events:+-M "\\${par_many_spliced_events}"} \\\\ - \\${par_max_kmer_content:+-K "\\${par_max_kmer_content}"} \\\\ - \\${par_max_mismatch_pvalue:+-V "\\${par_max_mismatch_pvalue}"} \\\\ - \\${par_fragment_length:+-F "\\${par_fragment_length}"} \\\\ - \\${par_max_reads:+-U "\\${par_max_reads}"} \\\\ - \\${par_quantile:+-Q "\\${par_quantile}"} \\\\ - \\${par_exonic_fraction:+-e "\\${par_exonic_fraction}"} \\\\ - \\${par_top_n:+-T "\\${par_top_n}"} \\\\ - \\${par_covered_fraction:+-C "\\${par_covered_fraction}"} \\\\ - \\${par_max_itd_length:+-l "\\${par_max_itd_length}"} \\\\ - \\${par_min_itd_allele_fraction:+-z "\\${par_min_itd_allele_fraction}"} \\\\ - \\${par_min_itd_supporting_reads:+-Z "\\${par_min_itd_supporting_reads}"} \\\\ - \\${par_skip_duplicate_marking:+-u} \\\\ - \\${par_extra_information:+-X} \\\\ +# build command arguments array +cmd_args=( + # required arguments + -x "\\$par_bam" + -a "\\$par_genome" + -g "\\$par_gene_annotation" + -o "\\$par_fusions" + + # optional input files + \\${par_known_fusions:+-k "\\$par_known_fusions"} + \\${par_blacklist:+-b "\\$par_blacklist"} + \\${par_structural_variants:+-d "\\$par_structural_variants"} + \\${par_tags:+-t "\\$par_tags"} + \\${par_protein_domains:+-p "\\$par_protein_domains"} + + # optional output files + \\${par_fusions_discarded:+-O "\\$par_fusions_discarded"} + + # filter and analysis options + \\${par_max_genomic_breakpoint_distance:+-D "\\$par_max_genomic_breakpoint_distance"} + \\${par_strandedness:+-s "\\$par_strandedness"} + \\${par_interesting_contigs:+-i "\\$par_interesting_contigs"} + \\${par_viral_contigs:+-v "\\$par_viral_contigs"} + \\${par_disable_filters:+-f "\\$par_disable_filters"} + + # statistical thresholds + \\${par_max_e_value:+-E "\\$par_max_e_value"} + \\${par_min_supporting_reads:+-S "\\$par_min_supporting_reads"} + \\${par_max_mismappers:+-m "\\$par_max_mismappers"} + \\${par_max_homolog_identity:+-L "\\$par_max_homolog_identity"} + \\${par_homopolymer_length:+-H "\\$par_homopolymer_length"} + \\${par_read_through_distance:+-R "\\$par_read_through_distance"} + \\${par_min_anchor_length:+-A "\\$par_min_anchor_length"} + \\${par_many_spliced_events:+-M "\\$par_many_spliced_events"} + \\${par_max_kmer_content:+-K "\\$par_max_kmer_content"} + \\${par_max_mismatch_pvalue:+-V "\\$par_max_mismatch_pvalue"} + \\${par_fragment_length:+-F "\\$par_fragment_length"} + \\${par_max_reads:+-U "\\$par_max_reads"} + \\${par_quantile:+-Q "\\$par_quantile"} + \\${par_exonic_fraction:+-e "\\$par_exonic_fraction"} + \\${par_top_n:+-T "\\$par_top_n"} + \\${par_covered_fraction:+-C "\\$par_covered_fraction"} + + # internal tandem duplication options + \\${par_max_itd_length:+-l "\\$par_max_itd_length"} + \\${par_min_itd_allele_fraction:+-z "\\$par_min_itd_allele_fraction"} + \\${par_min_itd_supporting_reads:+-Z "\\$par_min_itd_supporting_reads"} + + # boolean flags + \\${par_skip_duplicate_marking:+-u} + \\${par_extra_information:+-X} \\${par_fill_gaps:+-I} +) + +# execute arriba +arriba "\\${cmd_args[@]}" VIASHMAIN bash "$tempscript" ''' @@ -4572,7 +4385,6 @@ meta["defaults"] = [ "image" : "vsh/biobox/arriba", "tag" : "main" }, - "cpus" : 1, "tag" : "$id" }'''), diff --git a/target/nextflow/arriba/nextflow.config b/target/nextflow/arriba/nextflow.config index 4c8611ff..f5a0e222 100644 --- a/target/nextflow/arriba/nextflow.config +++ b/target/nextflow/arriba/nextflow.config @@ -3,7 +3,7 @@ manifest { mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' version = 'main' - description = 'Detect gene fusions from RNA-Seq data' + description = 'Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data. It was developed for the use in a clinical research setting. Therefore, short runtimes and high sensitivity were important design criteria.\n\nArriba is based on the STAR RNA-Seq aligner and post-processes the alignments (output from STAR) to:\n\n1. detect split reads and discordant mates, which are indicative of structural rearrangements,\n2. find reads supporting gene fusions (i.e., reads spanning the breakpoints of gene fusions),\n3. perform various filtering steps to remove false positives, and\n4. output the final predictions in a standardized format.\n\nIn contrast to many other fusion detection tools, Arriba does not require to reduce the STAR parameter `--alignIntronMax` (maximum intron size). Reducing this parameter impairs detection of long introns and may affect expression quantification. Arriba reliably filters translocation-based false positives even when large maximum intron sizes are used.\n\n**Important**: Arriba requires BAM files that were aligned with STAR using specific chimeric alignment parameters, particularly `--chimOutType WithinBAM HardClip`. See the [official workflow documentation](https://github.com/suhrig/arriba/blob/master/run_arriba.sh) for the complete set of recommended STAR parameters.\n' author = 'Robrecht Cannoodt' } diff --git a/target/nextflow/arriba/nextflow_schema.json b/target/nextflow/arriba/nextflow_schema.json index 190a60dc..f802ccc0 100644 --- a/target/nextflow/arriba/nextflow_schema.json +++ b/target/nextflow/arriba/nextflow_schema.json @@ -1,7 +1,7 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", "title": "arriba", - "description": "Detect gene fusions from RNA-Seq data", + "description": "Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data. It was developed for the use in a clinical research setting. Therefore, short runtimes and high sensitivity were important design criteria.\n\nArriba is based on the STAR RNA-Seq aligner and post-processes the alignments (output from STAR) to:\n\n1. detect split reads and discordant mates, which are indicative of structural rearrangements,\n2. find reads supporting gene fusions (i.e., reads spanning the breakpoints of gene fusions),\n3. perform various filtering steps to remove false positives, and\n4. output the final predictions in a standardized format.\n\nIn contrast to many other fusion detection tools, Arriba does not require to reduce the STAR parameter `--alignIntronMax` (maximum intron size). Reducing this parameter impairs detection of long introns and may affect expression quantification. Arriba reliably filters translocation-based false positives even when large maximum intron sizes are used.\n\n**Important**: Arriba requires BAM files that were aligned with STAR using specific chimeric alignment parameters, particularly `--chimOutType WithinBAM HardClip`. See the [official workflow documentation](https://github.com/suhrig/arriba/blob/master/run_arriba.sh) for the complete set of recommended STAR parameters.\n", "type": "object", "$defs": { "inputs": { diff --git a/target/nextflow/bases2fastq/.config.vsh.yaml b/target/nextflow/bases2fastq/.config.vsh.yaml index e4611ab4..12d974c3 100644 --- a/target/nextflow/bases2fastq/.config.vsh.yaml +++ b/target/nextflow/bases2fastq/.config.vsh.yaml @@ -352,6 +352,7 @@ scope: target: "public" requirements: commands: + - "bases2fastq" - "ps" keywords: - "demultiplex" @@ -431,7 +432,7 @@ runners: engines: - type: "docker" id: "docker" - image: "elembio/bases2fastq:2.2" + image: "elembio/bases2fastq:2.2.1" target_registry: "images.viash-hub.com" target_tag: "main" namespace_separator: "/" @@ -451,7 +452,7 @@ build_info: output: "target/nextflow/bases2fastq" executable: "target/nextflow/bases2fastq/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -473,138 +474,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bases2fastq/main.nf b/target/nextflow/bases2fastq/main.nf index a92c4ef7..80a955ac 100644 --- a/target/nextflow/bases2fastq/main.nf +++ b/target/nextflow/bases2fastq/main.nf @@ -3451,6 +3451,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bases2fastq", "ps" ] }, @@ -3544,7 +3545,7 @@ meta = [ { "type" : "docker", "id" : "docker", - "image" : "elembio/bases2fastq:2.2", + "image" : "elembio/bases2fastq:2.2.1", "target_registry" : "images.viash-hub.com", "target_tag" : "main", "namespace_separator" : "/", @@ -3568,7 +3569,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bases2fastq", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3580,225 +3581,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bbmap/bbmap_bbsplit/.config.vsh.yaml b/target/nextflow/bbmap/bbmap_bbsplit/.config.vsh.yaml index 4ff45b38..490b685f 100644 --- a/target/nextflow/bbmap/bbmap_bbsplit/.config.vsh.yaml +++ b/target/nextflow/bbmap/bbmap_bbsplit/.config.vsh.yaml @@ -371,7 +371,7 @@ build_info: output: "target/nextflow/bbmap/bbmap_bbsplit" executable: "target/nextflow/bbmap/bbmap_bbsplit/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -393,138 +393,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bbmap/bbmap_bbsplit/main.nf b/target/nextflow/bbmap/bbmap_bbsplit/main.nf index c0e8c3d9..42039522 100644 --- a/target/nextflow/bbmap/bbmap_bbsplit/main.nf +++ b/target/nextflow/bbmap/bbmap_bbsplit/main.nf @@ -3450,7 +3450,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bbmap/bbmap_bbsplit", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3462,225 +3462,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bcftools/bcftools_annotate/.config.vsh.yaml b/target/nextflow/bcftools/bcftools_annotate/.config.vsh.yaml index 52fec9e0..b28e8eb6 100644 --- a/target/nextflow/bcftools/bcftools_annotate/.config.vsh.yaml +++ b/target/nextflow/bcftools/bcftools_annotate/.config.vsh.yaml @@ -340,6 +340,16 @@ argument_groups: direction: "input" multiple: false multiple_sep: ";" + - type: "integer" + name: "--verbosity" + alternatives: + - "-v" + description: "Verbosity level.\n" + info: null + required: false + direction: "input" + multiple: false + multiple_sep: ";" resources: - type: "bash_script" path: "script.sh" @@ -349,6 +359,8 @@ test_resources: - type: "bash_script" path: "test.sh" is_executable: true +- type: "file" + path: "test_helpers.sh" info: null status: "enabled" scope: @@ -356,6 +368,7 @@ scope: target: "public" requirements: commands: + - "bcftools" - "ps" keywords: - "Annotate" @@ -438,25 +451,15 @@ runners: engines: - type: "docker" id: "docker" - image: "debian:stable-slim" + image: "quay.io/biocontainers/bcftools:1.22--h3a4d415_1" target_registry: "images.viash-hub.com" target_tag: "main" namespace_separator: "/" setup: - - type: "apt" - packages: - - "bcftools" - - "procps" - interactive: false - type: "docker" run: - "echo \"bcftools: \\\"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftools\ \ //p')\\\"\" > /var/software_versions.txt\n" - test_setup: - - type: "apt" - packages: - - "tabix" - interactive: false entrypoint: [] cmd: null - type: "native" @@ -468,7 +471,7 @@ build_info: output: "target/nextflow/bcftools/bcftools_annotate" executable: "target/nextflow/bcftools/bcftools_annotate/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -490,138 +493,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bcftools/bcftools_annotate/main.nf b/target/nextflow/bcftools/bcftools_annotate/main.nf index 685bded8..806f401d 100644 --- a/target/nextflow/bcftools/bcftools_annotate/main.nf +++ b/target/nextflow/bcftools/bcftools_annotate/main.nf @@ -3393,6 +3393,18 @@ meta = [ "direction" : "input", "multiple" : false, "multiple_sep" : ";" + }, + { + "type" : "integer", + "name" : "--verbosity", + "alternatives" : [ + "-v" + ], + "description" : "Verbosity level.\n", + "required" : false, + "direction" : "input", + "multiple" : false, + "multiple_sep" : ";" } ] } @@ -3410,6 +3422,10 @@ meta = [ "type" : "bash_script", "path" : "test.sh", "is_executable" : true + }, + { + "type" : "file", + "path" : "/src/_utils/test_helpers.sh" } ], "status" : "enabled", @@ -3419,6 +3435,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bcftools", "ps" ] }, @@ -3517,34 +3534,17 @@ meta = [ { "type" : "docker", "id" : "docker", - "image" : "debian:stable-slim", + "image" : "quay.io/biocontainers/bcftools:1.22--h3a4d415_1", "target_registry" : "images.viash-hub.com", "target_tag" : "main", "namespace_separator" : "/", "setup" : [ - { - "type" : "apt", - "packages" : [ - "bcftools", - "procps" - ], - "interactive" : false - }, { "type" : "docker", "run" : [ "echo \\"bcftools: \\\\\\"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftools //p')\\\\\\"\\" > /var/software_versions.txt\n" ] } - ], - "test_setup" : [ - { - "type" : "apt", - "packages" : [ - "tabix" - ], - "interactive" : false - } ] }, { @@ -3558,7 +3558,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bcftools/bcftools_annotate", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3570,225 +3570,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", @@ -3844,6 +3630,7 @@ $( if [ ! -z ${VIASH_PAR_SAMPLES+x} ]; then echo "${VIASH_PAR_SAMPLES}" | sed "s $( if [ ! -z ${VIASH_PAR_SAMPLES_FILE+x} ]; then echo "${VIASH_PAR_SAMPLES_FILE}" | sed "s#'#'\\"'\\"'#g;s#.*#par_samples_file='&'#" ; else echo "# par_samples_file="; fi ) $( if [ ! -z ${VIASH_PAR_SINGLE_OVERLAPS+x} ]; then echo "${VIASH_PAR_SINGLE_OVERLAPS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_single_overlaps='&'#" ; else echo "# par_single_overlaps="; fi ) $( if [ ! -z ${VIASH_PAR_REMOVE+x} ]; then echo "${VIASH_PAR_REMOVE}" | sed "s#'#'\\"'\\"'#g;s#.*#par_remove='&'#" ; else echo "# par_remove="; fi ) +$( if [ ! -z ${VIASH_PAR_VERBOSITY+x} ]; then echo "${VIASH_PAR_VERBOSITY}" | sed "s#'#'\\"'\\"'#g;s#.*#par_verbosity='&'#" ; else echo "# par_verbosity="; fi ) $( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "${VIASH_META_NAME}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_name='&'#" ; else echo "# meta_name="; fi ) $( if [ ! -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then echo "${VIASH_META_FUNCTIONALITY_NAME}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_functionality_name='&'#" ; else echo "# meta_functionality_name="; fi ) $( if [ ! -z ${VIASH_META_RESOURCES_DIR+x} ]; then echo "${VIASH_META_RESOURCES_DIR}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_resources_dir='&'#" ; else echo "# meta_resources_dir="; fi ) @@ -3870,50 +3657,51 @@ set -eo pipefail # Unset parameters unset_if_false=( - par_force - par_keep_sites - par_no_version - par_single_overlaps + par_force + par_keep_sites + par_no_version + par_single_overlaps ) for par in \\${unset_if_false[@]}; do - test_val="\\${!par}" - [[ "\\$test_val" == "false" ]] && unset \\$par + test_val="\\${!par}" + [[ "\\$test_val" == "false" ]] && unset \\$par done # Execute bcftools annotate with the provided arguments bcftools annotate \\\\ - \\${par_annotations:+-a "\\$par_annotations"} \\\\ - \\${par_columns:+-c "\\$par_columns"} \\\\ - \\${par_columns_file:+-C "\\$par_columns_file"} \\\\ - \\${par_exclude:+-e "\\$par_exclude"} \\\\ - \\${par_force:+--force} \\\\ - \\${par_header_line:+-H "\\$par_header_line"} \\\\ - \\${par_header_lines:+-h "\\$par_header_lines"} \\\\ - \\${par_set_id:+-I "\\$par_set_id"} \\\\ - \\${par_include:+-i "\\$par_include"} \\\\ - \\${par_keep_sites:+-k} \\\\ - \\${par_merge_logic:+-l "\\$par_merge_logic"} \\\\ - \\${par_mark_sites:+-m "\\$par_mark_sites"} \\\\ - \\${par_min_overlap:+--min-overlap "\\$par_min_overlap"} \\\\ - \\${par_no_version:+--no-version} \\\\ - \\${par_samples_file:+-S "\\$par_samples_file"} \\\\ - \\${par_output_type:+-O "\\$par_output_type"} \\\\ - \\${par_pair_logic:+--pair-logic "\\$par_pair_logic"} \\\\ - \\${par_regions:+-r "\\$par_regions"} \\\\ - \\${par_regions_file:+-R "\\$par_regions_file"} \\\\ - \\${par_regions_overlap:+--regions-overlap "\\$par_regions_overlap"} \\\\ - \\${par_rename_annotations:+--rename-annots "\\$par_rename_annotations"} \\\\ - \\${par_rename_chromosomes:+--rename-chrs "\\$par_rename_chromosomes"} \\\\ - \\${par_samples:+-s "\\$par_samples"} \\\\ - \\${par_single_overlaps:+--single-overlaps} \\\\ - \\${par_threads:+--threads "\\$par_threads"} \\\\ - \\${par_remove:+-x "\\$par_remove"} \\\\ - -o \\$par_output \\\\ - \\$par_input - + \\${par_annotations:+-a "\\$par_annotations"} \\\\ + \\${par_columns:+-c "\\$par_columns"} \\\\ + \\${par_columns_file:+-C "\\$par_columns_file"} \\\\ + \\${par_exclude:+-e "\\$par_exclude"} \\\\ + \\${par_force:+--force} \\\\ + \\${par_header_line:+-H "\\$par_header_line"} \\\\ + \\${par_header_lines:+-h "\\$par_header_lines"} \\\\ + \\${par_set_id:+-I "\\$par_set_id"} \\\\ + \\${par_include:+-i "\\$par_include"} \\\\ + \\${par_keep_sites:+-k} \\\\ + \\${par_merge_logic:+-l "\\$par_merge_logic"} \\\\ + \\${par_mark_sites:+-m "\\$par_mark_sites"} \\\\ + \\${par_min_overlap:+--min-overlap "\\$par_min_overlap"} \\\\ + \\${par_no_version:+--no-version} \\\\ + \\${par_samples_file:+-S "\\$par_samples_file"} \\\\ + \\${par_output_type:+-O "\\$par_output_type"} \\\\ + \\${par_pair_logic:+--pair-logic "\\$par_pair_logic"} \\\\ + \\${par_regions:+-r "\\$par_regions"} \\\\ + \\${par_regions_file:+-R "\\$par_regions_file"} \\\\ + \\${par_regions_overlap:+--regions-overlap "\\$par_regions_overlap"} \\\\ + \\${par_rename_annotations:+--rename-annots "\\$par_rename_annotations"} \\\\ + \\${par_rename_chromosomes:+--rename-chrs "\\$par_rename_chromosomes"} \\\\ + \\${par_samples:+-s "\\$par_samples"} \\\\ + \\${par_single_overlaps:+--single-overlaps} \\\\ + \\${par_remove:+-x "\\$par_remove"} \\\\ + \\${par_verbosity:+-v "\\$par_verbosity"} \\\\ + \\${meta_cpus:+--threads "\\$meta_cpus"} \\\\ + -o \\$par_output \\\\ + \\$par_input + - + VIASHMAIN bash "$tempscript" ''' diff --git a/target/nextflow/bcftools/bcftools_annotate/nextflow_schema.json b/target/nextflow/bcftools/bcftools_annotate/nextflow_schema.json index f40d2bcc..cbf2ddba 100644 --- a/target/nextflow/bcftools/bcftools_annotate/nextflow_schema.json +++ b/target/nextflow/bcftools/bcftools_annotate/nextflow_schema.json @@ -197,6 +197,11 @@ "type": "string", "description": "List of annotations to remove", "help_text": "Type: `string`, multiple: `False`. " + }, + "verbosity": { + "type": "integer", + "description": "Verbosity level.\n", + "help_text": "Type: `integer`, multiple: `False`. " } } }, diff --git a/target/nextflow/bcftools/bcftools_concat/.config.vsh.yaml b/target/nextflow/bcftools/bcftools_concat/.config.vsh.yaml index f43c0606..74857e93 100644 --- a/target/nextflow/bcftools/bcftools_concat/.config.vsh.yaml +++ b/target/nextflow/bcftools/bcftools_concat/.config.vsh.yaml @@ -17,8 +17,12 @@ argument_groups: name: "--input" alternatives: - "-i" - description: "Input VCF/BCF files to concatenate." + description: "Input VCF/BCF files to concatenate.\n\nAll source files must have\ + \ the same sample columns appearing in \nthe same order. Files must be sorted\ + \ by chr and position.\n" info: null + example: + - "input1.vcf.gz input2.vcf.gz" must_exist: true create_parent: true required: false @@ -29,8 +33,11 @@ argument_groups: name: "--file_list" alternatives: - "-f" - description: "Read the list of VCF/BCF files from a file, one file name per line." + description: "Read the list of VCF/BCF files from a file, one file name per line.\n\ + \nAlternative to providing multiple --input files.\n" info: null + example: + - "files_list.txt" must_exist: true create_parent: true required: false @@ -43,8 +50,11 @@ argument_groups: name: "--output" alternatives: - "-o" - description: "Output concatenated VCF/BCF file." + description: "Write output to a file.\n\nIf not specified, output goes to standard\ + \ output.\n" info: null + example: + - "concatenated.vcf.gz" must_exist: true create_parent: true required: true @@ -58,24 +68,28 @@ argument_groups: alternatives: - "-a" description: "First coordinate of the next file can precede last record of the\ - \ current file.\n" + \ current file.\n\nAllows overlapping records between files during concatenation.\n" info: null direction: "input" - type: "boolean_true" - name: "--compact_PS" + name: "--compact_ps" alternatives: - "-c" description: "Do not output PS tag at each site, only at the start of a new phase\ - \ set block.\n" + \ set block.\n\nReduces output size for phased data.\n" info: null direction: "input" - type: "string" - name: "--remove_duplicates" + name: "--rm_dups" alternatives: - "-d" - description: "Output duplicate records present in multiple files only once: .\n\ - \ \n" + description: "Output duplicate records present in multiple files only once.\n\n\ + **Options:**\n- `snps`: Remove duplicate SNPs\n- `indels`: Remove duplicate\ + \ indels \n- `both`: Remove duplicate SNPs and indels\n- `all`: Remove all\ + \ duplicates\n- `exact`: Remove exact duplicates only\n" info: null + example: + - "exact" required: false choices: - "snps" @@ -83,53 +97,75 @@ argument_groups: - "both" - "all" - "exact" - - "none" direction: "input" multiple: false multiple_sep: ";" + - type: "boolean_true" + name: "--remove_duplicates" + alternatives: + - "-D" + description: "Alias for --rm_dups exact.\n\nRemove exact duplicate records present\ + \ in multiple files.\n" + info: null + direction: "input" + - type: "boolean_true" + name: "--drop_genotypes" + alternatives: + - "-G" + description: "Drop individual genotype information.\n\nRemoves all sample-specific\ + \ data from output.\n" + info: null + direction: "input" - type: "boolean_true" name: "--ligate" alternatives: - "-l" - description: "Ligate phased VCFs by matching phase at overlapping haplotypes." + description: "Ligate phased VCFs by matching phase at overlapping haplotypes.\n\ + \nConnects phase information across files.\n" info: null direction: "input" - type: "boolean_true" name: "--ligate_force" - description: "Ligate even non-overlapping chunks, keep all sites." + description: "Ligate even non-overlapping chunks, keep all sites.\n\nForces ligation\ + \ without requiring overlap validation.\n" info: null direction: "input" - type: "boolean_true" name: "--ligate_warn" - description: "Drop sites in imperfect overlaps." + description: "Drop sites in imperfect overlaps.\n\nConservative ligation that\ + \ removes problematic sites.\n" info: null direction: "input" - type: "boolean_true" name: "--no_version" - description: "Do not append version and command line information to the header." + description: "Do not append version and command line to the header.\n\nProduces\ + \ cleaner output headers.\n" info: null direction: "input" - type: "boolean_true" name: "--naive" alternatives: - "-n" - description: "Concatenate files without recompression, a header check compatibility\ - \ is performed." + description: "Concatenate files without recompression.\n\nVery fast operation\ + \ with header compatibility check.\n" info: null direction: "input" - type: "boolean_true" name: "--naive_force" - description: "Same as --naive, but header compatibility is not checked. \nDangerous,\ - \ use with caution.\n" + description: "Same as --naive, but header compatibility is not checked.\n\n**Warning:**\ + \ Dangerous option, use with caution.\n" info: null direction: "input" - type: "string" name: "--output_type" alternatives: - "-O" - description: "Output type:\n u: uncompressed BCF\n z: compressed VCF\n b: compressed\ - \ BCF\n v: uncompressed VCF\n" + description: "Output type and compression level.\n\n**Options:**\n- `u`: uncompressed\ + \ BCF\n- `b`: compressed BCF \n- `v`: uncompressed VCF\n- `z`: compressed VCF\ + \ (with optional compression level 0-9)\n" info: null + example: + - "z" required: false choices: - "u" @@ -140,10 +176,11 @@ argument_groups: multiple: false multiple_sep: ";" - type: "integer" - name: "--min_PQ" + name: "--min_pq" alternatives: - "-q" - description: "Break phase set if phasing quality is lower than ." + description: "Break phase set if phasing quality is lower than specified value.\n\ + \nOnly relevant when working with phased data.\n" info: null example: - 30 @@ -155,11 +192,11 @@ argument_groups: name: "--regions" alternatives: - "-r" - description: "Restrict to comma-separated list of regions. \nFollowing formats\ - \ are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​].\n" + description: "Restrict to comma-separated list of regions.\n\n**Formats supported:**\ + \ chr|chr:pos|chr:beg-end|chr:beg-[,…​]\n" info: null example: - - "20:1000000-2000000" + - "chr20:1000000-2000000" required: false direction: "input" multiple: false @@ -168,10 +205,11 @@ argument_groups: name: "--regions_file" alternatives: - "-R" - description: "Restrict to regions listed in a file. \nRegions can be specified\ - \ either on a VCF, BED, or tab-delimited file (the default). \nFor more information\ - \ check manual.\n" + description: "Restrict to regions listed in a file.\n\nRegions can be specified\ + \ in VCF, BED, or tab-delimited format.\n" info: null + example: + - "regions.bed" must_exist: true create_parent: true required: false @@ -180,26 +218,46 @@ argument_groups: multiple_sep: ";" - type: "string" name: "--regions_overlap" - description: "This option controls how overlapping records are determined: \n\ - set to 'pos' or '0' if the VCF record has to have POS inside a region (this\ - \ corresponds to the default behavior of -t/-T); \nset to 'record' or '1' if\ - \ also overlapping records with POS outside a region should be included (this\ - \ is the default behavior of -r/-R, \nand includes indels with POS at the end\ - \ of a region, which are technically outside the region); \nor set to 'variant'\ - \ or '2' to include only true overlapping variation (compare the full VCF representation\ - \ \"TA>T-\" vs the true sequence variation \"A>-\").\n" + description: "Include if POS in the region (0), record overlaps (1), variant overlaps\ + \ (2).\n\n**Options:**\n- `0`: POS inside region (default for -t/-T)\n- `1`:\ + \ overlapping records included (default for -r/-R) \n- `2`: true overlapping\ + \ variation only\n" info: null + example: + - "1" required: false choices: - - "pos" - - "record" - - "variant" - "0" - "1" - "2" direction: "input" multiple: false multiple_sep: ";" + - type: "integer" + name: "--verbosity" + alternatives: + - "-v" + description: "Set verbosity level.\n\nControls amount of diagnostic output.\n" + info: null + example: + - 1 + required: false + direction: "input" + multiple: false + multiple_sep: ";" + - type: "string" + name: "--write_index" + alternatives: + - "-W" + description: "Automatically index the output files.\n\n**Format:** Specify index\ + \ format or use default.\n" + info: null + example: + - "tbi" + required: false + direction: "input" + multiple: false + multiple_sep: ";" resources: - type: "bash_script" path: "script.sh" @@ -215,6 +273,8 @@ test_resources: - type: "bash_script" path: "test.sh" is_executable: true +- type: "file" + path: "test_helpers.sh" info: null status: "enabled" scope: @@ -222,6 +282,7 @@ scope: target: "public" requirements: commands: + - "bcftools" - "ps" keywords: - "Concatenate" @@ -304,25 +365,14 @@ runners: engines: - type: "docker" id: "docker" - image: "debian:stable-slim" + image: "quay.io/biocontainers/bcftools:1.22--h3a4d415_1" target_registry: "images.viash-hub.com" target_tag: "main" namespace_separator: "/" setup: - - type: "apt" - packages: - - "bcftools" - - "procps" - interactive: false - type: "docker" run: - - "echo \"bcftools: \\\"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftools\ - \ //p')\\\"\" > /var/software_versions.txt\n" - test_setup: - - type: "apt" - packages: - - "tabix" - interactive: false + - "bcftools --version 2>&1 | head -1 | sed 's/bcftools /bcftools: /' > /var/software_versions.txt\n" entrypoint: [] cmd: null - type: "native" @@ -334,7 +384,7 @@ build_info: output: "target/nextflow/bcftools/bcftools_concat" executable: "target/nextflow/bcftools/bcftools_concat/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -356,138 +406,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bcftools/bcftools_concat/main.nf b/target/nextflow/bcftools/bcftools_concat/main.nf index ea038826..87b41ee9 100644 --- a/target/nextflow/bcftools/bcftools_concat/main.nf +++ b/target/nextflow/bcftools/bcftools_concat/main.nf @@ -3061,7 +3061,10 @@ meta = [ "alternatives" : [ "-i" ], - "description" : "Input VCF/BCF files to concatenate.", + "description" : "Input VCF/BCF files to concatenate.\n\nAll source files must have the same sample columns appearing in \nthe same order. Files must be sorted by chr and position.\n", + "example" : [ + "input1.vcf.gz input2.vcf.gz" + ], "must_exist" : true, "create_parent" : true, "required" : false, @@ -3075,7 +3078,10 @@ meta = [ "alternatives" : [ "-f" ], - "description" : "Read the list of VCF/BCF files from a file, one file name per line.", + "description" : "Read the list of VCF/BCF files from a file, one file name per line.\n\nAlternative to providing multiple --input files.\n", + "example" : [ + "files_list.txt" + ], "must_exist" : true, "create_parent" : true, "required" : false, @@ -3094,7 +3100,10 @@ meta = [ "alternatives" : [ "-o" ], - "description" : "Output concatenated VCF/BCF file.", + "description" : "Write output to a file.\n\nIf not specified, output goes to standard output.\n", + "example" : [ + "concatenated.vcf.gz" + ], "must_exist" : true, "create_parent" : true, "required" : true, @@ -3113,63 +3122,83 @@ meta = [ "alternatives" : [ "-a" ], - "description" : "First coordinate of the next file can precede last record of the current file.\n", + "description" : "First coordinate of the next file can precede last record of the current file.\n\nAllows overlapping records between files during concatenation.\n", "direction" : "input" }, { "type" : "boolean_true", - "name" : "--compact_PS", + "name" : "--compact_ps", "alternatives" : [ "-c" ], - "description" : "Do not output PS tag at each site, only at the start of a new phase set block.\n", + "description" : "Do not output PS tag at each site, only at the start of a new phase set block.\n\nReduces output size for phased data.\n", "direction" : "input" }, { "type" : "string", - "name" : "--remove_duplicates", + "name" : "--rm_dups", "alternatives" : [ "-d" ], - "description" : "Output duplicate records present in multiple files only once: .\n \n", + "description" : "Output duplicate records present in multiple files only once.\n\n**Options:**\n- `snps`: Remove duplicate SNPs\n- `indels`: Remove duplicate indels \n- `both`: Remove duplicate SNPs and indels\n- `all`: Remove all duplicates\n- `exact`: Remove exact duplicates only\n", + "example" : [ + "exact" + ], "required" : false, "choices" : [ "snps", "indels", "both", "all", - "exact", - "none" + "exact" ], "direction" : "input", "multiple" : false, "multiple_sep" : ";" }, + { + "type" : "boolean_true", + "name" : "--remove_duplicates", + "alternatives" : [ + "-D" + ], + "description" : "Alias for --rm_dups exact.\n\nRemove exact duplicate records present in multiple files.\n", + "direction" : "input" + }, + { + "type" : "boolean_true", + "name" : "--drop_genotypes", + "alternatives" : [ + "-G" + ], + "description" : "Drop individual genotype information.\n\nRemoves all sample-specific data from output.\n", + "direction" : "input" + }, { "type" : "boolean_true", "name" : "--ligate", "alternatives" : [ "-l" ], - "description" : "Ligate phased VCFs by matching phase at overlapping haplotypes.", + "description" : "Ligate phased VCFs by matching phase at overlapping haplotypes.\n\nConnects phase information across files.\n", "direction" : "input" }, { "type" : "boolean_true", "name" : "--ligate_force", - "description" : "Ligate even non-overlapping chunks, keep all sites.", + "description" : "Ligate even non-overlapping chunks, keep all sites.\n\nForces ligation without requiring overlap validation.\n", "direction" : "input" }, { "type" : "boolean_true", "name" : "--ligate_warn", - "description" : "Drop sites in imperfect overlaps.", + "description" : "Drop sites in imperfect overlaps.\n\nConservative ligation that removes problematic sites.\n", "direction" : "input" }, { "type" : "boolean_true", "name" : "--no_version", - "description" : "Do not append version and command line information to the header.", + "description" : "Do not append version and command line to the header.\n\nProduces cleaner output headers.\n", "direction" : "input" }, { @@ -3178,13 +3207,13 @@ meta = [ "alternatives" : [ "-n" ], - "description" : "Concatenate files without recompression, a header check compatibility is performed.", + "description" : "Concatenate files without recompression.\n\nVery fast operation with header compatibility check.\n", "direction" : "input" }, { "type" : "boolean_true", "name" : "--naive_force", - "description" : "Same as --naive, but header compatibility is not checked. \nDangerous, use with caution.\n", + "description" : "Same as --naive, but header compatibility is not checked.\n\n**Warning:** Dangerous option, use with caution.\n", "direction" : "input" }, { @@ -3193,7 +3222,10 @@ meta = [ "alternatives" : [ "-O" ], - "description" : "Output type:\n u: uncompressed BCF\n z: compressed VCF\n b: compressed BCF\n v: uncompressed VCF\n", + "description" : "Output type and compression level.\n\n**Options:**\n- `u`: uncompressed BCF\n- `b`: compressed BCF \n- `v`: uncompressed VCF\n- `z`: compressed VCF (with optional compression level 0-9)\n", + "example" : [ + "z" + ], "required" : false, "choices" : [ "u", @@ -3207,11 +3239,11 @@ meta = [ }, { "type" : "integer", - "name" : "--min_PQ", + "name" : "--min_pq", "alternatives" : [ "-q" ], - "description" : "Break phase set if phasing quality is lower than .", + "description" : "Break phase set if phasing quality is lower than specified value.\n\nOnly relevant when working with phased data.\n", "example" : [ 30 ], @@ -3226,9 +3258,9 @@ meta = [ "alternatives" : [ "-r" ], - "description" : "Restrict to comma-separated list of regions. \nFollowing formats are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​].\n", + "description" : "Restrict to comma-separated list of regions.\n\n**Formats supported:** chr|chr:pos|chr:beg-end|chr:beg-[,…​]\n", "example" : [ - "20:1000000-2000000" + "chr20:1000000-2000000" ], "required" : false, "direction" : "input", @@ -3241,7 +3273,10 @@ meta = [ "alternatives" : [ "-R" ], - "description" : "Restrict to regions listed in a file. \nRegions can be specified either on a VCF, BED, or tab-delimited file (the default). \nFor more information check manual.\n", + "description" : "Restrict to regions listed in a file.\n\nRegions can be specified in VCF, BED, or tab-delimited format.\n", + "example" : [ + "regions.bed" + ], "must_exist" : true, "create_parent" : true, "required" : false, @@ -3252,12 +3287,12 @@ meta = [ { "type" : "string", "name" : "--regions_overlap", - "description" : "This option controls how overlapping records are determined: \nset to 'pos' or '0' if the VCF record has to have POS inside a region (this corresponds to the default behavior of -t/-T); \nset to 'record' or '1' if also overlapping records with POS outside a region should be included (this is the default behavior of -r/-R, \nand includes indels with POS at the end of a region, which are technically outside the region); \nor set to 'variant' or '2' to include only true overlapping variation (compare the full VCF representation \\"TA>T-\\" vs the true sequence variation \\"A>-\\").\n", + "description" : "Include if POS in the region (0), record overlaps (1), variant overlaps (2).\n\n**Options:**\n- `0`: POS inside region (default for -t/-T)\n- `1`: overlapping records included (default for -r/-R) \n- `2`: true overlapping variation only\n", + "example" : [ + "1" + ], "required" : false, "choices" : [ - "pos", - "record", - "variant", "0", "1", "2" @@ -3265,6 +3300,36 @@ meta = [ "direction" : "input", "multiple" : false, "multiple_sep" : ";" + }, + { + "type" : "integer", + "name" : "--verbosity", + "alternatives" : [ + "-v" + ], + "description" : "Set verbosity level.\n\nControls amount of diagnostic output.\n", + "example" : [ + 1 + ], + "required" : false, + "direction" : "input", + "multiple" : false, + "multiple_sep" : ";" + }, + { + "type" : "string", + "name" : "--write_index", + "alternatives" : [ + "-W" + ], + "description" : "Automatically index the output files.\n\n**Format:** Specify index format or use default.\n", + "example" : [ + "tbi" + ], + "required" : false, + "direction" : "input", + "multiple" : false, + "multiple_sep" : ";" } ] } @@ -3282,6 +3347,10 @@ meta = [ "type" : "bash_script", "path" : "test.sh", "is_executable" : true + }, + { + "type" : "file", + "path" : "/src/_utils/test_helpers.sh" } ], "status" : "enabled", @@ -3291,6 +3360,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bcftools", "ps" ] }, @@ -3389,34 +3459,17 @@ meta = [ { "type" : "docker", "id" : "docker", - "image" : "debian:stable-slim", + "image" : "quay.io/biocontainers/bcftools:1.22--h3a4d415_1", "target_registry" : "images.viash-hub.com", "target_tag" : "main", "namespace_separator" : "/", "setup" : [ - { - "type" : "apt", - "packages" : [ - "bcftools", - "procps" - ], - "interactive" : false - }, { "type" : "docker", "run" : [ - "echo \\"bcftools: \\\\\\"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftools //p')\\\\\\"\\" > /var/software_versions.txt\n" + "bcftools --version 2>&1 | head -1 | sed 's/bcftools /bcftools: /' > /var/software_versions.txt\n" ] } - ], - "test_setup" : [ - { - "type" : "apt", - "packages" : [ - "tabix" - ], - "interactive" : false - } ] }, { @@ -3430,7 +3483,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bcftools/bcftools_concat", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3442,225 +3495,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", @@ -3693,8 +3532,10 @@ $( if [ ! -z ${VIASH_PAR_INPUT+x} ]; then echo "${VIASH_PAR_INPUT}" | sed "s#'#' $( if [ ! -z ${VIASH_PAR_FILE_LIST+x} ]; then echo "${VIASH_PAR_FILE_LIST}" | sed "s#'#'\\"'\\"'#g;s#.*#par_file_list='&'#" ; else echo "# par_file_list="; fi ) $( if [ ! -z ${VIASH_PAR_OUTPUT+x} ]; then echo "${VIASH_PAR_OUTPUT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_output='&'#" ; else echo "# par_output="; fi ) $( if [ ! -z ${VIASH_PAR_ALLOW_OVERLAPS+x} ]; then echo "${VIASH_PAR_ALLOW_OVERLAPS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_allow_overlaps='&'#" ; else echo "# par_allow_overlaps="; fi ) -$( if [ ! -z ${VIASH_PAR_COMPACT_PS+x} ]; then echo "${VIASH_PAR_COMPACT_PS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_compact_PS='&'#" ; else echo "# par_compact_PS="; fi ) +$( if [ ! -z ${VIASH_PAR_COMPACT_PS+x} ]; then echo "${VIASH_PAR_COMPACT_PS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_compact_ps='&'#" ; else echo "# par_compact_ps="; fi ) +$( if [ ! -z ${VIASH_PAR_RM_DUPS+x} ]; then echo "${VIASH_PAR_RM_DUPS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_rm_dups='&'#" ; else echo "# par_rm_dups="; fi ) $( if [ ! -z ${VIASH_PAR_REMOVE_DUPLICATES+x} ]; then echo "${VIASH_PAR_REMOVE_DUPLICATES}" | sed "s#'#'\\"'\\"'#g;s#.*#par_remove_duplicates='&'#" ; else echo "# par_remove_duplicates="; fi ) +$( if [ ! -z ${VIASH_PAR_DROP_GENOTYPES+x} ]; then echo "${VIASH_PAR_DROP_GENOTYPES}" | sed "s#'#'\\"'\\"'#g;s#.*#par_drop_genotypes='&'#" ; else echo "# par_drop_genotypes="; fi ) $( if [ ! -z ${VIASH_PAR_LIGATE+x} ]; then echo "${VIASH_PAR_LIGATE}" | sed "s#'#'\\"'\\"'#g;s#.*#par_ligate='&'#" ; else echo "# par_ligate="; fi ) $( if [ ! -z ${VIASH_PAR_LIGATE_FORCE+x} ]; then echo "${VIASH_PAR_LIGATE_FORCE}" | sed "s#'#'\\"'\\"'#g;s#.*#par_ligate_force='&'#" ; else echo "# par_ligate_force="; fi ) $( if [ ! -z ${VIASH_PAR_LIGATE_WARN+x} ]; then echo "${VIASH_PAR_LIGATE_WARN}" | sed "s#'#'\\"'\\"'#g;s#.*#par_ligate_warn='&'#" ; else echo "# par_ligate_warn="; fi ) @@ -3702,10 +3543,12 @@ $( if [ ! -z ${VIASH_PAR_NO_VERSION+x} ]; then echo "${VIASH_PAR_NO_VERSION}" | $( if [ ! -z ${VIASH_PAR_NAIVE+x} ]; then echo "${VIASH_PAR_NAIVE}" | sed "s#'#'\\"'\\"'#g;s#.*#par_naive='&'#" ; else echo "# par_naive="; fi ) $( if [ ! -z ${VIASH_PAR_NAIVE_FORCE+x} ]; then echo "${VIASH_PAR_NAIVE_FORCE}" | sed "s#'#'\\"'\\"'#g;s#.*#par_naive_force='&'#" ; else echo "# par_naive_force="; fi ) $( if [ ! -z ${VIASH_PAR_OUTPUT_TYPE+x} ]; then echo "${VIASH_PAR_OUTPUT_TYPE}" | sed "s#'#'\\"'\\"'#g;s#.*#par_output_type='&'#" ; else echo "# par_output_type="; fi ) -$( if [ ! -z ${VIASH_PAR_MIN_PQ+x} ]; then echo "${VIASH_PAR_MIN_PQ}" | sed "s#'#'\\"'\\"'#g;s#.*#par_min_PQ='&'#" ; else echo "# par_min_PQ="; fi ) +$( if [ ! -z ${VIASH_PAR_MIN_PQ+x} ]; then echo "${VIASH_PAR_MIN_PQ}" | sed "s#'#'\\"'\\"'#g;s#.*#par_min_pq='&'#" ; else echo "# par_min_pq="; fi ) $( if [ ! -z ${VIASH_PAR_REGIONS+x} ]; then echo "${VIASH_PAR_REGIONS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_regions='&'#" ; else echo "# par_regions="; fi ) $( if [ ! -z ${VIASH_PAR_REGIONS_FILE+x} ]; then echo "${VIASH_PAR_REGIONS_FILE}" | sed "s#'#'\\"'\\"'#g;s#.*#par_regions_file='&'#" ; else echo "# par_regions_file="; fi ) $( if [ ! -z ${VIASH_PAR_REGIONS_OVERLAP+x} ]; then echo "${VIASH_PAR_REGIONS_OVERLAP}" | sed "s#'#'\\"'\\"'#g;s#.*#par_regions_overlap='&'#" ; else echo "# par_regions_overlap="; fi ) +$( if [ ! -z ${VIASH_PAR_VERBOSITY+x} ]; then echo "${VIASH_PAR_VERBOSITY}" | sed "s#'#'\\"'\\"'#g;s#.*#par_verbosity='&'#" ; else echo "# par_verbosity="; fi ) +$( if [ ! -z ${VIASH_PAR_WRITE_INDEX+x} ]; then echo "${VIASH_PAR_WRITE_INDEX}" | sed "s#'#'\\"'\\"'#g;s#.*#par_write_index='&'#" ; else echo "# par_write_index="; fi ) $( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "${VIASH_META_NAME}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_name='&'#" ; else echo "# meta_name="; fi ) $( if [ ! -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then echo "${VIASH_META_FUNCTIONALITY_NAME}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_functionality_name='&'#" ; else echo "# meta_functionality_name="; fi ) $( if [ ! -z ${VIASH_META_RESOURCES_DIR+x} ]; then echo "${VIASH_META_RESOURCES_DIR}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_resources_dir='&'#" ; else echo "# meta_resources_dir="; fi ) @@ -3727,55 +3570,71 @@ $( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}" ## VIASH END -# Exit on error set -eo pipefail -# Unset parameters +# Unset false boolean parameters unset_if_false=( - par_allow_overlaps - par_compact_PS - par_ligate - par_ligate_force - par_ligate_warn - par_no_version - par_naive - par_naive_force + par_allow_overlaps + par_compact_ps + par_remove_duplicates + par_drop_genotypes + par_ligate + par_ligate_force + par_ligate_warn + par_no_version + par_naive + par_naive_force ) for par in \\${unset_if_false[@]}; do - test_val="\\${!par}" - [[ "\\$test_val" == "false" ]] && unset \\$par + test_val="\\${!par}" + [[ "\\$test_val" == "false" ]] && unset \\$par done -# Check to see whether the par_input or the par_file_list is set +# Check that either input files or file_list is provided if [[ -z "\\${par_input}" && -z "\\${par_file_list}" ]]; then - echo "Error: One of the parameters '--input' or '--file_list' must be used." - exit 1 + echo "Error: One of the parameters '--input' or '--file_list' must be used." + exit 1 fi -# Create input array -IFS=";" read -ra input <<< \\$par_input +# Handle multiple input files (semicolon-separated from Viash) +if [[ -n "\\$par_input" ]]; then + IFS=';' read -ra input_files <<< "\\$par_input" +fi -# Execute bcftools concat with the provided arguments -bcftools concat \\\\ - \\${par_allow_overlaps:+-a} \\\\ - \\${par_compact_PS:+-c} \\\\ - \\${par_remove_duplicates:+-d "\\$par_remove_duplicates"} \\\\ - \\${par_ligate:+-l} \\\\ - \\${par_ligate_force:+--ligate-force} \\\\ - \\${par_ligate_warn:+--ligate-warn} \\\\ - \\${par_no_version:+--no-version} \\\\ - \\${par_naive:+-n} \\\\ - \\${par_naive_force:+--naive-force} \\\\ - \\${par_output_type:+--O "\\$par_output_type"} \\\\ - \\${par_min_PQ:+-q "\\$par_min_PQ"} \\\\ - \\${par_regions:+-r "\\$par_regions"} \\\\ - \\${par_regions_file:+-R "\\$par_regions_file"} \\\\ - \\${par_regions_overlap:+--regions-overlap "\\$par_regions_overlap"} \\\\ - \\${meta_cpus:+--threads "\\$meta_cpus"} \\\\ - -o \\$par_output \\\\ - \\${par_file_list:+-f "\\$par_file_list"} \\\\ - \\${input[@]} \\\\ +# Build command array +cmd_args=( + bcftools concat + \\${par_allow_overlaps:+--allow-overlaps} + \\${par_compact_ps:+--compact-PS} + \\${par_rm_dups:+--rm-dups "\\$par_rm_dups"} + \\${par_remove_duplicates:+--remove-duplicates} + \\${par_drop_genotypes:+--drop-genotypes} + \\${par_ligate:+--ligate} + \\${par_ligate_force:+--ligate-force} + \\${par_ligate_warn:+--ligate-warn} + \\${par_no_version:+--no-version} + \\${par_naive:+--naive} + \\${par_naive_force:+--naive-force} + \\${par_output_type:+--output-type "\\$par_output_type"} + \\${par_min_pq:+--min-PQ "\\$par_min_pq"} + \\${par_regions:+--regions "\\$par_regions"} + \\${par_regions_file:+--regions-file "\\$par_regions_file"} + \\${par_regions_overlap:+--regions-overlap "\\$par_regions_overlap"} + \\${meta_cpus:+--threads "\\$meta_cpus"} + \\${par_verbosity:+--verbosity "\\$par_verbosity"} + \\${par_write_index:+--write-index="\\$par_write_index"} + \\${par_output:+--output "\\$par_output"} + \\${par_file_list:+--file-list "\\$par_file_list"} +) + +# Add input files to command array +if [[ -n "\\$par_input" ]]; then + cmd_args+=("\\${input_files[@]}") +fi + +# Execute command +"\\${cmd_args[@]}" VIASHMAIN bash "$tempscript" ''' diff --git a/target/nextflow/bcftools/bcftools_concat/nextflow_schema.json b/target/nextflow/bcftools/bcftools_concat/nextflow_schema.json index db79851f..694e9a95 100644 --- a/target/nextflow/bcftools/bcftools_concat/nextflow_schema.json +++ b/target/nextflow/bcftools/bcftools_concat/nextflow_schema.json @@ -15,14 +15,14 @@ "type": "string" }, "format": "path", - "description": "Input VCF/BCF files to concatenate.", - "help_text": "Type: `file`, multiple: `True`, direction: `input`. " + "description": "Input VCF/BCF files to concatenate.\n\nAll source files must have the same sample columns appearing in \nthe same order", + "help_text": "Type: `file`, multiple: `True`, direction: `input`, example: `[\"input1.vcf.gz input2.vcf.gz\"]`. " }, "file_list": { "type": "string", "format": "path", - "description": "Read the list of VCF/BCF files from a file, one file name per line.", - "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + "description": "Read the list of VCF/BCF files from a file, one file name per line.\n\nAlternative to providing multiple --input files.\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"files_list.txt\"`. " } } }, @@ -34,9 +34,9 @@ "output": { "type": "string", "format": "path", - "description": "Output concatenated VCF/BCF file.", - "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output\"`, direction: `output`. ", - "default": "$id.$key.output" + "description": "Write output to a file.\n\nIf not specified, output goes to standard output.\n", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.gz\"`, direction: `output`, example: `\"concatenated.vcf.gz\"`. ", + "default": "$id.$key.output.gz" } } }, @@ -47,69 +47,80 @@ "properties": { "allow_overlaps": { "type": "boolean", - "description": "First coordinate of the next file can precede last record of the current file.\n", + "description": "First coordinate of the next file can precede last record of the current file.\n\nAllows overlapping records between files during concatenation.\n", "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", "default": false }, - "compact_PS": { + "compact_ps": { "type": "boolean", - "description": "Do not output PS tag at each site, only at the start of a new phase set block.\n", + "description": "Do not output PS tag at each site, only at the start of a new phase set block.\n\nReduces output size for phased data.\n", "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", "default": false }, - "remove_duplicates": { + "rm_dups": { "type": "string", - "description": "Output duplicate records present in multiple files only once: .\n \n", - "help_text": "Type: `string`, multiple: `False`, choices: ``snps`, `indels`, `both`, `all`, `exact`, `none``. ", + "description": "Output duplicate records present in multiple files only once.\n\n**Options:**\n- `snps`: Remove duplicate SNPs\n- `indels`: Remove duplicate indels \n- `both`: Remove duplicate SNPs and indels\n- `all`: Remove all duplicates\n- `exact`: Remove exact duplicates only\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"exact\"`, choices: ``snps`, `indels`, `both`, `all`, `exact``. ", "enum": [ "snps", "indels", "both", "all", - "exact", - "none" + "exact" ] }, + "remove_duplicates": { + "type": "boolean", + "description": "Alias for --rm_dups exact.\n\nRemove exact duplicate records present in multiple files.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "drop_genotypes": { + "type": "boolean", + "description": "Drop individual genotype information.\n\nRemoves all sample-specific data from output.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, "ligate": { "type": "boolean", - "description": "Ligate phased VCFs by matching phase at overlapping haplotypes.", + "description": "Ligate phased VCFs by matching phase at overlapping haplotypes.\n\nConnects phase information across files.\n", "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", "default": false }, "ligate_force": { "type": "boolean", - "description": "Ligate even non-overlapping chunks, keep all sites.", + "description": "Ligate even non-overlapping chunks, keep all sites.\n\nForces ligation without requiring overlap validation.\n", "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", "default": false }, "ligate_warn": { "type": "boolean", - "description": "Drop sites in imperfect overlaps.", + "description": "Drop sites in imperfect overlaps.\n\nConservative ligation that removes problematic sites.\n", "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", "default": false }, "no_version": { "type": "boolean", - "description": "Do not append version and command line information to the header.", + "description": "Do not append version and command line to the header.\n\nProduces cleaner output headers.\n", "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", "default": false }, "naive": { "type": "boolean", - "description": "Concatenate files without recompression, a header check compatibility is performed.", + "description": "Concatenate files without recompression.\n\nVery fast operation with header compatibility check.\n", "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", "default": false }, "naive_force": { "type": "boolean", - "description": "Same as --naive, but header compatibility is not checked", + "description": "Same as --naive, but header compatibility is not checked.\n\n**Warning:** Dangerous option, use with caution.\n", "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", "default": false }, "output_type": { "type": "string", - "description": "Output type:\n u: uncompressed BCF\n z: compressed VCF\n b: compressed BCF\n v: uncompressed VCF\n", - "help_text": "Type: `string`, multiple: `False`, choices: ``u`, `z`, `b`, `v``. ", + "description": "Output type and compression level.\n\n**Options:**\n- `u`: uncompressed BCF\n- `b`: compressed BCF \n- `v`: uncompressed VCF\n- `z`: compressed VCF (with optional compression level 0-9)\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"z\"`, choices: ``u`, `z`, `b`, `v``. ", "enum": [ "u", "z", @@ -117,34 +128,41 @@ "v" ] }, - "min_PQ": { + "min_pq": { "type": "integer", - "description": "Break phase set if phasing quality is lower than .", + "description": "Break phase set if phasing quality is lower than specified value.\n\nOnly relevant when working with phased data.\n", "help_text": "Type: `integer`, multiple: `False`, example: `30`. " }, "regions": { "type": "string", - "description": "Restrict to comma-separated list of regions", - "help_text": "Type: `string`, multiple: `False`, example: `\"20:1000000-2000000\"`. " + "description": "Restrict to comma-separated list of regions.\n\n**Formats supported:** chr|chr:pos|chr:beg-end|chr:beg-[,…​]\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"chr20:1000000-2000000\"`. " }, "regions_file": { "type": "string", "format": "path", - "description": "Restrict to regions listed in a file", - "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + "description": "Restrict to regions listed in a file.\n\nRegions can be specified in VCF, BED, or tab-delimited format.\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"regions.bed\"`. " }, "regions_overlap": { "type": "string", - "description": "This option controls how overlapping records are determined: \nset to 'pos' or '0' if the VCF record has to have POS inside a region (this corresponds to the default behavior of -t/-T); \nset to 'record' or '1' if also overlapping records with POS outside a region should be included (this is the default behavior of -r/-R, \nand includes indels with POS at the end of a region, which are technically outside the region); \nor set to 'variant' or '2' to include only true overlapping variation (compare the full VCF representation \"TA>T-\" vs the true sequence variation \"A>-\").\n", - "help_text": "Type: `string`, multiple: `False`, choices: ``pos`, `record`, `variant`, `0`, `1`, `2``. ", + "description": "Include if POS in the region (0), record overlaps (1), variant overlaps (2).\n\n**Options:**\n- `0`: POS inside region (default for -t/-T)\n- `1`: overlapping records included (default for -r/-R) \n- `2`: true overlapping variation only\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"1\"`, choices: ``0`, `1`, `2``. ", "enum": [ - "pos", - "record", - "variant", "0", "1", "2" ] + }, + "verbosity": { + "type": "integer", + "description": "Set verbosity level.\n\nControls amount of diagnostic output.\n", + "help_text": "Type: `integer`, multiple: `False`, example: `1`. " + }, + "write_index": { + "type": "string", + "description": "Automatically index the output files.\n\n**Format:** Specify index format or use default.\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"tbi\"`. " } } }, diff --git a/target/nextflow/bcftools/bcftools_norm/.config.vsh.yaml b/target/nextflow/bcftools/bcftools_norm/.config.vsh.yaml index fb506960..22f1ea54 100644 --- a/target/nextflow/bcftools/bcftools_norm/.config.vsh.yaml +++ b/target/nextflow/bcftools/bcftools_norm/.config.vsh.yaml @@ -15,10 +15,11 @@ argument_groups: arguments: - type: "file" name: "--input" - alternatives: - - "-i" - description: "Input VCF/BCF file." + description: "Input VCF/BCF file.\n\nThe file to be normalized, left-aligned,\ + \ and/or processed.\n" info: null + example: + - "input.vcf.gz" must_exist: true create_parent: true required: true @@ -31,8 +32,11 @@ argument_groups: name: "--output" alternatives: - "-o" - description: "Output normalized VCF/BCF file." + description: "Write output to a file.\n\nIf not specified, output goes to standard\ + \ output.\n" info: null + example: + - "normalized.vcf.gz" must_exist: true create_parent: true required: true @@ -45,14 +49,18 @@ argument_groups: name: "--atomize" alternatives: - "-a" - description: "Decompose complex variants (e.g., MNVs become consecutive SNVs).\n" + description: "Decompose complex variants (e.g., MNVs become consecutive SNVs).\n\ + \nBreaks down complex variants into simpler components.\n" info: null direction: "input" - type: "string" name: "--atom_overlaps" description: "Use the star allele (*) for overlapping alleles or set to missing\ - \ (.).\n" + \ (.).\n\n**Options:**\n- `*`: Use star allele for overlaps (default)\n- `.`:\ + \ Set overlapping alleles to missing\n" info: null + example: + - "*" required: false choices: - "." @@ -65,8 +73,12 @@ argument_groups: alternatives: - "-c" description: "Check REF alleles and exit (e), warn (w), exclude (x), or set (s)\ - \ bad sites.\n" + \ bad sites.\n\n**Options:**\n- `e`: exit on REF mismatch (default)\n- `w`:\ + \ warn about REF mismatches\n- `x`: exclude sites with REF mismatches\n- `s`:\ + \ set/fix REF mismatches\n" info: null + example: + - "w" required: false choices: - "e" @@ -76,13 +88,25 @@ argument_groups: direction: "input" multiple: false multiple_sep: ";" + - type: "boolean_true" + name: "--remove_duplicates_flag" + alternatives: + - "-D" + description: "Remove duplicate lines of the same type.\n\nShorthand for --rm_dup\ + \ exact.\n" + info: null + direction: "input" - type: "string" - name: "--remove_duplicates" + name: "--rm_dup" alternatives: - "-d" - description: "Remove duplicate snps, indels, both, all, exact matches, or none\ - \ (old -D option)." + description: "Remove duplicate snps|indels|both|all|exact.\n\n**Options:**\n-\ + \ `snps`: Remove duplicate SNPs\n- `indels`: Remove duplicate indels\n- `both`:\ + \ Remove duplicate SNPs and indels\n- `all`: Remove all duplicates\n- `exact`:\ + \ Remove exact duplicates only\n" info: null + example: + - "exact" required: false choices: - "snps" @@ -90,7 +114,19 @@ argument_groups: - "both" - "all" - "exact" - - "none" + direction: "input" + multiple: false + multiple_sep: ";" + - type: "string" + name: "--exclude" + alternatives: + - "-e" + description: "Do not normalize records for which the expression is true.\n\nUses\ + \ bcftools expression syntax (see man page for details).\n" + info: null + example: + - "INFO/DP<10" + required: false direction: "input" multiple: false multiple_sep: ";" @@ -98,8 +134,11 @@ argument_groups: name: "--fasta_ref" alternatives: - "-f" - description: "Reference fasta sequence file." + description: "Reference sequence file.\n\nRequired for checking REF alleles and\ + \ left-alignment.\n" info: null + example: + - "reference.fa" must_exist: true create_parent: true required: false @@ -108,15 +147,45 @@ argument_groups: multiple_sep: ";" - type: "boolean_true" name: "--force" - description: "Try to proceed even if malformed tags are encountered. \nExperimental,\ - \ use at your own risk.\n" + description: "Try to proceed even if malformed tags are encountered.\n\n**Warning:**\ + \ Experimental feature, use at your own risk.\n" info: null direction: "input" + - type: "file" + name: "--gff_annot" + alternatives: + - "-g" + description: "Follow HGVS 3'rule and right-align variants in transcripts on the\ + \ forward strand.\n\nUses GFF annotation file for transcript information.\n" + info: null + example: + - "genes.gff" + must_exist: true + create_parent: true + required: false + direction: "input" + multiple: false + multiple_sep: ";" + - type: "string" + name: "--include" + alternatives: + - "-i" + description: "Normalize only records for which the expression is true.\n\nUses\ + \ bcftools expression syntax (see man page for details).\n" + info: null + example: + - "QUAL>=30" + required: false + direction: "input" + multiple: false + multiple_sep: ";" - type: "string" name: "--keep_sum" - description: "Keep vector sum constant when splitting multiallelics (see github\ - \ issue #360).\n" + description: "Keep vector sum constant when splitting multiallelics.\n\nComma-separated\ + \ list of INFO tags (see github issue #360).\n" info: null + example: + - "AC,AF" required: false direction: "input" multiple: false @@ -125,9 +194,12 @@ argument_groups: name: "--multiallelics" alternatives: - "-m" - description: "Split multiallelics (-) or join biallelics (+), type: snps, indels,\ - \ both, any [default: both].\n" + description: "Split multiallelics (-) or join biallelics (+), type: snps|indels|both|any.\n\ + \n**Options:**\n- `-both`: Split multiallelic sites (default)\n- `+both`: Join\ + \ biallelic sites\n- Use `snps`, `indels`, `any` for specific variant types\n" info: null + example: + - "-both" required: false choices: - "+snps" @@ -141,25 +213,56 @@ argument_groups: direction: "input" multiple: false multiple_sep: ";" + - type: "string" + name: "--multi_overlaps" + description: "Fill in the reference (0) or missing (.) allele when splitting multiallelics.\n\ + \n**Options:**\n- `0`: Fill with reference allele (default)\n- `.`: Fill with\ + \ missing allele\n" + info: null + example: + - "0" + required: false + choices: + - "0" + - "." + direction: "input" + multiple: false + multiple_sep: ";" - type: "boolean_true" name: "--no_version" - description: "Do not append version and command line information to the header." + description: "Do not append version and command line to the header.\n\nProduces\ + \ cleaner output headers.\n" info: null direction: "input" - type: "boolean_true" name: "--do_not_normalize" alternatives: - "-N" - description: "Do not normalize indels (with -m or -c s)." + description: "Do not normalize indels (with -m or -c s).\n\nSkips indel left-alignment\ + \ and normalization.\n" info: null direction: "input" + - type: "string" + name: "--old_rec_tag" + description: "Annotate modified records with INFO/STR indicating the original\ + \ variant.\n\nAdds specified INFO tag to track original variants.\n" + info: null + example: + - "OLD_VARIANT" + required: false + direction: "input" + multiple: false + multiple_sep: ";" - type: "string" name: "--output_type" alternatives: - - "--O" - description: "Output type:\n u: uncompressed BCF\n z: compressed VCF\n b: compressed\ - \ BCF\n v: uncompressed VCF\n" + - "-O" + description: "Output type and compression level.\n\n**Options:**\n- `u`: uncompressed\ + \ BCF\n- `b`: compressed BCF\n- `v`: uncompressed VCF (default)\n- `z`: compressed\ + \ VCF (with optional compression level 0-9)\n" info: null + example: + - "z" required: false choices: - "u" @@ -169,24 +272,15 @@ argument_groups: direction: "input" multiple: false multiple_sep: ";" - - type: "string" - name: "--old_rec_tag" - description: "Annotate modified records with INFO/STR indicating the original\ - \ variant." - info: null - required: false - direction: "input" - multiple: false - multiple_sep: ";" - type: "string" name: "--regions" alternatives: - - "--r" - description: "Restrict to comma-separated list of regions. \nFollowing formats\ - \ are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​].\n" + - "-r" + description: "Restrict to comma-separated list of regions.\n\n**Formats supported:**\ + \ chr|chr:pos|chr:beg-end|chr:beg-[,…​]\n" info: null example: - - "20:1000000-2000000" + - "chr20:1000000-2000000" required: false direction: "input" multiple: false @@ -194,11 +288,12 @@ argument_groups: - type: "file" name: "--regions_file" alternatives: - - "--R" - description: "Restrict to regions listed in a file. \nRegions can be specified\ - \ either on a VCF, BED, or tab-delimited file (the default). \nFor more information\ - \ check manual.\n" + - "-R" + description: "Restrict to regions listed in a file.\n\nRegions can be specified\ + \ in VCF, BED, or tab-delimited format.\n" info: null + example: + - "regions.bed" must_exist: true create_parent: true required: false @@ -207,52 +302,54 @@ argument_groups: multiple_sep: ";" - type: "string" name: "--regions_overlap" - description: "This option controls how overlapping records are determined: \n\ - set to 'pos' or '0' if the VCF record has to have POS inside a region (this\ - \ corresponds to the default behavior of -t/-T); \nset to 'record' or '1' if\ - \ also overlapping records with POS outside a region should be included (this\ - \ is the default behavior of -r/-R, \nand includes indels with POS at the end\ - \ of a region, which are technically outside the region); \nor set to 'variant'\ - \ or '2' to include only true overlapping variation (compare the full VCF representation\ - \ \"TA>T-\" vs the true sequence variation \"A>-\").\n" + description: "Include if POS in the region (0), record overlaps (1), variant overlaps\ + \ (2).\n\n**Options:**\n- `0`: POS inside region (default for -t/-T)\n- `1`:\ + \ overlapping records included (default for -r/-R)\n- `2`: true overlapping\ + \ variation only\n" info: null + example: + - "1" required: false choices: - - "pos" - - "record" - - "variant" - "0" - "1" - "2" direction: "input" multiple: false multiple_sep: ";" - - type: "integer" - name: "--site_win" - alternatives: - - "-w" - description: "Buffer for sorting lines that changed position during realignment.\n" - info: null - required: false - direction: "input" - multiple: false - multiple_sep: ";" - type: "boolean_true" name: "--strict_filter" alternatives: - "-s" description: "When merging (-m+), merged site is PASS only if all sites being\ - \ merged PASS." + \ merged PASS.\n\nStricter FILTER handling during multiallelic joining.\n" info: null direction: "input" + - type: "string" + name: "--sort" + alternatives: + - "-S" + description: "Sort order: chr_pos,lex.\n\n**Options:**\n- `chr_pos`: Sort by chromosome\ + \ and position (default)\n- `lex`: Lexicographic sort\n" + info: null + example: + - "chr_pos" + required: false + choices: + - "chr_pos" + - "lex" + direction: "input" + multiple: false + multiple_sep: ";" - type: "string" name: "--targets" alternatives: - "-t" - description: "Similar to --regions but streams rather than index-jumps." + description: "Similar to --regions but streams rather than index-jumps.\n\nMore\ + \ efficient for processing many small regions.\n" info: null example: - - "20:1000000-2000000" + - "chr20:1000000-2000000" required: false direction: "input" multiple: false @@ -261,8 +358,11 @@ argument_groups: name: "--targets_file" alternatives: - "-T" - description: "Similar to --regions_file but streams rather than index-jumps." + description: "Similar to --regions_file but streams rather than index-jumps.\n\ + \nMore efficient for processing many regions from file.\n" info: null + example: + - "targets.bed" must_exist: true create_parent: true required: false @@ -272,19 +372,56 @@ argument_groups: - type: "string" name: "--targets_overlap" description: "Include if POS in the region (0), record overlaps (1), variant overlaps\ - \ (2).\nSimilar to --regions_overlap.\n" + \ (2).\n\nSimilar to --regions_overlap but for streaming mode.\n" info: null + example: + - "0" required: false choices: - - "pos" - - "record" - - "variant" - "0" - "1" - "2" direction: "input" multiple: false multiple_sep: ";" + - type: "integer" + name: "--verbosity" + alternatives: + - "-v" + description: "Verbosity level.\n\nControls amount of diagnostic output.\n" + info: null + example: + - 1 + required: false + direction: "input" + multiple: false + multiple_sep: ";" + - type: "integer" + name: "--site_win" + alternatives: + - "-w" + description: "Buffer for sorting lines which changed position during realignment.\n\ + \nLarger values use more memory but handle more complex rearrangements.\n" + info: null + example: + - 1000 + required: false + direction: "input" + multiple: false + multiple_sep: ";" + - type: "string" + name: "--write_index" + alternatives: + - "-W" + description: "Automatically index the output files.\n\n**Format:** Specify index\ + \ format or use default.\n" + info: null + example: + - "tbi" + required: false + direction: "input" + multiple: false + multiple_sep: ";" resources: - type: "bash_script" path: "script.sh" @@ -296,6 +433,8 @@ test_resources: - type: "bash_script" path: "test.sh" is_executable: true +- type: "file" + path: "test_helpers.sh" info: null status: "enabled" scope: @@ -303,6 +442,7 @@ scope: target: "public" requirements: commands: + - "bcftools" - "ps" keywords: - "Normalize" @@ -385,25 +525,14 @@ runners: engines: - type: "docker" id: "docker" - image: "debian:stable-slim" + image: "quay.io/biocontainers/bcftools:1.22--h3a4d415_1" target_registry: "images.viash-hub.com" target_tag: "main" namespace_separator: "/" setup: - - type: "apt" - packages: - - "bcftools" - - "procps" - interactive: false - type: "docker" run: - - "echo \"bcftools: \\\"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftools\ - \ //p')\\\"\" > /var/software_versions.txt\n" - test_setup: - - type: "apt" - packages: - - "tabix" - interactive: false + - "bcftools --version 2>&1 | head -1 | sed 's/bcftools /bcftools: /' > /var/software_versions.txt\n" entrypoint: [] cmd: null - type: "native" @@ -415,7 +544,7 @@ build_info: output: "target/nextflow/bcftools/bcftools_norm" executable: "target/nextflow/bcftools/bcftools_norm/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -437,138 +566,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bcftools/bcftools_norm/main.nf b/target/nextflow/bcftools/bcftools_norm/main.nf index 069402c5..a4583ad0 100644 --- a/target/nextflow/bcftools/bcftools_norm/main.nf +++ b/target/nextflow/bcftools/bcftools_norm/main.nf @@ -3058,10 +3058,10 @@ meta = [ { "type" : "file", "name" : "--input", - "alternatives" : [ - "-i" + "description" : "Input VCF/BCF file.\n\nThe file to be normalized, left-aligned, and/or processed.\n", + "example" : [ + "input.vcf.gz" ], - "description" : "Input VCF/BCF file.", "must_exist" : true, "create_parent" : true, "required" : true, @@ -3080,7 +3080,10 @@ meta = [ "alternatives" : [ "-o" ], - "description" : "Output normalized VCF/BCF file.", + "description" : "Write output to a file.\n\nIf not specified, output goes to standard output.\n", + "example" : [ + "normalized.vcf.gz" + ], "must_exist" : true, "create_parent" : true, "required" : true, @@ -3099,13 +3102,16 @@ meta = [ "alternatives" : [ "-a" ], - "description" : "Decompose complex variants (e.g., MNVs become consecutive SNVs).\n", + "description" : "Decompose complex variants (e.g., MNVs become consecutive SNVs).\n\nBreaks down complex variants into simpler components.\n", "direction" : "input" }, { "type" : "string", "name" : "--atom_overlaps", - "description" : "Use the star allele (*) for overlapping alleles or set to missing (.).\n", + "description" : "Use the star allele (*) for overlapping alleles or set to missing (.).\n\n**Options:**\n- `*`: Use star allele for overlaps (default)\n- `.`: Set overlapping alleles to missing\n", + "example" : [ + "*" + ], "required" : false, "choices" : [ ".", @@ -3121,7 +3127,10 @@ meta = [ "alternatives" : [ "-c" ], - "description" : "Check REF alleles and exit (e), warn (w), exclude (x), or set (s) bad sites.\n", + "description" : "Check REF alleles and exit (e), warn (w), exclude (x), or set (s) bad sites.\n\n**Options:**\n- `e`: exit on REF mismatch (default)\n- `w`: warn about REF mismatches\n- `x`: exclude sites with REF mismatches\n- `s`: set/fix REF mismatches\n", + "example" : [ + "w" + ], "required" : false, "choices" : [ "e", @@ -3133,33 +3142,62 @@ meta = [ "multiple" : false, "multiple_sep" : ";" }, + { + "type" : "boolean_true", + "name" : "--remove_duplicates_flag", + "alternatives" : [ + "-D" + ], + "description" : "Remove duplicate lines of the same type.\n\nShorthand for --rm_dup exact.\n", + "direction" : "input" + }, { "type" : "string", - "name" : "--remove_duplicates", + "name" : "--rm_dup", "alternatives" : [ "-d" ], - "description" : "Remove duplicate snps, indels, both, all, exact matches, or none (old -D option).", + "description" : "Remove duplicate snps|indels|both|all|exact.\n\n**Options:**\n- `snps`: Remove duplicate SNPs\n- `indels`: Remove duplicate indels\n- `both`: Remove duplicate SNPs and indels\n- `all`: Remove all duplicates\n- `exact`: Remove exact duplicates only\n", + "example" : [ + "exact" + ], "required" : false, "choices" : [ "snps", "indels", "both", "all", - "exact", - "none" + "exact" ], "direction" : "input", "multiple" : false, "multiple_sep" : ";" }, + { + "type" : "string", + "name" : "--exclude", + "alternatives" : [ + "-e" + ], + "description" : "Do not normalize records for which the expression is true.\n\nUses bcftools expression syntax (see man page for details).\n", + "example" : [ + "INFO/DP<10" + ], + "required" : false, + "direction" : "input", + "multiple" : false, + "multiple_sep" : ";" + }, { "type" : "file", "name" : "--fasta_ref", "alternatives" : [ "-f" ], - "description" : "Reference fasta sequence file.", + "description" : "Reference sequence file.\n\nRequired for checking REF alleles and left-alignment.\n", + "example" : [ + "reference.fa" + ], "must_exist" : true, "create_parent" : true, "required" : false, @@ -3170,13 +3208,48 @@ meta = [ { "type" : "boolean_true", "name" : "--force", - "description" : "Try to proceed even if malformed tags are encountered. \nExperimental, use at your own risk.\n", + "description" : "Try to proceed even if malformed tags are encountered.\n\n**Warning:** Experimental feature, use at your own risk.\n", "direction" : "input" }, + { + "type" : "file", + "name" : "--gff_annot", + "alternatives" : [ + "-g" + ], + "description" : "Follow HGVS 3'rule and right-align variants in transcripts on the forward strand.\n\nUses GFF annotation file for transcript information.\n", + "example" : [ + "genes.gff" + ], + "must_exist" : true, + "create_parent" : true, + "required" : false, + "direction" : "input", + "multiple" : false, + "multiple_sep" : ";" + }, + { + "type" : "string", + "name" : "--include", + "alternatives" : [ + "-i" + ], + "description" : "Normalize only records for which the expression is true.\n\nUses bcftools expression syntax (see man page for details).\n", + "example" : [ + "QUAL>=30" + ], + "required" : false, + "direction" : "input", + "multiple" : false, + "multiple_sep" : ";" + }, { "type" : "string", "name" : "--keep_sum", - "description" : "Keep vector sum constant when splitting multiallelics (see github issue #360).\n", + "description" : "Keep vector sum constant when splitting multiallelics.\n\nComma-separated list of INFO tags (see github issue #360).\n", + "example" : [ + "AC,AF" + ], "required" : false, "direction" : "input", "multiple" : false, @@ -3188,7 +3261,10 @@ meta = [ "alternatives" : [ "-m" ], - "description" : "Split multiallelics (-) or join biallelics (+), type: snps, indels, both, any [default: both].\n", + "description" : "Split multiallelics (-) or join biallelics (+), type: snps|indels|both|any.\n\n**Options:**\n- `-both`: Split multiallelic sites (default)\n- `+both`: Join biallelic sites\n- Use `snps`, `indels`, `any` for specific variant types\n", + "example" : [ + "-both" + ], "required" : false, "choices" : [ "+snps", @@ -3204,10 +3280,26 @@ meta = [ "multiple" : false, "multiple_sep" : ";" }, + { + "type" : "string", + "name" : "--multi_overlaps", + "description" : "Fill in the reference (0) or missing (.) allele when splitting multiallelics.\n\n**Options:**\n- `0`: Fill with reference allele (default)\n- `.`: Fill with missing allele\n", + "example" : [ + "0" + ], + "required" : false, + "choices" : [ + "0", + "." + ], + "direction" : "input", + "multiple" : false, + "multiple_sep" : ";" + }, { "type" : "boolean_true", "name" : "--no_version", - "description" : "Do not append version and command line information to the header.", + "description" : "Do not append version and command line to the header.\n\nProduces cleaner output headers.\n", "direction" : "input" }, { @@ -3216,16 +3308,31 @@ meta = [ "alternatives" : [ "-N" ], - "description" : "Do not normalize indels (with -m or -c s).", + "description" : "Do not normalize indels (with -m or -c s).\n\nSkips indel left-alignment and normalization.\n", "direction" : "input" }, + { + "type" : "string", + "name" : "--old_rec_tag", + "description" : "Annotate modified records with INFO/STR indicating the original variant.\n\nAdds specified INFO tag to track original variants.\n", + "example" : [ + "OLD_VARIANT" + ], + "required" : false, + "direction" : "input", + "multiple" : false, + "multiple_sep" : ";" + }, { "type" : "string", "name" : "--output_type", "alternatives" : [ - "--O" + "-O" + ], + "description" : "Output type and compression level.\n\n**Options:**\n- `u`: uncompressed BCF\n- `b`: compressed BCF\n- `v`: uncompressed VCF (default)\n- `z`: compressed VCF (with optional compression level 0-9)\n", + "example" : [ + "z" ], - "description" : "Output type:\n u: uncompressed BCF\n z: compressed VCF\n b: compressed BCF\n v: uncompressed VCF\n", "required" : false, "choices" : [ "u", @@ -3237,24 +3344,15 @@ meta = [ "multiple" : false, "multiple_sep" : ";" }, - { - "type" : "string", - "name" : "--old_rec_tag", - "description" : "Annotate modified records with INFO/STR indicating the original variant.", - "required" : false, - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - }, { "type" : "string", "name" : "--regions", "alternatives" : [ - "--r" + "-r" ], - "description" : "Restrict to comma-separated list of regions. \nFollowing formats are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​].\n", + "description" : "Restrict to comma-separated list of regions.\n\n**Formats supported:** chr|chr:pos|chr:beg-end|chr:beg-[,…​]\n", "example" : [ - "20:1000000-2000000" + "chr20:1000000-2000000" ], "required" : false, "direction" : "input", @@ -3265,9 +3363,12 @@ meta = [ "type" : "file", "name" : "--regions_file", "alternatives" : [ - "--R" + "-R" + ], + "description" : "Restrict to regions listed in a file.\n\nRegions can be specified in VCF, BED, or tab-delimited format.\n", + "example" : [ + "regions.bed" ], - "description" : "Restrict to regions listed in a file. \nRegions can be specified either on a VCF, BED, or tab-delimited file (the default). \nFor more information check manual.\n", "must_exist" : true, "create_parent" : true, "required" : false, @@ -3278,12 +3379,12 @@ meta = [ { "type" : "string", "name" : "--regions_overlap", - "description" : "This option controls how overlapping records are determined: \nset to 'pos' or '0' if the VCF record has to have POS inside a region (this corresponds to the default behavior of -t/-T); \nset to 'record' or '1' if also overlapping records with POS outside a region should be included (this is the default behavior of -r/-R, \nand includes indels with POS at the end of a region, which are technically outside the region); \nor set to 'variant' or '2' to include only true overlapping variation (compare the full VCF representation \\"TA>T-\\" vs the true sequence variation \\"A>-\\").\n", + "description" : "Include if POS in the region (0), record overlaps (1), variant overlaps (2).\n\n**Options:**\n- `0`: POS inside region (default for -t/-T)\n- `1`: overlapping records included (default for -r/-R)\n- `2`: true overlapping variation only\n", + "example" : [ + "1" + ], "required" : false, "choices" : [ - "pos", - "record", - "variant", "0", "1", "2" @@ -3292,36 +3393,43 @@ meta = [ "multiple" : false, "multiple_sep" : ";" }, - { - "type" : "integer", - "name" : "--site_win", - "alternatives" : [ - "-w" - ], - "description" : "Buffer for sorting lines that changed position during realignment.\n", - "required" : false, - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - }, { "type" : "boolean_true", "name" : "--strict_filter", "alternatives" : [ "-s" ], - "description" : "When merging (-m+), merged site is PASS only if all sites being merged PASS.", + "description" : "When merging (-m+), merged site is PASS only if all sites being merged PASS.\n\nStricter FILTER handling during multiallelic joining.\n", "direction" : "input" }, + { + "type" : "string", + "name" : "--sort", + "alternatives" : [ + "-S" + ], + "description" : "Sort order: chr_pos,lex.\n\n**Options:**\n- `chr_pos`: Sort by chromosome and position (default)\n- `lex`: Lexicographic sort\n", + "example" : [ + "chr_pos" + ], + "required" : false, + "choices" : [ + "chr_pos", + "lex" + ], + "direction" : "input", + "multiple" : false, + "multiple_sep" : ";" + }, { "type" : "string", "name" : "--targets", "alternatives" : [ "-t" ], - "description" : "Similar to --regions but streams rather than index-jumps.", + "description" : "Similar to --regions but streams rather than index-jumps.\n\nMore efficient for processing many small regions.\n", "example" : [ - "20:1000000-2000000" + "chr20:1000000-2000000" ], "required" : false, "direction" : "input", @@ -3334,7 +3442,10 @@ meta = [ "alternatives" : [ "-T" ], - "description" : "Similar to --regions_file but streams rather than index-jumps.", + "description" : "Similar to --regions_file but streams rather than index-jumps.\n\nMore efficient for processing many regions from file.\n", + "example" : [ + "targets.bed" + ], "must_exist" : true, "create_parent" : true, "required" : false, @@ -3345,12 +3456,12 @@ meta = [ { "type" : "string", "name" : "--targets_overlap", - "description" : "Include if POS in the region (0), record overlaps (1), variant overlaps (2).\nSimilar to --regions_overlap.\n", + "description" : "Include if POS in the region (0), record overlaps (1), variant overlaps (2).\n\nSimilar to --regions_overlap but for streaming mode.\n", + "example" : [ + "0" + ], "required" : false, "choices" : [ - "pos", - "record", - "variant", "0", "1", "2" @@ -3358,6 +3469,51 @@ meta = [ "direction" : "input", "multiple" : false, "multiple_sep" : ";" + }, + { + "type" : "integer", + "name" : "--verbosity", + "alternatives" : [ + "-v" + ], + "description" : "Verbosity level.\n\nControls amount of diagnostic output.\n", + "example" : [ + 1 + ], + "required" : false, + "direction" : "input", + "multiple" : false, + "multiple_sep" : ";" + }, + { + "type" : "integer", + "name" : "--site_win", + "alternatives" : [ + "-w" + ], + "description" : "Buffer for sorting lines which changed position during realignment.\n\nLarger values use more memory but handle more complex rearrangements.\n", + "example" : [ + 1000 + ], + "required" : false, + "direction" : "input", + "multiple" : false, + "multiple_sep" : ";" + }, + { + "type" : "string", + "name" : "--write_index", + "alternatives" : [ + "-W" + ], + "description" : "Automatically index the output files.\n\n**Format:** Specify index format or use default.\n", + "example" : [ + "tbi" + ], + "required" : false, + "direction" : "input", + "multiple" : false, + "multiple_sep" : ";" } ] } @@ -3375,6 +3531,10 @@ meta = [ "type" : "bash_script", "path" : "test.sh", "is_executable" : true + }, + { + "type" : "file", + "path" : "/src/_utils/test_helpers.sh" } ], "status" : "enabled", @@ -3384,6 +3544,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bcftools", "ps" ] }, @@ -3482,34 +3643,17 @@ meta = [ { "type" : "docker", "id" : "docker", - "image" : "debian:stable-slim", + "image" : "quay.io/biocontainers/bcftools:1.22--h3a4d415_1", "target_registry" : "images.viash-hub.com", "target_tag" : "main", "namespace_separator" : "/", "setup" : [ - { - "type" : "apt", - "packages" : [ - "bcftools", - "procps" - ], - "interactive" : false - }, { "type" : "docker", "run" : [ - "echo \\"bcftools: \\\\\\"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftools //p')\\\\\\"\\" > /var/software_versions.txt\n" + "bcftools --version 2>&1 | head -1 | sed 's/bcftools /bcftools: /' > /var/software_versions.txt\n" ] } - ], - "test_setup" : [ - { - "type" : "apt", - "packages" : [ - "tabix" - ], - "interactive" : false - } ] }, { @@ -3523,7 +3667,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bcftools/bcftools_norm", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3535,225 +3679,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", @@ -3787,23 +3717,31 @@ $( if [ ! -z ${VIASH_PAR_OUTPUT+x} ]; then echo "${VIASH_PAR_OUTPUT}" | sed "s#' $( if [ ! -z ${VIASH_PAR_ATOMIZE+x} ]; then echo "${VIASH_PAR_ATOMIZE}" | sed "s#'#'\\"'\\"'#g;s#.*#par_atomize='&'#" ; else echo "# par_atomize="; fi ) $( if [ ! -z ${VIASH_PAR_ATOM_OVERLAPS+x} ]; then echo "${VIASH_PAR_ATOM_OVERLAPS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_atom_overlaps='&'#" ; else echo "# par_atom_overlaps="; fi ) $( if [ ! -z ${VIASH_PAR_CHECK_REF+x} ]; then echo "${VIASH_PAR_CHECK_REF}" | sed "s#'#'\\"'\\"'#g;s#.*#par_check_ref='&'#" ; else echo "# par_check_ref="; fi ) -$( if [ ! -z ${VIASH_PAR_REMOVE_DUPLICATES+x} ]; then echo "${VIASH_PAR_REMOVE_DUPLICATES}" | sed "s#'#'\\"'\\"'#g;s#.*#par_remove_duplicates='&'#" ; else echo "# par_remove_duplicates="; fi ) +$( if [ ! -z ${VIASH_PAR_REMOVE_DUPLICATES_FLAG+x} ]; then echo "${VIASH_PAR_REMOVE_DUPLICATES_FLAG}" | sed "s#'#'\\"'\\"'#g;s#.*#par_remove_duplicates_flag='&'#" ; else echo "# par_remove_duplicates_flag="; fi ) +$( if [ ! -z ${VIASH_PAR_RM_DUP+x} ]; then echo "${VIASH_PAR_RM_DUP}" | sed "s#'#'\\"'\\"'#g;s#.*#par_rm_dup='&'#" ; else echo "# par_rm_dup="; fi ) +$( if [ ! -z ${VIASH_PAR_EXCLUDE+x} ]; then echo "${VIASH_PAR_EXCLUDE}" | sed "s#'#'\\"'\\"'#g;s#.*#par_exclude='&'#" ; else echo "# par_exclude="; fi ) $( if [ ! -z ${VIASH_PAR_FASTA_REF+x} ]; then echo "${VIASH_PAR_FASTA_REF}" | sed "s#'#'\\"'\\"'#g;s#.*#par_fasta_ref='&'#" ; else echo "# par_fasta_ref="; fi ) $( if [ ! -z ${VIASH_PAR_FORCE+x} ]; then echo "${VIASH_PAR_FORCE}" | sed "s#'#'\\"'\\"'#g;s#.*#par_force='&'#" ; else echo "# par_force="; fi ) +$( if [ ! -z ${VIASH_PAR_GFF_ANNOT+x} ]; then echo "${VIASH_PAR_GFF_ANNOT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_gff_annot='&'#" ; else echo "# par_gff_annot="; fi ) +$( if [ ! -z ${VIASH_PAR_INCLUDE+x} ]; then echo "${VIASH_PAR_INCLUDE}" | sed "s#'#'\\"'\\"'#g;s#.*#par_include='&'#" ; else echo "# par_include="; fi ) $( if [ ! -z ${VIASH_PAR_KEEP_SUM+x} ]; then echo "${VIASH_PAR_KEEP_SUM}" | sed "s#'#'\\"'\\"'#g;s#.*#par_keep_sum='&'#" ; else echo "# par_keep_sum="; fi ) $( if [ ! -z ${VIASH_PAR_MULTIALLELICS+x} ]; then echo "${VIASH_PAR_MULTIALLELICS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_multiallelics='&'#" ; else echo "# par_multiallelics="; fi ) +$( if [ ! -z ${VIASH_PAR_MULTI_OVERLAPS+x} ]; then echo "${VIASH_PAR_MULTI_OVERLAPS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_multi_overlaps='&'#" ; else echo "# par_multi_overlaps="; fi ) $( if [ ! -z ${VIASH_PAR_NO_VERSION+x} ]; then echo "${VIASH_PAR_NO_VERSION}" | sed "s#'#'\\"'\\"'#g;s#.*#par_no_version='&'#" ; else echo "# par_no_version="; fi ) $( if [ ! -z ${VIASH_PAR_DO_NOT_NORMALIZE+x} ]; then echo "${VIASH_PAR_DO_NOT_NORMALIZE}" | sed "s#'#'\\"'\\"'#g;s#.*#par_do_not_normalize='&'#" ; else echo "# par_do_not_normalize="; fi ) -$( if [ ! -z ${VIASH_PAR_OUTPUT_TYPE+x} ]; then echo "${VIASH_PAR_OUTPUT_TYPE}" | sed "s#'#'\\"'\\"'#g;s#.*#par_output_type='&'#" ; else echo "# par_output_type="; fi ) $( if [ ! -z ${VIASH_PAR_OLD_REC_TAG+x} ]; then echo "${VIASH_PAR_OLD_REC_TAG}" | sed "s#'#'\\"'\\"'#g;s#.*#par_old_rec_tag='&'#" ; else echo "# par_old_rec_tag="; fi ) +$( if [ ! -z ${VIASH_PAR_OUTPUT_TYPE+x} ]; then echo "${VIASH_PAR_OUTPUT_TYPE}" | sed "s#'#'\\"'\\"'#g;s#.*#par_output_type='&'#" ; else echo "# par_output_type="; fi ) $( if [ ! -z ${VIASH_PAR_REGIONS+x} ]; then echo "${VIASH_PAR_REGIONS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_regions='&'#" ; else echo "# par_regions="; fi ) $( if [ ! -z ${VIASH_PAR_REGIONS_FILE+x} ]; then echo "${VIASH_PAR_REGIONS_FILE}" | sed "s#'#'\\"'\\"'#g;s#.*#par_regions_file='&'#" ; else echo "# par_regions_file="; fi ) $( if [ ! -z ${VIASH_PAR_REGIONS_OVERLAP+x} ]; then echo "${VIASH_PAR_REGIONS_OVERLAP}" | sed "s#'#'\\"'\\"'#g;s#.*#par_regions_overlap='&'#" ; else echo "# par_regions_overlap="; fi ) -$( if [ ! -z ${VIASH_PAR_SITE_WIN+x} ]; then echo "${VIASH_PAR_SITE_WIN}" | sed "s#'#'\\"'\\"'#g;s#.*#par_site_win='&'#" ; else echo "# par_site_win="; fi ) $( if [ ! -z ${VIASH_PAR_STRICT_FILTER+x} ]; then echo "${VIASH_PAR_STRICT_FILTER}" | sed "s#'#'\\"'\\"'#g;s#.*#par_strict_filter='&'#" ; else echo "# par_strict_filter="; fi ) +$( if [ ! -z ${VIASH_PAR_SORT+x} ]; then echo "${VIASH_PAR_SORT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_sort='&'#" ; else echo "# par_sort="; fi ) $( if [ ! -z ${VIASH_PAR_TARGETS+x} ]; then echo "${VIASH_PAR_TARGETS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_targets='&'#" ; else echo "# par_targets="; fi ) $( if [ ! -z ${VIASH_PAR_TARGETS_FILE+x} ]; then echo "${VIASH_PAR_TARGETS_FILE}" | sed "s#'#'\\"'\\"'#g;s#.*#par_targets_file='&'#" ; else echo "# par_targets_file="; fi ) $( if [ ! -z ${VIASH_PAR_TARGETS_OVERLAP+x} ]; then echo "${VIASH_PAR_TARGETS_OVERLAP}" | sed "s#'#'\\"'\\"'#g;s#.*#par_targets_overlap='&'#" ; else echo "# par_targets_overlap="; fi ) +$( if [ ! -z ${VIASH_PAR_VERBOSITY+x} ]; then echo "${VIASH_PAR_VERBOSITY}" | sed "s#'#'\\"'\\"'#g;s#.*#par_verbosity='&'#" ; else echo "# par_verbosity="; fi ) +$( if [ ! -z ${VIASH_PAR_SITE_WIN+x} ]; then echo "${VIASH_PAR_SITE_WIN}" | sed "s#'#'\\"'\\"'#g;s#.*#par_site_win='&'#" ; else echo "# par_site_win="; fi ) +$( if [ ! -z ${VIASH_PAR_WRITE_INDEX+x} ]; then echo "${VIASH_PAR_WRITE_INDEX}" | sed "s#'#'\\"'\\"'#g;s#.*#par_write_index='&'#" ; else echo "# par_write_index="; fi ) $( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "${VIASH_META_NAME}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_name='&'#" ; else echo "# meta_name="; fi ) $( if [ ! -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then echo "${VIASH_META_FUNCTIONALITY_NAME}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_functionality_name='&'#" ; else echo "# meta_functionality_name="; fi ) $( if [ ! -z ${VIASH_META_RESOURCES_DIR+x} ]; then echo "${VIASH_META_RESOURCES_DIR}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_resources_dir='&'#" ; else echo "# meta_resources_dir="; fi ) @@ -3825,50 +3763,61 @@ $( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}" ## VIASH END -# Exit on error set -eo pipefail -# Unset parameters +# Unset false boolean parameters unset_if_false=( - par_atomize - par_remove_duplicates - par_force - par_no_version - par_do_not_normalize - par_strict_filter + par_atomize + par_remove_duplicates_flag + par_force + par_no_version + par_do_not_normalize + par_strict_filter ) for par in \\${unset_if_false[@]}; do - test_val="\\${!par}" - [[ "\\$test_val" == "false" ]] && unset \\$par + test_val="\\${!par}" + [[ "\\$test_val" == "false" ]] && unset \\$par done -# Execute bcftools norm with the provided arguments -bcftools norm \\\\ - \\${par_atomize:+--atomize} \\\\ - \\${par_atom_overlaps:+--atom-overlaps "\\$par_atom_overlaps"} \\\\ - \\${par_check_ref:+-c "\\$par_check_ref"} \\\\ - \\${par_remove_duplicates:+-d "\\$par_remove_duplicates"} \\\\ - \\${par_fasta_ref:+-f "\\$par_fasta_ref"} \\\\ - \\${par_force:+--force} \\\\ - \\${par_keep_sum:+--keep-sum "\\$par_keep_sum"} \\\\ - \\${par_multiallelics:+-m "\\$par_multiallelics"} \\\\ - \\${par_no_version:+--no-version} \\\\ - \\${par_do_not_normalize:+-N} \\\\ - \\${par_old_rec_tag:+--old-rec-tag "\\$par_old_rec_tag"} \\\\ - \\${par_regions:+-r "\\$par_regions"} \\\\ - \\${par_regions_file:+-R "\\$par_regions_file"} \\\\ - \\${par_regions_overlap:+--regions-overlap "\\$par_regions_overlap"} \\\\ - \\${par_site_win:+-w "\\$par_site_win"} \\\\ - \\${par_strict_filter:+-s} \\\\ - \\${par_targets:+-t "\\$par_targets"} \\\\ - \\${par_targets_file:+-T "\\$par_targets_file"} \\\\ - \\${par_targets_overlap:+--targets-overlap "\\$par_targets_overlap"} \\\\ - \\${meta_cpus:+--threads "\\$meta_cpus"} \\\\ - \\${par_output_type:+-O "\\$par_output_type"} \\\\ - -o \\$par_output \\\\ - \\$par_input - +# Build command array +cmd_args=( + bcftools norm + \\${par_atomize:+--atomize} + \\${par_atom_overlaps:+--atom-overlaps "\\$par_atom_overlaps"} + \\${par_check_ref:+--check-ref "\\$par_check_ref"} + \\${par_remove_duplicates_flag:+--remove-duplicates} + \\${par_rm_dup:+--rm-dup "\\$par_rm_dup"} + \\${par_exclude:+--exclude "\\$par_exclude"} + \\${par_fasta_ref:+--fasta-ref "\\$par_fasta_ref"} + \\${par_force:+--force} + \\${par_gff_annot:+--gff-annot "\\$par_gff_annot"} + \\${par_include:+--include "\\$par_include"} + \\${par_keep_sum:+--keep-sum "\\$par_keep_sum"} + \\${par_multiallelics:+--multiallelics "\\$par_multiallelics"} + \\${par_multi_overlaps:+--multi-overlaps "\\$par_multi_overlaps"} + \\${par_no_version:+--no-version} + \\${par_do_not_normalize:+--do-not-normalize} + \\${par_old_rec_tag:+--old-rec-tag "\\$par_old_rec_tag"} + \\${par_output_type:+--output-type "\\$par_output_type"} + \\${par_regions:+--regions "\\$par_regions"} + \\${par_regions_file:+--regions-file "\\$par_regions_file"} + \\${par_regions_overlap:+--regions-overlap "\\$par_regions_overlap"} + \\${par_strict_filter:+--strict-filter} + \\${par_sort:+--sort "\\$par_sort"} + \\${par_targets:+--targets "\\$par_targets"} + \\${par_targets_file:+--targets-file "\\$par_targets_file"} + \\${par_targets_overlap:+--targets-overlap "\\$par_targets_overlap"} + \\${meta_cpus:+--threads "\\$meta_cpus"} + \\${par_verbosity:+--verbosity "\\$par_verbosity"} + \\${par_site_win:+--site-win "\\$par_site_win"} + \\${par_write_index:+--write-index="\\$par_write_index"} + \\${par_output:+--output "\\$par_output"} + "\\$par_input" +) + +# Execute command +"\\${cmd_args[@]}" VIASHMAIN bash "$tempscript" ''' diff --git a/target/nextflow/bcftools/bcftools_norm/nextflow_schema.json b/target/nextflow/bcftools/bcftools_norm/nextflow_schema.json index f7bcc49f..70793465 100644 --- a/target/nextflow/bcftools/bcftools_norm/nextflow_schema.json +++ b/target/nextflow/bcftools/bcftools_norm/nextflow_schema.json @@ -13,8 +13,8 @@ "type": "string", "format": "path", "exists": true, - "description": "Input VCF/BCF file.", - "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. " + "description": "Input VCF/BCF file.\n\nThe file to be normalized, left-aligned, and/or processed.\n", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"input.vcf.gz\"`. " } } }, @@ -26,9 +26,9 @@ "output": { "type": "string", "format": "path", - "description": "Output normalized VCF/BCF file.", - "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output\"`, direction: `output`. ", - "default": "$id.$key.output" + "description": "Write output to a file.\n\nIf not specified, output goes to standard output.\n", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.gz\"`, direction: `output`, example: `\"normalized.vcf.gz\"`. ", + "default": "$id.$key.output.gz" } } }, @@ -39,14 +39,14 @@ "properties": { "atomize": { "type": "boolean", - "description": "Decompose complex variants (e.g., MNVs become consecutive SNVs).\n", + "description": "Decompose complex variants (e.g., MNVs become consecutive SNVs).\n\nBreaks down complex variants into simpler components.\n", "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", "default": false }, "atom_overlaps": { "type": "string", - "description": "Use the star allele (*) for overlapping alleles or set to missing (.).\n", - "help_text": "Type: `string`, multiple: `False`, choices: ``.`, `*``. ", + "description": "Use the star allele (*) for overlapping alleles or set to missing (.).\n\n**Options:**\n- `*`: Use star allele for overlaps (default)\n- `.`: Set overlapping alleles to missing\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"*\"`, choices: ``.`, `*``. ", "enum": [ ".", "*" @@ -54,8 +54,8 @@ }, "check_ref": { "type": "string", - "description": "Check REF alleles and exit (e), warn (w), exclude (x), or set (s) bad sites.\n", - "help_text": "Type: `string`, multiple: `False`, choices: ``e`, `w`, `x`, `s``. ", + "description": "Check REF alleles and exit (e), warn (w), exclude (x), or set (s) bad sites.\n\n**Options:**\n- `e`: exit on REF mismatch (default)\n- `w`: warn about REF mismatches\n- `x`: exclude sites with REF mismatches\n- `s`: set/fix REF mismatches\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"w\"`, choices: ``e`, `w`, `x`, `s``. ", "enum": [ "e", "w", @@ -63,40 +63,61 @@ "s" ] }, - "remove_duplicates": { + "remove_duplicates_flag": { + "type": "boolean", + "description": "Remove duplicate lines of the same type.\n\nShorthand for --rm_dup exact.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "rm_dup": { "type": "string", - "description": "Remove duplicate snps, indels, both, all, exact matches, or none (old -D option).", - "help_text": "Type: `string`, multiple: `False`, choices: ``snps`, `indels`, `both`, `all`, `exact`, `none``. ", + "description": "Remove duplicate snps|indels|both|all|exact.\n\n**Options:**\n- `snps`: Remove duplicate SNPs\n- `indels`: Remove duplicate indels\n- `both`: Remove duplicate SNPs and indels\n- `all`: Remove all duplicates\n- `exact`: Remove exact duplicates only\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"exact\"`, choices: ``snps`, `indels`, `both`, `all`, `exact``. ", "enum": [ "snps", "indels", "both", "all", - "exact", - "none" + "exact" ] }, + "exclude": { + "type": "string", + "description": "Do not normalize records for which the expression is true.\n\nUses bcftools expression syntax (see man page for details).\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"INFO/DP<10\"`. " + }, "fasta_ref": { "type": "string", "format": "path", - "description": "Reference fasta sequence file.", - "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + "description": "Reference sequence file.\n\nRequired for checking REF alleles and left-alignment.\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"reference.fa\"`. " }, "force": { "type": "boolean", - "description": "Try to proceed even if malformed tags are encountered", + "description": "Try to proceed even if malformed tags are encountered.\n\n**Warning:** Experimental feature, use at your own risk.\n", "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", "default": false }, + "gff_annot": { + "type": "string", + "format": "path", + "description": "Follow HGVS 3'rule and right-align variants in transcripts on the forward strand.\n\nUses GFF annotation file for transcript information.\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"genes.gff\"`. " + }, + "include": { + "type": "string", + "description": "Normalize only records for which the expression is true.\n\nUses bcftools expression syntax (see man page for details).\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"QUAL>=30\"`. " + }, "keep_sum": { "type": "string", - "description": "Keep vector sum constant when splitting multiallelics (see github issue #360).\n", - "help_text": "Type: `string`, multiple: `False`. " + "description": "Keep vector sum constant when splitting multiallelics.\n\nComma-separated list of INFO tags (see github issue #360).\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"AC,AF\"`. " }, "multiallelics": { "type": "string", - "description": "Split multiallelics (-) or join biallelics (+), type: snps, indels, both, any [default: both].\n", - "help_text": "Type: `string`, multiple: `False`, choices: ``+snps`, `+indels`, `+both`, `+any`, `-snps`, `-indels`, `-both`, `-any``. ", + "description": "Split multiallelics (-) or join biallelics (+), type: snps|indels|both|any.\n\n**Options:**\n- `-both`: Split multiallelic sites (default)\n- `+both`: Join biallelic sites\n- Use `snps`, `indels`, `any` for specific variant types\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"-both\"`, choices: ``+snps`, `+indels`, `+both`, `+any`, `-snps`, `-indels`, `-both`, `-any``. ", "enum": [ "+snps", "+indels", @@ -108,22 +129,36 @@ "-any" ] }, + "multi_overlaps": { + "type": "string", + "description": "Fill in the reference (0) or missing (.) allele when splitting multiallelics.\n\n**Options:**\n- `0`: Fill with reference allele (default)\n- `.`: Fill with missing allele\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"0\"`, choices: ``0`, `.``. ", + "enum": [ + "0", + "." + ] + }, "no_version": { "type": "boolean", - "description": "Do not append version and command line information to the header.", + "description": "Do not append version and command line to the header.\n\nProduces cleaner output headers.\n", "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", "default": false }, "do_not_normalize": { "type": "boolean", - "description": "Do not normalize indels (with -m or -c s).", + "description": "Do not normalize indels (with -m or -c s).\n\nSkips indel left-alignment and normalization.\n", "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", "default": false }, + "old_rec_tag": { + "type": "string", + "description": "Annotate modified records with INFO/STR indicating the original variant.\n\nAdds specified INFO tag to track original variants.\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"OLD_VARIANT\"`. " + }, "output_type": { "type": "string", - "description": "Output type:\n u: uncompressed BCF\n z: compressed VCF\n b: compressed BCF\n v: uncompressed VCF\n", - "help_text": "Type: `string`, multiple: `False`, choices: ``u`, `z`, `b`, `v``. ", + "description": "Output type and compression level.\n\n**Options:**\n- `u`: uncompressed BCF\n- `b`: compressed BCF\n- `v`: uncompressed VCF (default)\n- `z`: compressed VCF (with optional compression level 0-9)\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"z\"`, choices: ``u`, `z`, `b`, `v``. ", "enum": [ "u", "z", @@ -131,69 +166,77 @@ "v" ] }, - "old_rec_tag": { - "type": "string", - "description": "Annotate modified records with INFO/STR indicating the original variant.", - "help_text": "Type: `string`, multiple: `False`. " - }, "regions": { "type": "string", - "description": "Restrict to comma-separated list of regions", - "help_text": "Type: `string`, multiple: `False`, example: `\"20:1000000-2000000\"`. " + "description": "Restrict to comma-separated list of regions.\n\n**Formats supported:** chr|chr:pos|chr:beg-end|chr:beg-[,…​]\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"chr20:1000000-2000000\"`. " }, "regions_file": { "type": "string", "format": "path", - "description": "Restrict to regions listed in a file", - "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + "description": "Restrict to regions listed in a file.\n\nRegions can be specified in VCF, BED, or tab-delimited format.\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"regions.bed\"`. " }, "regions_overlap": { "type": "string", - "description": "This option controls how overlapping records are determined: \nset to 'pos' or '0' if the VCF record has to have POS inside a region (this corresponds to the default behavior of -t/-T); \nset to 'record' or '1' if also overlapping records with POS outside a region should be included (this is the default behavior of -r/-R, \nand includes indels with POS at the end of a region, which are technically outside the region); \nor set to 'variant' or '2' to include only true overlapping variation (compare the full VCF representation \"TA>T-\" vs the true sequence variation \"A>-\").\n", - "help_text": "Type: `string`, multiple: `False`, choices: ``pos`, `record`, `variant`, `0`, `1`, `2``. ", + "description": "Include if POS in the region (0), record overlaps (1), variant overlaps (2).\n\n**Options:**\n- `0`: POS inside region (default for -t/-T)\n- `1`: overlapping records included (default for -r/-R)\n- `2`: true overlapping variation only\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"1\"`, choices: ``0`, `1`, `2``. ", "enum": [ - "pos", - "record", - "variant", "0", "1", "2" ] }, - "site_win": { - "type": "integer", - "description": "Buffer for sorting lines that changed position during realignment.\n", - "help_text": "Type: `integer`, multiple: `False`. " - }, "strict_filter": { "type": "boolean", - "description": "When merging (-m+), merged site is PASS only if all sites being merged PASS.", + "description": "When merging (-m+), merged site is PASS only if all sites being merged PASS.\n\nStricter FILTER handling during multiallelic joining.\n", "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", "default": false }, + "sort": { + "type": "string", + "description": "Sort order: chr_pos,lex.\n\n**Options:**\n- `chr_pos`: Sort by chromosome and position (default)\n- `lex`: Lexicographic sort\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"chr_pos\"`, choices: ``chr_pos`, `lex``. ", + "enum": [ + "chr_pos", + "lex" + ] + }, "targets": { "type": "string", - "description": "Similar to --regions but streams rather than index-jumps.", - "help_text": "Type: `string`, multiple: `False`, example: `\"20:1000000-2000000\"`. " + "description": "Similar to --regions but streams rather than index-jumps.\n\nMore efficient for processing many small regions.\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"chr20:1000000-2000000\"`. " }, "targets_file": { "type": "string", "format": "path", - "description": "Similar to --regions_file but streams rather than index-jumps.", - "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + "description": "Similar to --regions_file but streams rather than index-jumps.\n\nMore efficient for processing many regions from file.\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"targets.bed\"`. " }, "targets_overlap": { "type": "string", - "description": "Include if POS in the region (0), record overlaps (1), variant overlaps (2).\nSimilar to --regions_overlap.\n", - "help_text": "Type: `string`, multiple: `False`, choices: ``pos`, `record`, `variant`, `0`, `1`, `2``. ", + "description": "Include if POS in the region (0), record overlaps (1), variant overlaps (2).\n\nSimilar to --regions_overlap but for streaming mode.\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"0\"`, choices: ``0`, `1`, `2``. ", "enum": [ - "pos", - "record", - "variant", "0", "1", "2" ] + }, + "verbosity": { + "type": "integer", + "description": "Verbosity level.\n\nControls amount of diagnostic output.\n", + "help_text": "Type: `integer`, multiple: `False`, example: `1`. " + }, + "site_win": { + "type": "integer", + "description": "Buffer for sorting lines which changed position during realignment.\n\nLarger values use more memory but handle more complex rearrangements.\n", + "help_text": "Type: `integer`, multiple: `False`, example: `1000`. " + }, + "write_index": { + "type": "string", + "description": "Automatically index the output files.\n\n**Format:** Specify index format or use default.\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"tbi\"`. " } } }, diff --git a/target/nextflow/bcftools/bcftools_sort/.config.vsh.yaml b/target/nextflow/bcftools/bcftools_sort/.config.vsh.yaml index 418080b8..67a69e6e 100644 --- a/target/nextflow/bcftools/bcftools_sort/.config.vsh.yaml +++ b/target/nextflow/bcftools/bcftools_sort/.config.vsh.yaml @@ -5,7 +5,6 @@ authors: - name: "Theodoro Gasperin Terra Camargo" roles: - "author" - - "maintainer" info: links: email: "theodorogtc@gmail.com" @@ -16,10 +15,11 @@ argument_groups: arguments: - type: "file" name: "--input" - alternatives: - - "-i" - description: "Input VCF/BCF file." + description: "Input VCF/BCF file to sort.\n\nThe file to be sorted by genomic\ + \ coordinates.\n" info: null + example: + - "input.vcf.gz" must_exist: true create_parent: true required: true @@ -32,8 +32,11 @@ argument_groups: name: "--output" alternatives: - "-o" - description: "Output sorted VCF/BCF file." + description: "Write output to a file.\n\nIf not specified, output goes to standard\ + \ output.\n" info: null + example: + - "sorted.vcf.gz" must_exist: true create_parent: true required: true @@ -46,16 +49,38 @@ argument_groups: name: "--output_type" alternatives: - "-O" - description: "Compresses or uncompresses the output.\nThe options are:\n b: compressed\ - \ BCF, \n u: uncompressed BCF, \n z: compressed VCF, \n v: uncompressed VCF.\ - \ \n" + description: "Output file type.\n\n**Options:**\n- u: uncompressed BCF\n- b: compressed\ + \ BCF \n- v: uncompressed VCF\n- z: compressed VCF\n- 0-9: compression level\ + \ for compressed formats\n\n**Default:** v (uncompressed VCF)\n" info: null - required: false - choices: - - "b" - - "u" + example: - "z" - - "v" + required: false + direction: "input" + multiple: false + multiple_sep: ";" + - type: "integer" + name: "--verbosity" + alternatives: + - "-v" + description: "Verbosity level.\n\nHigher values increase verbosity of output messages.\n" + info: null + example: + - 1 + required: false + direction: "input" + multiple: false + multiple_sep: ";" + - type: "string" + name: "--write_index" + alternatives: + - "-W" + description: "Automatically index the output files.\n\n**Format:** Specify index\ + \ format or use default.\n" + info: null + example: + - "tbi" + required: false direction: "input" multiple: false multiple_sep: ";" @@ -63,13 +88,13 @@ resources: - type: "bash_script" path: "script.sh" is_executable: true -description: "Sorts VCF/BCF files.\n" +description: "Sort VCF/BCF file.\n" test_resources: - type: "bash_script" path: "test.sh" is_executable: true - type: "file" - path: "test_data" + path: "test_helpers.sh" info: null status: "enabled" scope: @@ -77,6 +102,7 @@ scope: target: "public" requirements: commands: + - "bcftools" - "ps" keywords: - "Sort" @@ -159,20 +185,14 @@ runners: engines: - type: "docker" id: "docker" - image: "debian:stable-slim" + image: "quay.io/biocontainers/bcftools:1.22--h3a4d415_1" target_registry: "images.viash-hub.com" target_tag: "main" namespace_separator: "/" setup: - - type: "apt" - packages: - - "bcftools" - - "procps" - interactive: false - type: "docker" run: - - "echo \"bcftools: \\\"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftools\ - \ //p')\\\"\" > /var/software_versions.txt\n" + - "bcftools --version 2>&1 | head -1 | sed 's/bcftools /bcftools: /' > /var/software_versions.txt\n" entrypoint: [] cmd: null - type: "native" @@ -184,7 +204,7 @@ build_info: output: "target/nextflow/bcftools/bcftools_sort" executable: "target/nextflow/bcftools/bcftools_sort/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -206,138 +226,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bcftools/bcftools_sort/main.nf b/target/nextflow/bcftools/bcftools_sort/main.nf index e5c44d52..2b04ccc6 100644 --- a/target/nextflow/bcftools/bcftools_sort/main.nf +++ b/target/nextflow/bcftools/bcftools_sort/main.nf @@ -10,7 +10,7 @@ // files. // // Component authors: -// * Theodoro Gasperin Terra Camargo (author, maintainer) +// * Theodoro Gasperin Terra Camargo (author) //////////////////////////// // VDSL3 helper functions // @@ -3040,8 +3040,7 @@ meta = [ { "name" : "Theodoro Gasperin Terra Camargo", "roles" : [ - "author", - "maintainer" + "author" ], "info" : { "links" : { @@ -3059,10 +3058,10 @@ meta = [ { "type" : "file", "name" : "--input", - "alternatives" : [ - "-i" + "description" : "Input VCF/BCF file to sort.\n\nThe file to be sorted by genomic coordinates.\n", + "example" : [ + "input.vcf.gz" ], - "description" : "Input VCF/BCF file.", "must_exist" : true, "create_parent" : true, "required" : true, @@ -3081,7 +3080,10 @@ meta = [ "alternatives" : [ "-o" ], - "description" : "Output sorted VCF/BCF file.", + "description" : "Write output to a file.\n\nIf not specified, output goes to standard output.\n", + "example" : [ + "sorted.vcf.gz" + ], "must_exist" : true, "create_parent" : true, "required" : true, @@ -3100,14 +3102,41 @@ meta = [ "alternatives" : [ "-O" ], - "description" : "Compresses or uncompresses the output.\nThe options are:\n b: compressed BCF, \n u: uncompressed BCF, \n z: compressed VCF, \n v: uncompressed VCF. \n", - "required" : false, - "choices" : [ - "b", - "u", - "z", - "v" + "description" : "Output file type.\n\n**Options:**\n- u: uncompressed BCF\n- b: compressed BCF \n- v: uncompressed VCF\n- z: compressed VCF\n- 0-9: compression level for compressed formats\n\n**Default:** v (uncompressed VCF)\n", + "example" : [ + "z" ], + "required" : false, + "direction" : "input", + "multiple" : false, + "multiple_sep" : ";" + }, + { + "type" : "integer", + "name" : "--verbosity", + "alternatives" : [ + "-v" + ], + "description" : "Verbosity level.\n\nHigher values increase verbosity of output messages.\n", + "example" : [ + 1 + ], + "required" : false, + "direction" : "input", + "multiple" : false, + "multiple_sep" : ";" + }, + { + "type" : "string", + "name" : "--write_index", + "alternatives" : [ + "-W" + ], + "description" : "Automatically index the output files.\n\n**Format:** Specify index format or use default.\n", + "example" : [ + "tbi" + ], + "required" : false, "direction" : "input", "multiple" : false, "multiple_sep" : ";" @@ -3122,7 +3151,7 @@ meta = [ "is_executable" : true } ], - "description" : "Sorts VCF/BCF files.\n", + "description" : "Sort VCF/BCF file.\n", "test_resources" : [ { "type" : "bash_script", @@ -3131,7 +3160,7 @@ meta = [ }, { "type" : "file", - "path" : "test_data" + "path" : "/src/_utils/test_helpers.sh" } ], "status" : "enabled", @@ -3141,6 +3170,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bcftools", "ps" ] }, @@ -3239,23 +3269,15 @@ meta = [ { "type" : "docker", "id" : "docker", - "image" : "debian:stable-slim", + "image" : "quay.io/biocontainers/bcftools:1.22--h3a4d415_1", "target_registry" : "images.viash-hub.com", "target_tag" : "main", "namespace_separator" : "/", "setup" : [ - { - "type" : "apt", - "packages" : [ - "bcftools", - "procps" - ], - "interactive" : false - }, { "type" : "docker", "run" : [ - "echo \\"bcftools: \\\\\\"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftools //p')\\\\\\"\\" > /var/software_versions.txt\n" + "bcftools --version 2>&1 | head -1 | sed 's/bcftools /bcftools: /' > /var/software_versions.txt\n" ] } ] @@ -3271,7 +3293,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bcftools/bcftools_sort", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3283,225 +3305,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", @@ -3533,6 +3341,8 @@ cat > "$tempscript" << VIASHMAIN $( if [ ! -z ${VIASH_PAR_INPUT+x} ]; then echo "${VIASH_PAR_INPUT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_input='&'#" ; else echo "# par_input="; fi ) $( if [ ! -z ${VIASH_PAR_OUTPUT+x} ]; then echo "${VIASH_PAR_OUTPUT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_output='&'#" ; else echo "# par_output="; fi ) $( if [ ! -z ${VIASH_PAR_OUTPUT_TYPE+x} ]; then echo "${VIASH_PAR_OUTPUT_TYPE}" | sed "s#'#'\\"'\\"'#g;s#.*#par_output_type='&'#" ; else echo "# par_output_type="; fi ) +$( if [ ! -z ${VIASH_PAR_VERBOSITY+x} ]; then echo "${VIASH_PAR_VERBOSITY}" | sed "s#'#'\\"'\\"'#g;s#.*#par_verbosity='&'#" ; else echo "# par_verbosity="; fi ) +$( if [ ! -z ${VIASH_PAR_WRITE_INDEX+x} ]; then echo "${VIASH_PAR_WRITE_INDEX}" | sed "s#'#'\\"'\\"'#g;s#.*#par_write_index='&'#" ; else echo "# par_write_index="; fi ) $( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "${VIASH_META_NAME}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_name='&'#" ; else echo "# meta_name="; fi ) $( if [ ! -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then echo "${VIASH_META_FUNCTIONALITY_NAME}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_functionality_name='&'#" ; else echo "# meta_functionality_name="; fi ) $( if [ ! -z ${VIASH_META_RESOURCES_DIR+x} ]; then echo "${VIASH_META_RESOURCES_DIR}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_resources_dir='&'#" ; else echo "# meta_resources_dir="; fi ) @@ -3554,16 +3364,29 @@ $( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}" ## VIASH END -# Exit on error set -eo pipefail -# Execute bedtools bamtofastq with the provided arguments -bcftools sort \\\\ - -o "\\$par_output" \\\\ - \\${par_output_type:+-O "\\$par_output_type"} \\\\ - \\${meta_memory_mb:+-m "\\${meta_memory_mb}M"} \\\\ - \\${meta_temp_dir:+-T "\\$meta_temp_dir"} \\\\ - \\$par_input \\\\ +# Create temporary directory for bcftools if meta_temp_dir is available +if [[ -n "\\$meta_temp_dir" ]]; then + bcftools_temp_dir=\\$(mktemp -d "\\$meta_temp_dir/bcftools_sort.XXXXXX") + # Set up cleanup trap + trap 'rm -rf "\\$bcftools_temp_dir"' EXIT +fi + +# Build command array +cmd_args=( + bcftools sort + \\${meta_memory_mb:+--max-mem "\\${meta_memory_mb}M"} + \\${par_output_type:+--output-type "\\$par_output_type"} + \\${bcftools_temp_dir:+--temp-dir "\\$bcftools_temp_dir"} + \\${par_verbosity:+--verbosity "\\$par_verbosity"} + \\${par_write_index:+--write-index="\\$par_write_index"} + \\${par_output:+--output "\\$par_output"} + "\\$par_input" +) + +# Execute command +"\\${cmd_args[@]}" VIASHMAIN bash "$tempscript" ''' diff --git a/target/nextflow/bcftools/bcftools_sort/nextflow.config b/target/nextflow/bcftools/bcftools_sort/nextflow.config index 7d436cbb..19d9fda4 100644 --- a/target/nextflow/bcftools/bcftools_sort/nextflow.config +++ b/target/nextflow/bcftools/bcftools_sort/nextflow.config @@ -3,7 +3,7 @@ manifest { mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' version = 'main' - description = 'Sorts VCF/BCF files.\n' + description = 'Sort VCF/BCF file.\n' author = 'Theodoro Gasperin Terra Camargo' } diff --git a/target/nextflow/bcftools/bcftools_sort/nextflow_schema.json b/target/nextflow/bcftools/bcftools_sort/nextflow_schema.json index e4c1303d..16adc38d 100644 --- a/target/nextflow/bcftools/bcftools_sort/nextflow_schema.json +++ b/target/nextflow/bcftools/bcftools_sort/nextflow_schema.json @@ -1,7 +1,7 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", "title": "bcftools_sort", - "description": "Sorts VCF/BCF files.\n", + "description": "Sort VCF/BCF file.\n", "type": "object", "$defs": { "inputs": { @@ -13,8 +13,8 @@ "type": "string", "format": "path", "exists": true, - "description": "Input VCF/BCF file.", - "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. " + "description": "Input VCF/BCF file to sort.\n\nThe file to be sorted by genomic coordinates.\n", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"input.vcf.gz\"`. " } } }, @@ -26,9 +26,9 @@ "output": { "type": "string", "format": "path", - "description": "Output sorted VCF/BCF file.", - "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output\"`, direction: `output`. ", - "default": "$id.$key.output" + "description": "Write output to a file.\n\nIf not specified, output goes to standard output.\n", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.gz\"`, direction: `output`, example: `\"sorted.vcf.gz\"`. ", + "default": "$id.$key.output.gz" } } }, @@ -39,14 +39,18 @@ "properties": { "output_type": { "type": "string", - "description": "Compresses or uncompresses the output.\nThe options are:\n b: compressed BCF, \n u: uncompressed BCF, \n z: compressed VCF, \n v: uncompressed VCF", - "help_text": "Type: `string`, multiple: `False`, choices: ``b`, `u`, `z`, `v``. ", - "enum": [ - "b", - "u", - "z", - "v" - ] + "description": "Output file type.\n\n**Options:**\n- u: uncompressed BCF\n- b: compressed BCF \n- v: uncompressed VCF\n- z: compressed VCF\n- 0-9: compression level for compressed formats\n\n**Default:** v (uncompressed VCF)\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"z\"`. " + }, + "verbosity": { + "type": "integer", + "description": "Verbosity level.\n\nHigher values increase verbosity of output messages.\n", + "help_text": "Type: `integer`, multiple: `False`, example: `1`. " + }, + "write_index": { + "type": "string", + "description": "Automatically index the output files.\n\n**Format:** Specify index format or use default.\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"tbi\"`. " } } }, diff --git a/target/nextflow/bcftools/bcftools_stats/.config.vsh.yaml b/target/nextflow/bcftools/bcftools_stats/.config.vsh.yaml index 4bf87acf..c98ccd3b 100644 --- a/target/nextflow/bcftools/bcftools_stats/.config.vsh.yaml +++ b/target/nextflow/bcftools/bcftools_stats/.config.vsh.yaml @@ -15,10 +15,12 @@ argument_groups: arguments: - type: "file" name: "--input" - alternatives: - - "-i" - description: "Input VCF/BCF file. Maximum of two files." + description: "Input VCF/BCF file(s). Maximum of two files can be provided.\nWhen\ + \ two files are given, the program generates separate stats \nfor intersection\ + \ and the complements.\n" info: null + example: + - "input.vcf.gz" must_exist: true create_parent: true required: true @@ -31,8 +33,11 @@ argument_groups: name: "--output" alternatives: - "-o" - description: "Output txt statistics file." + description: "Write output to a file. The output is a text file which can be \n\ + plotted using plot-vcfstats.\n" info: null + example: + - "stats.txt" must_exist: true create_parent: true required: true @@ -42,10 +47,8 @@ argument_groups: - name: "Options" arguments: - type: "string" - name: "--allele_frequency_bins" - alternatives: - - "--af_bins" - description: "Allele frequency bins, a list of bin values (0.1,0.5,1).\n" + name: "--af_bins" + description: "Allele frequency bins, a list of comma-separated bin values.\n" info: null example: - "0.1,0.5,1" @@ -53,44 +56,25 @@ argument_groups: direction: "input" multiple: false multiple_sep: ";" - - type: "file" - name: "--allele_frequency_bins_file" - alternatives: - - "--af_bins_file" - description: "Same as allele_frequency_bins, but in a file.\nFormat of file is\ - \ one value per line. \ne.g. \n 0.1\n 0.5\n 1\n" - info: null - must_exist: true - create_parent: true - required: false - direction: "input" - multiple: false - multiple_sep: ";" - type: "string" - name: "--allele_frequency_tag" - alternatives: - - "--af_tag" + name: "--af_tag" description: "Allele frequency tag to use, by default estimated from AN,AC or\ \ GT.\n" info: null + example: + - "AF" required: false direction: "input" multiple: false multiple_sep: ";" - - type: "boolean_true" - name: "--first_allele_only" - alternatives: - - "--first_only" - description: "Include only 1st allele at multiallelic sites.\n" - info: null - direction: "input" - type: "string" name: "--collapse" alternatives: - - "--c" - description: "Treat as identical records with .\n\ - See https://samtools.github.io/bcftools/bcftools.html#common_options for details.\n" + - "-c" + description: "Treat as identical records with .\n" info: null + example: + - "snps" required: false choices: - "snps" @@ -105,8 +89,8 @@ argument_groups: - type: "string" name: "--depth" alternatives: - - "--d" - description: "Depth distribution: min,max,bin size.\n" + - "-d" + description: "Depth distribution: min,max,bin size [0:200:1].\n" info: null example: - "0,500,1" @@ -117,12 +101,11 @@ argument_groups: - type: "string" name: "--exclude" alternatives: - - "--e" - description: "Exclude sites for which the expression is true.\nSee https://samtools.github.io/bcftools/bcftools.html#expressions\ - \ for details.\n" + - "-e" + description: "Exclude sites for which the expression is true.\n" info: null example: - - "QUAL < 30 && DP < 10" + - "QUAL < 30" required: false direction: "input" multiple: false @@ -130,12 +113,13 @@ argument_groups: - type: "file" name: "--exons" alternatives: - - "--E" - description: "tab-delimited file with exons for indel frameshifts statistics.\ - \ \nThe columns of the file are CHR, FROM, TO, with 1-based, inclusive, positions.\ - \ \nThe file is BGZF-compressed and indexed with tabix (e.g. tabix -s1 -b2 -e3\ - \ file.gz).\n" + - "-E" + description: "Tab-delimited file with exons for indel frameshifts statistics.\n\ + The columns of the file are CHR, FROM, TO, with 1-based positions.\nThe file\ + \ should be BGZF-compressed and indexed with tabix.\n" info: null + example: + - "exons.bed.gz" must_exist: true create_parent: true required: false @@ -145,55 +129,63 @@ argument_groups: - type: "string" name: "--apply_filters" alternatives: - - "--f" - description: "Require at least one of the listed FILTER strings (e.g. \"PASS,.\"\ - ).\n" + - "-f" + description: "Require at least one of the listed FILTER strings.\n" info: null + example: + - "PASS,." required: false direction: "input" multiple: false multiple_sep: ";" - type: "file" - name: "--fasta_reference" + name: "--fasta_ref" alternatives: - - "--F" + - "-F" description: "Faidx indexed reference sequence file to determine INDEL context.\n" info: null + example: + - "reference.fa" must_exist: true create_parent: true required: false direction: "input" multiple: false multiple_sep: ";" + - type: "boolean_true" + name: "--first_allele_only" + alternatives: + - "--1st-allele-only" + description: "Include only 1st allele at multiallelic sites.\n" + info: null + direction: "input" - type: "string" name: "--include" alternatives: - - "--i" - description: "Select sites for which the expression is true.\nSee https://samtools.github.io/bcftools/bcftools.html#expressions\ - \ for details.\n" + - "-i" + description: "Select sites for which the expression is true.\n" info: null example: - - "QUAL >= 30 && DP >= 10" + - "QUAL >= 30" required: false direction: "input" multiple: false multiple_sep: ";" - type: "boolean_true" - name: "--split_by_ID" + name: "--split_by_id" alternatives: - - "--I" + - "-I" description: "Collect stats for sites with ID separately (known vs novel).\n" info: null direction: "input" - type: "string" name: "--regions" alternatives: - - "--r" - description: "Restrict to comma-separated list of regions. \nFollowing formats\ - \ are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​].\n" + - "-r" + description: "Restrict to comma-separated list of regions.\n" info: null example: - - "20:1000000-2000000" + - "chr20:1000000-2000000" required: false direction: "input" multiple: false @@ -201,11 +193,11 @@ argument_groups: - type: "file" name: "--regions_file" alternatives: - - "--R" - description: "Restrict to regions listed in a file. \nRegions can be specified\ - \ either on a VCF, BED, or tab-delimited file (the default). \nFor more information\ - \ check manual.\n" + - "-R" + description: "Restrict to regions listed in a file.\n" info: null + example: + - "regions.bed" must_exist: true create_parent: true required: false @@ -214,14 +206,8 @@ argument_groups: multiple_sep: ";" - type: "string" name: "--regions_overlap" - description: "This option controls how overlapping records are determined: \n\ - set to 'pos' or '0' if the VCF record has to have POS inside a region (this\ - \ corresponds to the default behavior of -t/-T); \nset to 'record' or '1' if\ - \ also overlapping records with POS outside a region should be included (this\ - \ is the default behavior of -r/-R, \nand includes indels with POS at the end\ - \ of a region, which are technically outside the region); \nor set to 'variant'\ - \ or '2' to include only true overlapping variation (compare the full VCF representation\ - \ \"TA>T-\" vs the true sequence variation \"A>-\").\n" + description: "Include if POS in the region (pos), record overlaps (record), \n\ + variant overlaps (variant). Can also use numeric equivalents 0, 1, 2.\n" info: null required: false choices: @@ -237,9 +223,11 @@ argument_groups: - type: "string" name: "--samples" alternatives: - - "--s" + - "-s" description: "List of samples for sample stats, \"-\" to include all samples.\n" info: null + example: + - "sample1,sample2" required: false direction: "input" multiple: false @@ -247,10 +235,11 @@ argument_groups: - type: "file" name: "--samples_file" alternatives: - - "--S" - description: "File of samples to include.\ne.g. \n sample1 1\n sample2 \ - \ 2\n sample3 2\n" + - "-S" + description: "File of samples to include.\n" info: null + example: + - "samples.txt" must_exist: true create_parent: true required: false @@ -260,21 +249,12 @@ argument_groups: - type: "string" name: "--targets" alternatives: - - "--t" - description: "Similar as -r, --regions, but the next position is accessed by streaming\ - \ the whole VCF/BCF \nrather than using the tbi/csi index. Both -r and -t options\ - \ can be applied simultaneously: -r uses the \nindex to jump to a region and\ - \ -t discards positions which are not in the targets. Unlike -r, targets \n\ - can be prefixed with \"^\" to request logical complement. For example, \"^X,Y,MT\"\ - \ indicates that \nsequences X, Y and MT should be skipped. Yet another difference\ - \ between the -t/-T and -r/-R is \nthat -r/-R checks for proper overlaps and\ - \ considers both POS and the end position of an indel, \nwhile -t/-T considers\ - \ the POS coordinate only (by default; see also --regions-overlap and --targets-overlap).\ - \ \nNote that -t cannot be used in combination with -T.\nFollowing formats are\ - \ supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​].\n" + - "-t" + description: "Similar to regions, but streams rather than using index.\nTargets\ + \ can be prefixed with \"^\" for logical complement.\n" info: null example: - - "20:1000000-2000000" + - "chr20:1000000-2000000" required: false direction: "input" multiple: false @@ -282,9 +262,11 @@ argument_groups: - type: "file" name: "--targets_file" alternatives: - - "--T" - description: "Similar to --regions_file option but streams rather than index-jumps.\n" + - "-T" + description: "Similar to regions_file but streams rather than index-jumps.\n" info: null + example: + - "targets.bed" must_exist: true create_parent: true required: false @@ -292,9 +274,9 @@ argument_groups: multiple: false multiple_sep: ";" - type: "string" - name: "--targets_overlaps" - description: "Include if POS in the region (0), record overlaps (1), variant overlaps\ - \ (2).\n" + name: "--targets_overlap" + description: "Include if POS in the region (pos), record overlaps (record), \n\ + variant overlaps (variant). Can also use numeric equivalents 0, 1, 2.\n" info: null required: false choices: @@ -310,11 +292,12 @@ argument_groups: - type: "string" name: "--user_tstv" alternatives: - - "--u" - description: "Collect Ts/Tv stats for any tag using the given binning [0:1:100].\n\ - Format is .\nA subfield can be selected as e.g. 'PV4[0]', here\ - \ the first value of the PV4 tag.\n" + - "-u" + description: "Collect Ts/Tv stats for any tag using the given binning.\nFormat\ + \ is TAG[:min:max:n]. Default binning is [0:1:100].\n" info: null + example: + - "QUAL:0:40:40" required: false direction: "input" multiple: false @@ -322,7 +305,7 @@ argument_groups: - type: "boolean_true" name: "--verbose" alternatives: - - "--v" + - "-v" description: "Produce verbose per-site and per-sample output.\n" info: null direction: "input" @@ -345,6 +328,7 @@ scope: target: "public" requirements: commands: + - "bcftools" - "ps" keywords: - "Stats" @@ -427,25 +411,14 @@ runners: engines: - type: "docker" id: "docker" - image: "debian:stable-slim" + image: "quay.io/biocontainers/bcftools:1.22--h3a4d415_1" target_registry: "images.viash-hub.com" target_tag: "main" namespace_separator: "/" setup: - - type: "apt" - packages: - - "bcftools" - - "procps" - interactive: false - type: "docker" run: - - "echo \"bcftools: \\\"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftools\ - \ //p')\\\"\" > /var/software_versions.txt\n" - test_setup: - - type: "apt" - packages: - - "tabix" - interactive: false + - "bcftools --version | head -1 | sed 's/bcftools /bcftools: /' > /var/software_versions.txt\n" entrypoint: [] cmd: null - type: "native" @@ -457,7 +430,7 @@ build_info: output: "target/nextflow/bcftools/bcftools_stats" executable: "target/nextflow/bcftools/bcftools_stats/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -479,138 +452,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bcftools/bcftools_stats/main.nf b/target/nextflow/bcftools/bcftools_stats/main.nf index f1a610e6..088e481e 100644 --- a/target/nextflow/bcftools/bcftools_stats/main.nf +++ b/target/nextflow/bcftools/bcftools_stats/main.nf @@ -3058,10 +3058,10 @@ meta = [ { "type" : "file", "name" : "--input", - "alternatives" : [ - "-i" + "description" : "Input VCF/BCF file(s). Maximum of two files can be provided.\nWhen two files are given, the program generates separate stats \nfor intersection and the complements.\n", + "example" : [ + "input.vcf.gz" ], - "description" : "Input VCF/BCF file. Maximum of two files.", "must_exist" : true, "create_parent" : true, "required" : true, @@ -3080,7 +3080,10 @@ meta = [ "alternatives" : [ "-o" ], - "description" : "Output txt statistics file.", + "description" : "Write output to a file. The output is a text file which can be \nplotted using plot-vcfstats.\n", + "example" : [ + "stats.txt" + ], "must_exist" : true, "create_parent" : true, "required" : true, @@ -3095,11 +3098,8 @@ meta = [ "arguments" : [ { "type" : "string", - "name" : "--allele_frequency_bins", - "alternatives" : [ - "--af_bins" - ], - "description" : "Allele frequency bins, a list of bin values (0.1,0.5,1).\n", + "name" : "--af_bins", + "description" : "Allele frequency bins, a list of comma-separated bin values.\n", "example" : [ "0.1,0.5,1" ], @@ -3108,48 +3108,28 @@ meta = [ "multiple" : false, "multiple_sep" : ";" }, - { - "type" : "file", - "name" : "--allele_frequency_bins_file", - "alternatives" : [ - "--af_bins_file" - ], - "description" : "Same as allele_frequency_bins, but in a file.\nFormat of file is one value per line. \ne.g. \n 0.1\n 0.5\n 1\n", - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - }, { "type" : "string", - "name" : "--allele_frequency_tag", - "alternatives" : [ - "--af_tag" - ], + "name" : "--af_tag", "description" : "Allele frequency tag to use, by default estimated from AN,AC or GT.\n", + "example" : [ + "AF" + ], "required" : false, "direction" : "input", "multiple" : false, "multiple_sep" : ";" }, - { - "type" : "boolean_true", - "name" : "--first_allele_only", - "alternatives" : [ - "--first_only" - ], - "description" : "Include only 1st allele at multiallelic sites.\n", - "direction" : "input" - }, { "type" : "string", "name" : "--collapse", "alternatives" : [ - "--c" + "-c" + ], + "description" : "Treat as identical records with .\n", + "example" : [ + "snps" ], - "description" : "Treat as identical records with .\nSee https://samtools.github.io/bcftools/bcftools.html#common_options for details.\n", "required" : false, "choices" : [ "snps", @@ -3167,9 +3147,9 @@ meta = [ "type" : "string", "name" : "--depth", "alternatives" : [ - "--d" + "-d" ], - "description" : "Depth distribution: min,max,bin size.\n", + "description" : "Depth distribution: min,max,bin size [0:200:1].\n", "example" : [ "0,500,1" ], @@ -3182,11 +3162,11 @@ meta = [ "type" : "string", "name" : "--exclude", "alternatives" : [ - "--e" + "-e" ], - "description" : "Exclude sites for which the expression is true.\nSee https://samtools.github.io/bcftools/bcftools.html#expressions for details.\n", + "description" : "Exclude sites for which the expression is true.\n", "example" : [ - "QUAL < 30 && DP < 10" + "QUAL < 30" ], "required" : false, "direction" : "input", @@ -3197,9 +3177,12 @@ meta = [ "type" : "file", "name" : "--exons", "alternatives" : [ - "--E" + "-E" + ], + "description" : "Tab-delimited file with exons for indel frameshifts statistics.\nThe columns of the file are CHR, FROM, TO, with 1-based positions.\nThe file should be BGZF-compressed and indexed with tabix.\n", + "example" : [ + "exons.bed.gz" ], - "description" : "tab-delimited file with exons for indel frameshifts statistics. \nThe columns of the file are CHR, FROM, TO, with 1-based, inclusive, positions. \nThe file is BGZF-compressed and indexed with tabix (e.g. tabix -s1 -b2 -e3 file.gz).\n", "must_exist" : true, "create_parent" : true, "required" : false, @@ -3211,9 +3194,12 @@ meta = [ "type" : "string", "name" : "--apply_filters", "alternatives" : [ - "--f" + "-f" + ], + "description" : "Require at least one of the listed FILTER strings.\n", + "example" : [ + "PASS,." ], - "description" : "Require at least one of the listed FILTER strings (e.g. \\"PASS,.\\").\n", "required" : false, "direction" : "input", "multiple" : false, @@ -3221,11 +3207,14 @@ meta = [ }, { "type" : "file", - "name" : "--fasta_reference", + "name" : "--fasta_ref", "alternatives" : [ - "--F" + "-F" ], "description" : "Faidx indexed reference sequence file to determine INDEL context.\n", + "example" : [ + "reference.fa" + ], "must_exist" : true, "create_parent" : true, "required" : false, @@ -3233,15 +3222,24 @@ meta = [ "multiple" : false, "multiple_sep" : ";" }, + { + "type" : "boolean_true", + "name" : "--first_allele_only", + "alternatives" : [ + "--1st-allele-only" + ], + "description" : "Include only 1st allele at multiallelic sites.\n", + "direction" : "input" + }, { "type" : "string", "name" : "--include", "alternatives" : [ - "--i" + "-i" ], - "description" : "Select sites for which the expression is true.\nSee https://samtools.github.io/bcftools/bcftools.html#expressions for details.\n", + "description" : "Select sites for which the expression is true.\n", "example" : [ - "QUAL >= 30 && DP >= 10" + "QUAL >= 30" ], "required" : false, "direction" : "input", @@ -3250,9 +3248,9 @@ meta = [ }, { "type" : "boolean_true", - "name" : "--split_by_ID", + "name" : "--split_by_id", "alternatives" : [ - "--I" + "-I" ], "description" : "Collect stats for sites with ID separately (known vs novel).\n", "direction" : "input" @@ -3261,11 +3259,11 @@ meta = [ "type" : "string", "name" : "--regions", "alternatives" : [ - "--r" + "-r" ], - "description" : "Restrict to comma-separated list of regions. \nFollowing formats are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​].\n", + "description" : "Restrict to comma-separated list of regions.\n", "example" : [ - "20:1000000-2000000" + "chr20:1000000-2000000" ], "required" : false, "direction" : "input", @@ -3276,9 +3274,12 @@ meta = [ "type" : "file", "name" : "--regions_file", "alternatives" : [ - "--R" + "-R" + ], + "description" : "Restrict to regions listed in a file.\n", + "example" : [ + "regions.bed" ], - "description" : "Restrict to regions listed in a file. \nRegions can be specified either on a VCF, BED, or tab-delimited file (the default). \nFor more information check manual.\n", "must_exist" : true, "create_parent" : true, "required" : false, @@ -3289,7 +3290,7 @@ meta = [ { "type" : "string", "name" : "--regions_overlap", - "description" : "This option controls how overlapping records are determined: \nset to 'pos' or '0' if the VCF record has to have POS inside a region (this corresponds to the default behavior of -t/-T); \nset to 'record' or '1' if also overlapping records with POS outside a region should be included (this is the default behavior of -r/-R, \nand includes indels with POS at the end of a region, which are technically outside the region); \nor set to 'variant' or '2' to include only true overlapping variation (compare the full VCF representation \\"TA>T-\\" vs the true sequence variation \\"A>-\\").\n", + "description" : "Include if POS in the region (pos), record overlaps (record), \nvariant overlaps (variant). Can also use numeric equivalents 0, 1, 2.\n", "required" : false, "choices" : [ "pos", @@ -3307,9 +3308,12 @@ meta = [ "type" : "string", "name" : "--samples", "alternatives" : [ - "--s" + "-s" ], "description" : "List of samples for sample stats, \\"-\\" to include all samples.\n", + "example" : [ + "sample1,sample2" + ], "required" : false, "direction" : "input", "multiple" : false, @@ -3319,9 +3323,12 @@ meta = [ "type" : "file", "name" : "--samples_file", "alternatives" : [ - "--S" + "-S" + ], + "description" : "File of samples to include.\n", + "example" : [ + "samples.txt" ], - "description" : "File of samples to include.\ne.g. \n sample1 1\n sample2 2\n sample3 2\n", "must_exist" : true, "create_parent" : true, "required" : false, @@ -3333,11 +3340,11 @@ meta = [ "type" : "string", "name" : "--targets", "alternatives" : [ - "--t" + "-t" ], - "description" : "Similar as -r, --regions, but the next position is accessed by streaming the whole VCF/BCF \nrather than using the tbi/csi index. Both -r and -t options can be applied simultaneously: -r uses the \nindex to jump to a region and -t discards positions which are not in the targets. Unlike -r, targets \ncan be prefixed with \\"^\\" to request logical complement. For example, \\"^X,Y,MT\\" indicates that \nsequences X, Y and MT should be skipped. Yet another difference between the -t/-T and -r/-R is \nthat -r/-R checks for proper overlaps and considers both POS and the end position of an indel, \nwhile -t/-T considers the POS coordinate only (by default; see also --regions-overlap and --targets-overlap). \nNote that -t cannot be used in combination with -T.\nFollowing formats are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​].\n", + "description" : "Similar to regions, but streams rather than using index.\nTargets can be prefixed with \\"^\\" for logical complement.\n", "example" : [ - "20:1000000-2000000" + "chr20:1000000-2000000" ], "required" : false, "direction" : "input", @@ -3348,9 +3355,12 @@ meta = [ "type" : "file", "name" : "--targets_file", "alternatives" : [ - "--T" + "-T" + ], + "description" : "Similar to regions_file but streams rather than index-jumps.\n", + "example" : [ + "targets.bed" ], - "description" : "Similar to --regions_file option but streams rather than index-jumps.\n", "must_exist" : true, "create_parent" : true, "required" : false, @@ -3360,8 +3370,8 @@ meta = [ }, { "type" : "string", - "name" : "--targets_overlaps", - "description" : "Include if POS in the region (0), record overlaps (1), variant overlaps (2).\n", + "name" : "--targets_overlap", + "description" : "Include if POS in the region (pos), record overlaps (record), \nvariant overlaps (variant). Can also use numeric equivalents 0, 1, 2.\n", "required" : false, "choices" : [ "pos", @@ -3379,9 +3389,12 @@ meta = [ "type" : "string", "name" : "--user_tstv", "alternatives" : [ - "--u" + "-u" + ], + "description" : "Collect Ts/Tv stats for any tag using the given binning.\nFormat is TAG[:min:max:n]. Default binning is [0:1:100].\n", + "example" : [ + "QUAL:0:40:40" ], - "description" : "Collect Ts/Tv stats for any tag using the given binning [0:1:100].\nFormat is .\nA subfield can be selected as e.g. 'PV4[0]', here the first value of the PV4 tag.\n", "required" : false, "direction" : "input", "multiple" : false, @@ -3391,7 +3404,7 @@ meta = [ "type" : "boolean_true", "name" : "--verbose", "alternatives" : [ - "--v" + "-v" ], "description" : "Produce verbose per-site and per-sample output.\n", "direction" : "input" @@ -3421,6 +3434,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bcftools", "ps" ] }, @@ -3519,34 +3533,17 @@ meta = [ { "type" : "docker", "id" : "docker", - "image" : "debian:stable-slim", + "image" : "quay.io/biocontainers/bcftools:1.22--h3a4d415_1", "target_registry" : "images.viash-hub.com", "target_tag" : "main", "namespace_separator" : "/", "setup" : [ - { - "type" : "apt", - "packages" : [ - "bcftools", - "procps" - ], - "interactive" : false - }, { "type" : "docker", "run" : [ - "echo \\"bcftools: \\\\\\"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftools //p')\\\\\\"\\" > /var/software_versions.txt\n" + "bcftools --version | head -1 | sed 's/bcftools /bcftools: /' > /var/software_versions.txt\n" ] } - ], - "test_setup" : [ - { - "type" : "apt", - "packages" : [ - "tabix" - ], - "interactive" : false - } ] }, { @@ -3560,7 +3557,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bcftools/bcftools_stats", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3572,225 +3569,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", @@ -3821,18 +3604,17 @@ cat > "$tempscript" << VIASHMAIN # The following code has been auto-generated by Viash. $( if [ ! -z ${VIASH_PAR_INPUT+x} ]; then echo "${VIASH_PAR_INPUT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_input='&'#" ; else echo "# par_input="; fi ) $( if [ ! -z ${VIASH_PAR_OUTPUT+x} ]; then echo "${VIASH_PAR_OUTPUT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_output='&'#" ; else echo "# par_output="; fi ) -$( if [ ! -z ${VIASH_PAR_ALLELE_FREQUENCY_BINS+x} ]; then echo "${VIASH_PAR_ALLELE_FREQUENCY_BINS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_allele_frequency_bins='&'#" ; else echo "# par_allele_frequency_bins="; fi ) -$( if [ ! -z ${VIASH_PAR_ALLELE_FREQUENCY_BINS_FILE+x} ]; then echo "${VIASH_PAR_ALLELE_FREQUENCY_BINS_FILE}" | sed "s#'#'\\"'\\"'#g;s#.*#par_allele_frequency_bins_file='&'#" ; else echo "# par_allele_frequency_bins_file="; fi ) -$( if [ ! -z ${VIASH_PAR_ALLELE_FREQUENCY_TAG+x} ]; then echo "${VIASH_PAR_ALLELE_FREQUENCY_TAG}" | sed "s#'#'\\"'\\"'#g;s#.*#par_allele_frequency_tag='&'#" ; else echo "# par_allele_frequency_tag="; fi ) -$( if [ ! -z ${VIASH_PAR_FIRST_ALLELE_ONLY+x} ]; then echo "${VIASH_PAR_FIRST_ALLELE_ONLY}" | sed "s#'#'\\"'\\"'#g;s#.*#par_first_allele_only='&'#" ; else echo "# par_first_allele_only="; fi ) +$( if [ ! -z ${VIASH_PAR_AF_BINS+x} ]; then echo "${VIASH_PAR_AF_BINS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_af_bins='&'#" ; else echo "# par_af_bins="; fi ) +$( if [ ! -z ${VIASH_PAR_AF_TAG+x} ]; then echo "${VIASH_PAR_AF_TAG}" | sed "s#'#'\\"'\\"'#g;s#.*#par_af_tag='&'#" ; else echo "# par_af_tag="; fi ) $( if [ ! -z ${VIASH_PAR_COLLAPSE+x} ]; then echo "${VIASH_PAR_COLLAPSE}" | sed "s#'#'\\"'\\"'#g;s#.*#par_collapse='&'#" ; else echo "# par_collapse="; fi ) $( if [ ! -z ${VIASH_PAR_DEPTH+x} ]; then echo "${VIASH_PAR_DEPTH}" | sed "s#'#'\\"'\\"'#g;s#.*#par_depth='&'#" ; else echo "# par_depth="; fi ) $( if [ ! -z ${VIASH_PAR_EXCLUDE+x} ]; then echo "${VIASH_PAR_EXCLUDE}" | sed "s#'#'\\"'\\"'#g;s#.*#par_exclude='&'#" ; else echo "# par_exclude="; fi ) $( if [ ! -z ${VIASH_PAR_EXONS+x} ]; then echo "${VIASH_PAR_EXONS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_exons='&'#" ; else echo "# par_exons="; fi ) $( if [ ! -z ${VIASH_PAR_APPLY_FILTERS+x} ]; then echo "${VIASH_PAR_APPLY_FILTERS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_apply_filters='&'#" ; else echo "# par_apply_filters="; fi ) -$( if [ ! -z ${VIASH_PAR_FASTA_REFERENCE+x} ]; then echo "${VIASH_PAR_FASTA_REFERENCE}" | sed "s#'#'\\"'\\"'#g;s#.*#par_fasta_reference='&'#" ; else echo "# par_fasta_reference="; fi ) +$( if [ ! -z ${VIASH_PAR_FASTA_REF+x} ]; then echo "${VIASH_PAR_FASTA_REF}" | sed "s#'#'\\"'\\"'#g;s#.*#par_fasta_ref='&'#" ; else echo "# par_fasta_ref="; fi ) +$( if [ ! -z ${VIASH_PAR_FIRST_ALLELE_ONLY+x} ]; then echo "${VIASH_PAR_FIRST_ALLELE_ONLY}" | sed "s#'#'\\"'\\"'#g;s#.*#par_first_allele_only='&'#" ; else echo "# par_first_allele_only="; fi ) $( if [ ! -z ${VIASH_PAR_INCLUDE+x} ]; then echo "${VIASH_PAR_INCLUDE}" | sed "s#'#'\\"'\\"'#g;s#.*#par_include='&'#" ; else echo "# par_include="; fi ) -$( if [ ! -z ${VIASH_PAR_SPLIT_BY_ID+x} ]; then echo "${VIASH_PAR_SPLIT_BY_ID}" | sed "s#'#'\\"'\\"'#g;s#.*#par_split_by_ID='&'#" ; else echo "# par_split_by_ID="; fi ) +$( if [ ! -z ${VIASH_PAR_SPLIT_BY_ID+x} ]; then echo "${VIASH_PAR_SPLIT_BY_ID}" | sed "s#'#'\\"'\\"'#g;s#.*#par_split_by_id='&'#" ; else echo "# par_split_by_id="; fi ) $( if [ ! -z ${VIASH_PAR_REGIONS+x} ]; then echo "${VIASH_PAR_REGIONS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_regions='&'#" ; else echo "# par_regions="; fi ) $( if [ ! -z ${VIASH_PAR_REGIONS_FILE+x} ]; then echo "${VIASH_PAR_REGIONS_FILE}" | sed "s#'#'\\"'\\"'#g;s#.*#par_regions_file='&'#" ; else echo "# par_regions_file="; fi ) $( if [ ! -z ${VIASH_PAR_REGIONS_OVERLAP+x} ]; then echo "${VIASH_PAR_REGIONS_OVERLAP}" | sed "s#'#'\\"'\\"'#g;s#.*#par_regions_overlap='&'#" ; else echo "# par_regions_overlap="; fi ) @@ -3840,7 +3622,7 @@ $( if [ ! -z ${VIASH_PAR_SAMPLES+x} ]; then echo "${VIASH_PAR_SAMPLES}" | sed "s $( if [ ! -z ${VIASH_PAR_SAMPLES_FILE+x} ]; then echo "${VIASH_PAR_SAMPLES_FILE}" | sed "s#'#'\\"'\\"'#g;s#.*#par_samples_file='&'#" ; else echo "# par_samples_file="; fi ) $( if [ ! -z ${VIASH_PAR_TARGETS+x} ]; then echo "${VIASH_PAR_TARGETS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_targets='&'#" ; else echo "# par_targets="; fi ) $( if [ ! -z ${VIASH_PAR_TARGETS_FILE+x} ]; then echo "${VIASH_PAR_TARGETS_FILE}" | sed "s#'#'\\"'\\"'#g;s#.*#par_targets_file='&'#" ; else echo "# par_targets_file="; fi ) -$( if [ ! -z ${VIASH_PAR_TARGETS_OVERLAPS+x} ]; then echo "${VIASH_PAR_TARGETS_OVERLAPS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_targets_overlaps='&'#" ; else echo "# par_targets_overlaps="; fi ) +$( if [ ! -z ${VIASH_PAR_TARGETS_OVERLAP+x} ]; then echo "${VIASH_PAR_TARGETS_OVERLAP}" | sed "s#'#'\\"'\\"'#g;s#.*#par_targets_overlap='&'#" ; else echo "# par_targets_overlap="; fi ) $( if [ ! -z ${VIASH_PAR_USER_TSTV+x} ]; then echo "${VIASH_PAR_USER_TSTV}" | sed "s#'#'\\"'\\"'#g;s#.*#par_user_tstv='&'#" ; else echo "# par_user_tstv="; fi ) $( if [ ! -z ${VIASH_PAR_VERBOSE+x} ]; then echo "${VIASH_PAR_VERBOSE}" | sed "s#'#'\\"'\\"'#g;s#.*#par_verbose='&'#" ; else echo "# par_verbose="; fi ) $( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "${VIASH_META_NAME}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_name='&'#" ; else echo "# meta_name="; fi ) @@ -3864,56 +3646,55 @@ $( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}" ## VIASH END -# Exit on error set -eo pipefail -# Unset parameters -unset_if_false=( - par_first_allele_only - par_split_by_ID - par_verbose -) +# Unset false boolean parameters +[[ "\\$par_first_allele_only" == "false" ]] && unset par_first_allele_only +[[ "\\$par_split_by_id" == "false" ]] && unset par_split_by_id +[[ "\\$par_verbose" == "false" ]] && unset par_verbose -for par in \\${unset_if_false[@]}; do - test_val="\\${!par}" - [[ "\\$test_val" == "false" ]] && unset \\$par -done +# Handle multiple input files (semicolon-separated) +IFS=';' read -ra input_files <<< "\\$par_input" -# Create input array -IFS=";" read -ra input <<< \\$par_input - -# Check the size of the input array -if [[ \\${#input[@]} -gt 2 ]]; then - echo "Error: --input only takes a max of two files!" - exit 1 +# Validate input files (maximum 2 allowed) +if [[ \\${#input_files[@]} -gt 2 ]]; then + echo "Error: Maximum of two input files allowed" >&2 + exit 1 fi -# Execute bcftools stats with the provided arguments -bcftools stats \\\\ - \\${par_first_allele_only:+--1st-allele-only} \\\\ - \\${par_split_by_ID:+--split-by-ID} \\\\ - \\${par_verbose:+--verbose} \\\\ - \\${par_allele_frequency_bins:+--af-bins "\\${par_allele_frequency_bins}"} \\\\ - \\${par_allele_frequency_bins_file:+--af-bins "\\${par_allele_frequency_bins_file}"} \\\\ - \\${par_allele_frequency_tag:+--af-tag "\\${par_allele_frequency_tag}"} \\\\ - \\${par_collapse:+-c "\\${par_collapse}"} \\\\ - \\${par_depth:+-d "\\${par_depth}"} \\\\ - \\${par_exclude:+-e "\\${par_exclude}"} \\\\ - \\${par_exons:+-E "\\${par_exons}"} \\\\ - \\${par_apply_filters:+-f "\\${par_apply_filters}"} \\\\ - \\${par_fasta_reference:+-F "\\${par_fasta_reference}"} \\\\ - \\${par_include:+-i "\\${par_include}"} \\\\ - \\${par_regions:+-r "\\${par_regions}"} \\\\ - \\${par_regions_file:+-R "\\${par_regions_file}"} \\\\ - \\${par_regions_overlap:+--regions-overlap "\\${par_regions_overlap}"} \\\\ - \\${par_samples:+-s "\\${par_samples}"} \\\\ - \\${par_samples_file:+-S "\\${par_samples_file}"} \\\\ - \\${par_targets:+-t "\\${par_targets}"} \\\\ - \\${par_targets_file:+-T "\\${par_targets_file}"} \\\\ - \\${par_targets_overlaps:+--targets-overlap "\\${par_targets_overlaps}"} \\\\ - \\${par_user_tstv:+-u "\\${par_user_tstv}"} \\\\ - "\\${input[@]}" \\\\ - > \\$par_output +# Build command array +cmd_args=( + "bcftools" "stats" + \\${par_af_bins:+--af-bins "\\$par_af_bins"} + \\${par_af_tag:+--af-tag "\\$par_af_tag"} + \\${par_collapse:+-c "\\$par_collapse"} + \\${par_depth:+-d "\\$par_depth"} + \\${par_exclude:+-e "\\$par_exclude"} + \\${par_exons:+-E "\\$par_exons"} + \\${par_apply_filters:+-f "\\$par_apply_filters"} + \\${par_fasta_ref:+-F "\\$par_fasta_ref"} + \\${par_first_allele_only:+--1st-allele-only} + \\${par_include:+-i "\\$par_include"} + \\${par_split_by_id:+-I} + \\${par_regions:+-r "\\$par_regions"} + \\${par_regions_file:+-R "\\$par_regions_file"} + \\${par_regions_overlap:+--regions-overlap "\\$par_regions_overlap"} + \\${par_samples:+-s "\\$par_samples"} + \\${par_samples_file:+-S "\\$par_samples_file"} + \\${par_targets:+-t "\\$par_targets"} + \\${par_targets_file:+-T "\\$par_targets_file"} + \\${par_targets_overlap:+--targets-overlap "\\$par_targets_overlap"} + \\${par_user_tstv:+-u "\\$par_user_tstv"} + \\${par_verbose:+-v} +) + +# Add input files +for file in "\\${input_files[@]}"; do + cmd_args+=("\\$file") +done + +# Execute command and redirect output +"\\${cmd_args[@]}" > "\\$par_output" VIASHMAIN bash "$tempscript" ''' diff --git a/target/nextflow/bcftools/bcftools_stats/nextflow_schema.json b/target/nextflow/bcftools/bcftools_stats/nextflow_schema.json index fbc5ccbf..b08b8866 100644 --- a/target/nextflow/bcftools/bcftools_stats/nextflow_schema.json +++ b/target/nextflow/bcftools/bcftools_stats/nextflow_schema.json @@ -16,8 +16,8 @@ }, "format": "path", "exists": true, - "description": "Input VCF/BCF file", - "help_text": "Type: `file`, multiple: `True`, required, direction: `input`. " + "description": "Input VCF/BCF file(s)", + "help_text": "Type: `file`, multiple: `True`, required, direction: `input`, example: `[\"input.vcf.gz\"]`. " } } }, @@ -29,9 +29,9 @@ "output": { "type": "string", "format": "path", - "description": "Output txt statistics file.", - "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output\"`, direction: `output`. ", - "default": "$id.$key.output" + "description": "Write output to a file", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.txt\"`, direction: `output`, example: `\"stats.txt\"`. ", + "default": "$id.$key.output.txt" } } }, @@ -40,32 +40,20 @@ "type": "object", "description": "No description", "properties": { - "allele_frequency_bins": { + "af_bins": { "type": "string", - "description": "Allele frequency bins, a list of bin values (0.1,0.5,1).\n", + "description": "Allele frequency bins, a list of comma-separated bin values.\n", "help_text": "Type: `string`, multiple: `False`, example: `\"0.1,0.5,1\"`. " }, - "allele_frequency_bins_file": { - "type": "string", - "format": "path", - "description": "Same as allele_frequency_bins, but in a file.\nFormat of file is one value per line", - "help_text": "Type: `file`, multiple: `False`, direction: `input`. " - }, - "allele_frequency_tag": { + "af_tag": { "type": "string", "description": "Allele frequency tag to use, by default estimated from AN,AC or GT.\n", - "help_text": "Type: `string`, multiple: `False`. " - }, - "first_allele_only": { - "type": "boolean", - "description": "Include only 1st allele at multiallelic sites.\n", - "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", - "default": false + "help_text": "Type: `string`, multiple: `False`, example: `\"AF\"`. " }, "collapse": { "type": "string", - "description": "Treat as identical records with .\nSee https://samtools.github.io/bcftools/bcftools.html#common_options for details.\n", - "help_text": "Type: `string`, multiple: `False`, choices: ``snps`, `indels`, `both`, `all`, `some`, `none``. ", + "description": "Treat as identical records with .\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"snps\"`, choices: ``snps`, `indels`, `both`, `all`, `some`, `none``. ", "enum": [ "snps", "indels", @@ -77,37 +65,43 @@ }, "depth": { "type": "string", - "description": "Depth distribution: min,max,bin size.\n", + "description": "Depth distribution: min,max,bin size [0:200:1].\n", "help_text": "Type: `string`, multiple: `False`, example: `\"0,500,1\"`. " }, "exclude": { "type": "string", - "description": "Exclude sites for which the expression is true.\nSee https://samtools.github.io/bcftools/bcftools.html#expressions for details.\n", - "help_text": "Type: `string`, multiple: `False`, example: `\"QUAL < 30 && DP < 10\"`. " + "description": "Exclude sites for which the expression is true.\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"QUAL < 30\"`. " }, "exons": { "type": "string", "format": "path", - "description": "tab-delimited file with exons for indel frameshifts statistics", - "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + "description": "Tab-delimited file with exons for indel frameshifts statistics.\nThe columns of the file are CHR, FROM, TO, with 1-based positions.\nThe file should be BGZF-compressed and indexed with tabix.\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"exons.bed.gz\"`. " }, "apply_filters": { "type": "string", - "description": "Require at least one of the listed FILTER strings (e.g", - "help_text": "Type: `string`, multiple: `False`. " + "description": "Require at least one of the listed FILTER strings.\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"PASS,.\"`. " }, - "fasta_reference": { + "fasta_ref": { "type": "string", "format": "path", "description": "Faidx indexed reference sequence file to determine INDEL context.\n", - "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"reference.fa\"`. " + }, + "first_allele_only": { + "type": "boolean", + "description": "Include only 1st allele at multiallelic sites.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false }, "include": { "type": "string", - "description": "Select sites for which the expression is true.\nSee https://samtools.github.io/bcftools/bcftools.html#expressions for details.\n", - "help_text": "Type: `string`, multiple: `False`, example: `\"QUAL >= 30 && DP >= 10\"`. " + "description": "Select sites for which the expression is true.\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"QUAL >= 30\"`. " }, - "split_by_ID": { + "split_by_id": { "type": "boolean", "description": "Collect stats for sites with ID separately (known vs novel).\n", "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", @@ -115,18 +109,18 @@ }, "regions": { "type": "string", - "description": "Restrict to comma-separated list of regions", - "help_text": "Type: `string`, multiple: `False`, example: `\"20:1000000-2000000\"`. " + "description": "Restrict to comma-separated list of regions.\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"chr20:1000000-2000000\"`. " }, "regions_file": { "type": "string", "format": "path", - "description": "Restrict to regions listed in a file", - "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + "description": "Restrict to regions listed in a file.\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"regions.bed\"`. " }, "regions_overlap": { "type": "string", - "description": "This option controls how overlapping records are determined: \nset to 'pos' or '0' if the VCF record has to have POS inside a region (this corresponds to the default behavior of -t/-T); \nset to 'record' or '1' if also overlapping records with POS outside a region should be included (this is the default behavior of -r/-R, \nand includes indels with POS at the end of a region, which are technically outside the region); \nor set to 'variant' or '2' to include only true overlapping variation (compare the full VCF representation \"TA>T-\" vs the true sequence variation \"A>-\").\n", + "description": "Include if POS in the region (pos), record overlaps (record), \nvariant overlaps (variant)", "help_text": "Type: `string`, multiple: `False`, choices: ``pos`, `record`, `variant`, `0`, `1`, `2``. ", "enum": [ "pos", @@ -140,28 +134,28 @@ "samples": { "type": "string", "description": "List of samples for sample stats, \"-\" to include all samples.\n", - "help_text": "Type: `string`, multiple: `False`. " + "help_text": "Type: `string`, multiple: `False`, example: `\"sample1,sample2\"`. " }, "samples_file": { "type": "string", "format": "path", - "description": "File of samples to include.\ne.g", - "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + "description": "File of samples to include.\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"samples.txt\"`. " }, "targets": { "type": "string", - "description": "Similar as -r, --regions, but the next position is accessed by streaming the whole VCF/BCF \nrather than using the tbi/csi index", - "help_text": "Type: `string`, multiple: `False`, example: `\"20:1000000-2000000\"`. " + "description": "Similar to regions, but streams rather than using index.\nTargets can be prefixed with \"^\" for logical complement.\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"chr20:1000000-2000000\"`. " }, "targets_file": { "type": "string", "format": "path", - "description": "Similar to --regions_file option but streams rather than index-jumps.\n", - "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + "description": "Similar to regions_file but streams rather than index-jumps.\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"targets.bed\"`. " }, - "targets_overlaps": { + "targets_overlap": { "type": "string", - "description": "Include if POS in the region (0), record overlaps (1), variant overlaps (2).\n", + "description": "Include if POS in the region (pos), record overlaps (record), \nvariant overlaps (variant)", "help_text": "Type: `string`, multiple: `False`, choices: ``pos`, `record`, `variant`, `0`, `1`, `2``. ", "enum": [ "pos", @@ -174,8 +168,8 @@ }, "user_tstv": { "type": "string", - "description": "Collect Ts/Tv stats for any tag using the given binning [0:1:100].\nFormat is .\nA subfield can be selected as e.g", - "help_text": "Type: `string`, multiple: `False`. " + "description": "Collect Ts/Tv stats for any tag using the given binning.\nFormat is TAG[:min:max:n]", + "help_text": "Type: `string`, multiple: `False`, example: `\"QUAL:0:40:40\"`. " }, "verbose": { "type": "boolean", diff --git a/target/nextflow/bcl_convert/.config.vsh.yaml b/target/nextflow/bcl_convert/.config.vsh.yaml index 80a0def5..5126b078 100644 --- a/target/nextflow/bcl_convert/.config.vsh.yaml +++ b/target/nextflow/bcl_convert/.config.vsh.yaml @@ -431,7 +431,7 @@ build_info: output: "target/nextflow/bcl_convert" executable: "target/nextflow/bcl_convert/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -453,138 +453,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bcl_convert/main.nf b/target/nextflow/bcl_convert/main.nf index c8271b3d..d8c518ef 100644 --- a/target/nextflow/bcl_convert/main.nf +++ b/target/nextflow/bcl_convert/main.nf @@ -3571,7 +3571,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bcl_convert", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3583,225 +3583,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml b/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml index 020c8de9..14b59086 100644 --- a/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml +++ b/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml @@ -166,6 +166,7 @@ scope: target: "public" requirements: commands: + - "cwl-runner" - "ps" keywords: - "genome" @@ -279,7 +280,7 @@ build_info: output: "target/nextflow/bd_rhapsody/bd_rhapsody_make_reference" executable: "target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -301,138 +302,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf b/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf index 7f078986..86edf729 100644 --- a/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf +++ b/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf @@ -3239,6 +3239,7 @@ meta = [ }, "requirements" : { "commands" : [ + "cwl-runner", "ps" ] }, @@ -3379,7 +3380,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bd_rhapsody/bd_rhapsody_make_reference", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3391,225 +3392,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/.config.vsh.yaml b/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/.config.vsh.yaml index c21bcdb7..f5a3df56 100644 --- a/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/.config.vsh.yaml +++ b/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/.config.vsh.yaml @@ -996,6 +996,7 @@ scope: target: "public" requirements: commands: + - "cwl-runner" - "ps" keywords: - "rna-seq" @@ -1120,7 +1121,7 @@ build_info: output: "target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis" executable: "target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -1142,138 +1143,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/main.nf b/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/main.nf index 76d714cb..0297ae7a 100644 --- a/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/main.nf +++ b/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/main.nf @@ -4271,6 +4271,7 @@ meta = [ }, "requirements" : { "commands" : [ + "cwl-runner", "ps" ] }, @@ -4426,7 +4427,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -4438,225 +4439,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bedtools/bedtools_annotate/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_annotate/.config.vsh.yaml index bd20e190..bd24e7eb 100644 --- a/target/nextflow/bedtools/bedtools_annotate/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_annotate/.config.vsh.yaml @@ -143,6 +143,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "Annotate" @@ -246,7 +247,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_annotate" executable: "target/nextflow/bedtools/bedtools_annotate/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -268,138 +269,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_annotate/main.nf b/target/nextflow/bedtools/bedtools_annotate/main.nf index 6a3590ba..fa7ed989 100644 --- a/target/nextflow/bedtools/bedtools_annotate/main.nf +++ b/target/nextflow/bedtools/bedtools_annotate/main.nf @@ -3197,6 +3197,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bedtools", "ps" ] }, @@ -3321,7 +3322,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_annotate", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3333,225 +3334,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bedtools/bedtools_bamtobed/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_bamtobed/.config.vsh.yaml index dadbca86..670c0fd0 100644 --- a/target/nextflow/bedtools/bedtools_bamtobed/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_bamtobed/.config.vsh.yaml @@ -163,6 +163,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "Converts" @@ -265,7 +266,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_bamtobed" executable: "target/nextflow/bedtools/bedtools_bamtobed/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -287,138 +288,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_bamtobed/main.nf b/target/nextflow/bedtools/bedtools_bamtobed/main.nf index 8a14a8c1..c5d8241e 100644 --- a/target/nextflow/bedtools/bedtools_bamtobed/main.nf +++ b/target/nextflow/bedtools/bedtools_bamtobed/main.nf @@ -3225,6 +3225,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bedtools", "ps" ] }, @@ -3348,7 +3349,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_bamtobed", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3360,225 +3361,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bedtools/bedtools_bamtofastq/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_bamtofastq/.config.vsh.yaml index e41c2d1f..738775d4 100644 --- a/target/nextflow/bedtools/bedtools_bamtofastq/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_bamtofastq/.config.vsh.yaml @@ -110,6 +110,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "Conversion" @@ -210,7 +211,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_bamtofastq" executable: "target/nextflow/bedtools/bedtools_bamtofastq/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -232,138 +233,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_bamtofastq/main.nf b/target/nextflow/bedtools/bedtools_bamtofastq/main.nf index 233f42fe..253256bd 100644 --- a/target/nextflow/bedtools/bedtools_bamtofastq/main.nf +++ b/target/nextflow/bedtools/bedtools_bamtofastq/main.nf @@ -3179,6 +3179,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bedtools", "ps" ] }, @@ -3300,7 +3301,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_bamtofastq", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3312,225 +3313,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bedtools/bedtools_bed12tobed6/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_bed12tobed6/.config.vsh.yaml index b2d48ec9..407a01ef 100644 --- a/target/nextflow/bedtools/bedtools_bed12tobed6/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_bed12tobed6/.config.vsh.yaml @@ -98,6 +98,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "Converts" @@ -198,7 +199,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_bed12tobed6" executable: "target/nextflow/bedtools/bedtools_bed12tobed6/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -220,138 +221,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_bed12tobed6/main.nf b/target/nextflow/bedtools/bedtools_bed12tobed6/main.nf index 6ce0ef9b..7fe03ec5 100644 --- a/target/nextflow/bedtools/bedtools_bed12tobed6/main.nf +++ b/target/nextflow/bedtools/bedtools_bed12tobed6/main.nf @@ -3165,6 +3165,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bedtools", "ps" ] }, @@ -3286,7 +3287,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_bed12tobed6", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3298,225 +3299,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bedtools/bedtools_bedpetobam/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_bedpetobam/.config.vsh.yaml index ea686dfc..b0280dfa 100644 --- a/target/nextflow/bedtools/bedtools_bedpetobam/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_bedpetobam/.config.vsh.yaml @@ -115,6 +115,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -218,7 +219,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_bedpetobam" executable: "target/nextflow/bedtools/bedtools_bedpetobam/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -240,138 +241,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_bedpetobam/main.nf b/target/nextflow/bedtools/bedtools_bedpetobam/main.nf index 5981eda0..0a489020 100644 --- a/target/nextflow/bedtools/bedtools_bedpetobam/main.nf +++ b/target/nextflow/bedtools/bedtools_bedpetobam/main.nf @@ -3177,6 +3177,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bedtools", "ps" ] }, @@ -3301,7 +3302,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_bedpetobam", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3313,225 +3314,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bedtools/bedtools_bedtobam/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_bedtobam/.config.vsh.yaml index 63f2e2cc..8f059c9c 100644 --- a/target/nextflow/bedtools/bedtools_bedtobam/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_bedtobam/.config.vsh.yaml @@ -132,6 +132,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "Converts" @@ -234,7 +235,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_bedtobam" executable: "target/nextflow/bedtools/bedtools_bedtobam/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -256,138 +257,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_bedtobam/main.nf b/target/nextflow/bedtools/bedtools_bedtobam/main.nf index 04ce1ec1..3daad1c0 100644 --- a/target/nextflow/bedtools/bedtools_bedtobam/main.nf +++ b/target/nextflow/bedtools/bedtools_bedtobam/main.nf @@ -3205,6 +3205,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bedtools", "ps" ] }, @@ -3328,7 +3329,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_bedtobam", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3340,225 +3341,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bedtools/bedtools_closest/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_closest/.config.vsh.yaml index 67250b76..3da5dee5 100644 --- a/target/nextflow/bedtools/bedtools_closest/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_closest/.config.vsh.yaml @@ -236,6 +236,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "Closest" @@ -340,7 +341,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_closest" executable: "target/nextflow/bedtools/bedtools_closest/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -362,138 +363,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_closest/main.nf b/target/nextflow/bedtools/bedtools_closest/main.nf index 572bf248..9537f3cf 100644 --- a/target/nextflow/bedtools/bedtools_closest/main.nf +++ b/target/nextflow/bedtools/bedtools_closest/main.nf @@ -3309,6 +3309,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bedtools", "ps" ] }, @@ -3434,7 +3435,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_closest", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3446,225 +3447,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bedtools/bedtools_cluster/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_cluster/.config.vsh.yaml index 29da8c57..e045883a 100644 --- a/target/nextflow/bedtools/bedtools_cluster/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_cluster/.config.vsh.yaml @@ -104,6 +104,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -207,7 +208,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_cluster" executable: "target/nextflow/bedtools/bedtools_cluster/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -229,138 +230,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_cluster/main.nf b/target/nextflow/bedtools/bedtools_cluster/main.nf index 9c688117..ea630a20 100644 --- a/target/nextflow/bedtools/bedtools_cluster/main.nf +++ b/target/nextflow/bedtools/bedtools_cluster/main.nf @@ -3166,6 +3166,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bedtools", "ps" ] }, @@ -3290,7 +3291,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_cluster", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3302,225 +3303,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bedtools/bedtools_complement/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_complement/.config.vsh.yaml index 4983d9c2..26900e28 100644 --- a/target/nextflow/bedtools/bedtools_complement/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_complement/.config.vsh.yaml @@ -105,6 +105,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -208,7 +209,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_complement" executable: "target/nextflow/bedtools/bedtools_complement/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -230,138 +231,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_complement/main.nf b/target/nextflow/bedtools/bedtools_complement/main.nf index 349d79f4..47dd47d5 100644 --- a/target/nextflow/bedtools/bedtools_complement/main.nf +++ b/target/nextflow/bedtools/bedtools_complement/main.nf @@ -3165,6 +3165,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bedtools", "ps" ] }, @@ -3289,7 +3290,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_complement", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3301,225 +3302,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bedtools/bedtools_coverage/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_coverage/.config.vsh.yaml index a5ed5a0d..9c058f11 100644 --- a/target/nextflow/bedtools/bedtools_coverage/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_coverage/.config.vsh.yaml @@ -257,6 +257,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -361,7 +362,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_coverage" executable: "target/nextflow/bedtools/bedtools_coverage/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -383,138 +384,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_coverage/main.nf b/target/nextflow/bedtools/bedtools_coverage/main.nf index bed5a0ed..db6da5fc 100644 --- a/target/nextflow/bedtools/bedtools_coverage/main.nf +++ b/target/nextflow/bedtools/bedtools_coverage/main.nf @@ -3332,6 +3332,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bedtools", "ps" ] }, @@ -3457,7 +3458,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_coverage", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3469,225 +3470,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bedtools/bedtools_expand/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_expand/.config.vsh.yaml index 04d8fe98..c9ade810 100644 --- a/target/nextflow/bedtools/bedtools_expand/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_expand/.config.vsh.yaml @@ -90,6 +90,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -193,7 +194,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_expand" executable: "target/nextflow/bedtools/bedtools_expand/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -215,138 +216,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_expand/main.nf b/target/nextflow/bedtools/bedtools_expand/main.nf index 4b591a5b..4bc71001 100644 --- a/target/nextflow/bedtools/bedtools_expand/main.nf +++ b/target/nextflow/bedtools/bedtools_expand/main.nf @@ -3153,6 +3153,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bedtools", "ps" ] }, @@ -3277,7 +3278,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_expand", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3289,225 +3290,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bedtools/bedtools_fisher/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_fisher/.config.vsh.yaml index d99bffbb..5aae5a97 100644 --- a/target/nextflow/bedtools/bedtools_fisher/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_fisher/.config.vsh.yaml @@ -238,6 +238,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -342,7 +343,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_fisher" executable: "target/nextflow/bedtools/bedtools_fisher/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -364,138 +365,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_fisher/main.nf b/target/nextflow/bedtools/bedtools_fisher/main.nf index 25dbcb51..1813e206 100644 --- a/target/nextflow/bedtools/bedtools_fisher/main.nf +++ b/target/nextflow/bedtools/bedtools_fisher/main.nf @@ -3316,6 +3316,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bedtools", "ps" ] }, @@ -3441,7 +3442,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_fisher", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3453,225 +3454,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bedtools/bedtools_flank/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_flank/.config.vsh.yaml index 341b46f7..f51069f5 100644 --- a/target/nextflow/bedtools/bedtools_flank/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_flank/.config.vsh.yaml @@ -169,6 +169,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -273,7 +274,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_flank" executable: "target/nextflow/bedtools/bedtools_flank/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -295,138 +296,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_flank/main.nf b/target/nextflow/bedtools/bedtools_flank/main.nf index 96872a81..53328c06 100644 --- a/target/nextflow/bedtools/bedtools_flank/main.nf +++ b/target/nextflow/bedtools/bedtools_flank/main.nf @@ -3234,6 +3234,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bedtools", "ps" ] }, @@ -3359,7 +3360,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_flank", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3371,225 +3372,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bedtools/bedtools_genomecov/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_genomecov/.config.vsh.yaml index 58a984e6..d3edc6f1 100644 --- a/target/nextflow/bedtools/bedtools_genomecov/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_genomecov/.config.vsh.yaml @@ -260,6 +260,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genome coverage" @@ -365,7 +366,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_genomecov" executable: "target/nextflow/bedtools/bedtools_genomecov/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -387,138 +388,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_genomecov/main.nf b/target/nextflow/bedtools/bedtools_genomecov/main.nf index aef6f4c2..e19541f0 100644 --- a/target/nextflow/bedtools/bedtools_genomecov/main.nf +++ b/target/nextflow/bedtools/bedtools_genomecov/main.nf @@ -3328,6 +3328,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bedtools", "ps" ] }, @@ -3454,7 +3455,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_genomecov", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3466,225 +3467,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml index a619077b..b6343258 100644 --- a/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml @@ -160,6 +160,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "sequencing" @@ -262,7 +263,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_getfasta" executable: "target/nextflow/bedtools/bedtools_getfasta/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -284,138 +285,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_getfasta/main.nf b/target/nextflow/bedtools/bedtools_getfasta/main.nf index d29d468a..083b3517 100644 --- a/target/nextflow/bedtools/bedtools_getfasta/main.nf +++ b/target/nextflow/bedtools/bedtools_getfasta/main.nf @@ -3233,6 +3233,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bedtools", "ps" ] }, @@ -3356,7 +3357,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_getfasta", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3368,225 +3369,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bedtools/bedtools_groupby/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_groupby/.config.vsh.yaml index 77961392..eaa81c26 100644 --- a/target/nextflow/bedtools/bedtools_groupby/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_groupby/.config.vsh.yaml @@ -184,6 +184,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "groupby" @@ -284,7 +285,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_groupby" executable: "target/nextflow/bedtools/bedtools_groupby/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -306,138 +307,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_groupby/main.nf b/target/nextflow/bedtools/bedtools_groupby/main.nf index 77b24bbf..ecba6cc7 100644 --- a/target/nextflow/bedtools/bedtools_groupby/main.nf +++ b/target/nextflow/bedtools/bedtools_groupby/main.nf @@ -3255,6 +3255,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bedtools", "ps" ] }, @@ -3376,7 +3377,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_groupby", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3388,225 +3389,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bedtools/bedtools_igv/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_igv/.config.vsh.yaml index 57814d07..137843f1 100644 --- a/target/nextflow/bedtools/bedtools_igv/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_igv/.config.vsh.yaml @@ -186,6 +186,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -290,7 +291,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_igv" executable: "target/nextflow/bedtools/bedtools_igv/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -312,138 +313,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_igv/main.nf b/target/nextflow/bedtools/bedtools_igv/main.nf index 7a4ef7c0..11a8e694 100644 --- a/target/nextflow/bedtools/bedtools_igv/main.nf +++ b/target/nextflow/bedtools/bedtools_igv/main.nf @@ -3256,6 +3256,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bedtools", "ps" ] }, @@ -3381,7 +3382,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_igv", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3393,225 +3394,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bedtools/bedtools_intersect/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_intersect/.config.vsh.yaml index fbfca336..01571e4e 100644 --- a/target/nextflow/bedtools/bedtools_intersect/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_intersect/.config.vsh.yaml @@ -313,6 +313,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "feature intersection" @@ -416,7 +417,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_intersect" executable: "target/nextflow/bedtools/bedtools_intersect/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -438,138 +439,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_intersect/main.nf b/target/nextflow/bedtools/bedtools_intersect/main.nf index 8c220eb2..0b305aa5 100644 --- a/target/nextflow/bedtools/bedtools_intersect/main.nf +++ b/target/nextflow/bedtools/bedtools_intersect/main.nf @@ -3396,6 +3396,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bedtools", "ps" ] }, @@ -3519,7 +3520,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_intersect", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3531,225 +3532,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bedtools/bedtools_jaccard/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_jaccard/.config.vsh.yaml index 93b2fd68..c961b50b 100644 --- a/target/nextflow/bedtools/bedtools_jaccard/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_jaccard/.config.vsh.yaml @@ -235,6 +235,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -340,7 +341,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_jaccard" executable: "target/nextflow/bedtools/bedtools_jaccard/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -362,138 +363,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_jaccard/main.nf b/target/nextflow/bedtools/bedtools_jaccard/main.nf index 3a3bb903..a7c1072f 100644 --- a/target/nextflow/bedtools/bedtools_jaccard/main.nf +++ b/target/nextflow/bedtools/bedtools_jaccard/main.nf @@ -3308,6 +3308,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bedtools", "ps" ] }, @@ -3434,7 +3435,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_jaccard", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3446,225 +3447,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bedtools/bedtools_links/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_links/.config.vsh.yaml index d3d94944..69e5daec 100644 --- a/target/nextflow/bedtools/bedtools_links/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_links/.config.vsh.yaml @@ -132,6 +132,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "HTML" @@ -236,7 +237,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_links" executable: "target/nextflow/bedtools/bedtools_links/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -258,138 +259,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_links/main.nf b/target/nextflow/bedtools/bedtools_links/main.nf index e86a21e3..b56e3e60 100644 --- a/target/nextflow/bedtools/bedtools_links/main.nf +++ b/target/nextflow/bedtools/bedtools_links/main.nf @@ -3201,6 +3201,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bedtools", "ps" ] }, @@ -3326,7 +3327,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_links", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3338,225 +3339,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bedtools/bedtools_makewindows/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_makewindows/.config.vsh.yaml index 0f2c5507..06b20bb2 100644 --- a/target/nextflow/bedtools/bedtools_makewindows/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_makewindows/.config.vsh.yaml @@ -173,6 +173,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -278,7 +279,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_makewindows" executable: "target/nextflow/bedtools/bedtools_makewindows/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -300,138 +301,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_makewindows/main.nf b/target/nextflow/bedtools/bedtools_makewindows/main.nf index accc802c..209886dd 100644 --- a/target/nextflow/bedtools/bedtools_makewindows/main.nf +++ b/target/nextflow/bedtools/bedtools_makewindows/main.nf @@ -3232,6 +3232,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bedtools", "ps" ] }, @@ -3358,7 +3359,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_makewindows", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3370,225 +3371,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bedtools/bedtools_map/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_map/.config.vsh.yaml index 77661235..61c903c5 100644 --- a/target/nextflow/bedtools/bedtools_map/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_map/.config.vsh.yaml @@ -298,6 +298,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -403,7 +404,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_map" executable: "target/nextflow/bedtools/bedtools_map/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -425,138 +426,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_map/main.nf b/target/nextflow/bedtools/bedtools_map/main.nf index 0de2eec1..2d541f56 100644 --- a/target/nextflow/bedtools/bedtools_map/main.nf +++ b/target/nextflow/bedtools/bedtools_map/main.nf @@ -3373,6 +3373,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bedtools", "ps" ] }, @@ -3499,7 +3500,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_map", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3511,225 +3512,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bedtools/bedtools_maskfasta/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_maskfasta/.config.vsh.yaml index f734119e..d738bc09 100644 --- a/target/nextflow/bedtools/bedtools_maskfasta/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_maskfasta/.config.vsh.yaml @@ -137,6 +137,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -239,7 +240,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_maskfasta" executable: "target/nextflow/bedtools/bedtools_maskfasta/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -261,138 +262,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_maskfasta/main.nf b/target/nextflow/bedtools/bedtools_maskfasta/main.nf index 4dca055b..6d2d0d42 100644 --- a/target/nextflow/bedtools/bedtools_maskfasta/main.nf +++ b/target/nextflow/bedtools/bedtools_maskfasta/main.nf @@ -3192,6 +3192,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bedtools", "ps" ] }, @@ -3315,7 +3316,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_maskfasta", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3327,225 +3328,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bedtools/bedtools_merge/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_merge/.config.vsh.yaml index 9555cb2d..e6c4edbc 100644 --- a/target/nextflow/bedtools/bedtools_merge/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_merge/.config.vsh.yaml @@ -224,6 +224,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "Merge" @@ -327,7 +328,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_merge" executable: "target/nextflow/bedtools/bedtools_merge/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -349,138 +350,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_merge/main.nf b/target/nextflow/bedtools/bedtools_merge/main.nf index 24622558..a4012a04 100644 --- a/target/nextflow/bedtools/bedtools_merge/main.nf +++ b/target/nextflow/bedtools/bedtools_merge/main.nf @@ -3286,6 +3286,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bedtools", "ps" ] }, @@ -3410,7 +3411,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_merge", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3422,225 +3423,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bedtools/bedtools_multicov/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_multicov/.config.vsh.yaml index c96b80fb..9796a39d 100644 --- a/target/nextflow/bedtools/bedtools_multicov/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_multicov/.config.vsh.yaml @@ -210,6 +210,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -314,7 +315,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_multicov" executable: "target/nextflow/bedtools/bedtools_multicov/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -336,138 +337,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_multicov/main.nf b/target/nextflow/bedtools/bedtools_multicov/main.nf index 52f6e9a3..68251132 100644 --- a/target/nextflow/bedtools/bedtools_multicov/main.nf +++ b/target/nextflow/bedtools/bedtools_multicov/main.nf @@ -3263,6 +3263,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bedtools", "ps" ] }, @@ -3388,7 +3389,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_multicov", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3400,225 +3401,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bedtools/bedtools_multiinter/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_multiinter/.config.vsh.yaml index f718d0a5..f68c0433 100644 --- a/target/nextflow/bedtools/bedtools_multiinter/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_multiinter/.config.vsh.yaml @@ -155,6 +155,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -260,7 +261,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_multiinter" executable: "target/nextflow/bedtools/bedtools_multiinter/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -282,138 +283,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_multiinter/main.nf b/target/nextflow/bedtools/bedtools_multiinter/main.nf index 2b8f13ac..00acc0e2 100644 --- a/target/nextflow/bedtools/bedtools_multiinter/main.nf +++ b/target/nextflow/bedtools/bedtools_multiinter/main.nf @@ -3205,6 +3205,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bedtools", "ps" ] }, @@ -3331,7 +3332,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_multiinter", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3343,225 +3344,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bedtools/bedtools_overlap/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_overlap/.config.vsh.yaml index 871ef399..04bf0386 100644 --- a/target/nextflow/bedtools/bedtools_overlap/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_overlap/.config.vsh.yaml @@ -102,6 +102,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -205,7 +206,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_overlap" executable: "target/nextflow/bedtools/bedtools_overlap/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -227,138 +228,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_overlap/main.nf b/target/nextflow/bedtools/bedtools_overlap/main.nf index 43abc5a8..b86ed255 100644 --- a/target/nextflow/bedtools/bedtools_overlap/main.nf +++ b/target/nextflow/bedtools/bedtools_overlap/main.nf @@ -3151,6 +3151,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bedtools", "ps" ] }, @@ -3275,7 +3276,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_overlap", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3287,225 +3288,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bedtools/bedtools_pairtobed/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_pairtobed/.config.vsh.yaml index 753c4c69..78c43c86 100644 --- a/target/nextflow/bedtools/bedtools_pairtobed/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_pairtobed/.config.vsh.yaml @@ -225,6 +225,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -329,7 +330,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_pairtobed" executable: "target/nextflow/bedtools/bedtools_pairtobed/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -351,138 +352,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_pairtobed/main.nf b/target/nextflow/bedtools/bedtools_pairtobed/main.nf index a57b3426..48d9beca 100644 --- a/target/nextflow/bedtools/bedtools_pairtobed/main.nf +++ b/target/nextflow/bedtools/bedtools_pairtobed/main.nf @@ -3274,6 +3274,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bedtools", "ps" ] }, @@ -3399,7 +3400,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_pairtobed", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3411,225 +3412,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bedtools/bedtools_pairtopair/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_pairtopair/.config.vsh.yaml index b868b0c6..d8421af3 100644 --- a/target/nextflow/bedtools/bedtools_pairtopair/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_pairtopair/.config.vsh.yaml @@ -184,6 +184,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -287,7 +288,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_pairtopair" executable: "target/nextflow/bedtools/bedtools_pairtopair/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -309,138 +310,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_pairtopair/main.nf b/target/nextflow/bedtools/bedtools_pairtopair/main.nf index cd960fb0..08c84d2f 100644 --- a/target/nextflow/bedtools/bedtools_pairtopair/main.nf +++ b/target/nextflow/bedtools/bedtools_pairtopair/main.nf @@ -3236,6 +3236,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bedtools", "ps" ] }, @@ -3360,7 +3361,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_pairtopair", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3372,225 +3373,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bedtools/bedtools_random/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_random/.config.vsh.yaml index 65a90bd3..1fcd9713 100644 --- a/target/nextflow/bedtools/bedtools_random/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_random/.config.vsh.yaml @@ -135,6 +135,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -239,7 +240,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_random" executable: "target/nextflow/bedtools/bedtools_random/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -261,138 +262,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_random/main.nf b/target/nextflow/bedtools/bedtools_random/main.nf index 76d4b959..d9b599b6 100644 --- a/target/nextflow/bedtools/bedtools_random/main.nf +++ b/target/nextflow/bedtools/bedtools_random/main.nf @@ -3187,6 +3187,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bedtools", "ps" ] }, @@ -3312,7 +3313,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_random", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3324,225 +3325,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bedtools/bedtools_reldist/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_reldist/.config.vsh.yaml index 2cc7e3c0..15c40067 100644 --- a/target/nextflow/bedtools/bedtools_reldist/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_reldist/.config.vsh.yaml @@ -116,6 +116,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -220,7 +221,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_reldist" executable: "target/nextflow/bedtools/bedtools_reldist/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -242,138 +243,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_reldist/main.nf b/target/nextflow/bedtools/bedtools_reldist/main.nf index 50500bd4..e6f04dff 100644 --- a/target/nextflow/bedtools/bedtools_reldist/main.nf +++ b/target/nextflow/bedtools/bedtools_reldist/main.nf @@ -3162,6 +3162,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bedtools", "ps" ] }, @@ -3287,7 +3288,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_reldist", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3299,225 +3300,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bedtools/bedtools_sample/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_sample/.config.vsh.yaml index 4574bc24..c28242fe 100644 --- a/target/nextflow/bedtools/bedtools_sample/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_sample/.config.vsh.yaml @@ -189,6 +189,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -292,7 +293,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_sample" executable: "target/nextflow/bedtools/bedtools_sample/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -314,138 +315,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_sample/main.nf b/target/nextflow/bedtools/bedtools_sample/main.nf index 94a2ddf0..03e484d5 100644 --- a/target/nextflow/bedtools/bedtools_sample/main.nf +++ b/target/nextflow/bedtools/bedtools_sample/main.nf @@ -3251,6 +3251,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bedtools", "ps" ] }, @@ -3375,7 +3376,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_sample", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3387,225 +3388,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bedtools/bedtools_shift/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_shift/.config.vsh.yaml index b880bc04..5205cbd5 100644 --- a/target/nextflow/bedtools/bedtools_shift/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_shift/.config.vsh.yaml @@ -169,6 +169,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -272,7 +273,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_shift" executable: "target/nextflow/bedtools/bedtools_shift/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -294,138 +295,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_shift/main.nf b/target/nextflow/bedtools/bedtools_shift/main.nf index 948d35f2..c63b5592 100644 --- a/target/nextflow/bedtools/bedtools_shift/main.nf +++ b/target/nextflow/bedtools/bedtools_shift/main.nf @@ -3221,6 +3221,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bedtools", "ps" ] }, @@ -3345,7 +3346,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_shift", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3357,225 +3358,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bedtools/bedtools_shuffle/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_shuffle/.config.vsh.yaml index 56f563fd..bee0e6ca 100644 --- a/target/nextflow/bedtools/bedtools_shuffle/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_shuffle/.config.vsh.yaml @@ -243,6 +243,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -347,7 +348,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_shuffle" executable: "target/nextflow/bedtools/bedtools_shuffle/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -369,138 +370,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_shuffle/main.nf b/target/nextflow/bedtools/bedtools_shuffle/main.nf index cba8fdf2..3b492767 100644 --- a/target/nextflow/bedtools/bedtools_shuffle/main.nf +++ b/target/nextflow/bedtools/bedtools_shuffle/main.nf @@ -3287,6 +3287,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bedtools", "ps" ] }, @@ -3412,7 +3413,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_shuffle", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3424,225 +3425,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bedtools/bedtools_slop/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_slop/.config.vsh.yaml index 3cf25420..1aa41460 100644 --- a/target/nextflow/bedtools/bedtools_slop/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_slop/.config.vsh.yaml @@ -183,6 +183,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -287,7 +288,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_slop" executable: "target/nextflow/bedtools/bedtools_slop/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -309,138 +310,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_slop/main.nf b/target/nextflow/bedtools/bedtools_slop/main.nf index d1b6842f..534b912a 100644 --- a/target/nextflow/bedtools/bedtools_slop/main.nf +++ b/target/nextflow/bedtools/bedtools_slop/main.nf @@ -3230,6 +3230,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bedtools", "ps" ] }, @@ -3355,7 +3356,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_slop", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3367,225 +3368,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bedtools/bedtools_sort/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_sort/.config.vsh.yaml index 425c8659..179360a8 100644 --- a/target/nextflow/bedtools/bedtools_sort/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_sort/.config.vsh.yaml @@ -172,6 +172,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "Sort" @@ -275,7 +276,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_sort" executable: "target/nextflow/bedtools/bedtools_sort/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -297,138 +298,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_sort/main.nf b/target/nextflow/bedtools/bedtools_sort/main.nf index f657d667..baa0a7a7 100644 --- a/target/nextflow/bedtools/bedtools_sort/main.nf +++ b/target/nextflow/bedtools/bedtools_sort/main.nf @@ -3229,6 +3229,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bedtools", "ps" ] }, @@ -3353,7 +3354,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_sort", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3365,225 +3366,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bedtools/bedtools_spacing/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_spacing/.config.vsh.yaml index 29eaede6..02b3cd43 100644 --- a/target/nextflow/bedtools/bedtools_spacing/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_spacing/.config.vsh.yaml @@ -134,6 +134,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -238,7 +239,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_spacing" executable: "target/nextflow/bedtools/bedtools_spacing/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -260,138 +261,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_spacing/main.nf b/target/nextflow/bedtools/bedtools_spacing/main.nf index b2646118..78af0e07 100644 --- a/target/nextflow/bedtools/bedtools_spacing/main.nf +++ b/target/nextflow/bedtools/bedtools_spacing/main.nf @@ -3186,6 +3186,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bedtools", "ps" ] }, @@ -3311,7 +3312,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_spacing", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3323,225 +3324,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bedtools/bedtools_split/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_split/.config.vsh.yaml index c22db36a..78ccd57f 100644 --- a/target/nextflow/bedtools/bedtools_split/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_split/.config.vsh.yaml @@ -138,6 +138,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -242,7 +243,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_split" executable: "target/nextflow/bedtools/bedtools_split/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -264,138 +265,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_split/main.nf b/target/nextflow/bedtools/bedtools_split/main.nf index d2d02a4d..62d03d12 100644 --- a/target/nextflow/bedtools/bedtools_split/main.nf +++ b/target/nextflow/bedtools/bedtools_split/main.nf @@ -3186,6 +3186,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bedtools", "ps" ] }, @@ -3311,7 +3312,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_split", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3323,225 +3324,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bedtools/bedtools_subtract/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_subtract/.config.vsh.yaml index 4f200624..b3caa7a9 100644 --- a/target/nextflow/bedtools/bedtools_subtract/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_subtract/.config.vsh.yaml @@ -318,6 +318,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -422,7 +423,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_subtract" executable: "target/nextflow/bedtools/bedtools_subtract/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -444,138 +445,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_subtract/main.nf b/target/nextflow/bedtools/bedtools_subtract/main.nf index 06a6b7dc..99fadd66 100644 --- a/target/nextflow/bedtools/bedtools_subtract/main.nf +++ b/target/nextflow/bedtools/bedtools_subtract/main.nf @@ -3364,6 +3364,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bedtools", "ps" ] }, @@ -3489,7 +3490,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_subtract", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3501,225 +3502,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bedtools/bedtools_summary/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_summary/.config.vsh.yaml index 1dcafdda..7018a9b6 100644 --- a/target/nextflow/bedtools/bedtools_summary/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_summary/.config.vsh.yaml @@ -106,6 +106,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -210,7 +211,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_summary" executable: "target/nextflow/bedtools/bedtools_summary/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -232,138 +233,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_summary/main.nf b/target/nextflow/bedtools/bedtools_summary/main.nf index b89c2c43..3889a19a 100644 --- a/target/nextflow/bedtools/bedtools_summary/main.nf +++ b/target/nextflow/bedtools/bedtools_summary/main.nf @@ -3154,6 +3154,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bedtools", "ps" ] }, @@ -3279,7 +3280,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_summary", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3291,225 +3292,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bedtools/bedtools_tag/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_tag/.config.vsh.yaml index a81d5b4d..a7727599 100644 --- a/target/nextflow/bedtools/bedtools_tag/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_tag/.config.vsh.yaml @@ -215,6 +215,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -319,7 +320,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_tag" executable: "target/nextflow/bedtools/bedtools_tag/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -341,138 +342,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_tag/main.nf b/target/nextflow/bedtools/bedtools_tag/main.nf index 8f69833f..95fa32f1 100644 --- a/target/nextflow/bedtools/bedtools_tag/main.nf +++ b/target/nextflow/bedtools/bedtools_tag/main.nf @@ -3254,6 +3254,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bedtools", "ps" ] }, @@ -3379,7 +3380,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_tag", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3391,225 +3392,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bedtools/bedtools_unionbedg/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_unionbedg/.config.vsh.yaml index 8586d6bf..18a3dfe5 100644 --- a/target/nextflow/bedtools/bedtools_unionbedg/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_unionbedg/.config.vsh.yaml @@ -97,6 +97,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -200,7 +201,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_unionbedg" executable: "target/nextflow/bedtools/bedtools_unionbedg/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -222,138 +223,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_unionbedg/main.nf b/target/nextflow/bedtools/bedtools_unionbedg/main.nf index 207d7a1d..07255844 100644 --- a/target/nextflow/bedtools/bedtools_unionbedg/main.nf +++ b/target/nextflow/bedtools/bedtools_unionbedg/main.nf @@ -3147,6 +3147,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bedtools", "ps" ] }, @@ -3271,7 +3272,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_unionbedg", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3283,225 +3284,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bedtools/bedtools_window/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_window/.config.vsh.yaml index 87f1167b..63630d61 100644 --- a/target/nextflow/bedtools/bedtools_window/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_window/.config.vsh.yaml @@ -261,6 +261,7 @@ scope: target: "public" requirements: commands: + - "bedtools" - "ps" keywords: - "genomics" @@ -365,7 +366,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_window" executable: "target/nextflow/bedtools/bedtools_window/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -387,138 +388,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_window/main.nf b/target/nextflow/bedtools/bedtools_window/main.nf index f241c2b4..aca44ab0 100644 --- a/target/nextflow/bedtools/bedtools_window/main.nf +++ b/target/nextflow/bedtools/bedtools_window/main.nf @@ -3311,6 +3311,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bedtools", "ps" ] }, @@ -3436,7 +3437,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_window", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3448,225 +3449,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bowtie2/bowtie2_align/.config.vsh.yaml b/target/nextflow/bowtie2/bowtie2_align/.config.vsh.yaml index 99c4993b..bb8f01ef 100644 --- a/target/nextflow/bowtie2/bowtie2_align/.config.vsh.yaml +++ b/target/nextflow/bowtie2/bowtie2_align/.config.vsh.yaml @@ -744,6 +744,7 @@ scope: target: "public" requirements: commands: + - "bowtie2" - "ps" keywords: - "Alignment" @@ -843,7 +844,7 @@ build_info: output: "target/nextflow/bowtie2/bowtie2_align" executable: "target/nextflow/bowtie2/bowtie2_align/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -865,138 +866,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bowtie2/bowtie2_align/main.nf b/target/nextflow/bowtie2/bowtie2_align/main.nf index 7803f585..94c527d3 100644 --- a/target/nextflow/bowtie2/bowtie2_align/main.nf +++ b/target/nextflow/bowtie2/bowtie2_align/main.nf @@ -3960,6 +3960,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bowtie2", "ps" ] }, @@ -4080,7 +4081,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bowtie2/bowtie2_align", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -4092,225 +4093,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bowtie2/bowtie2_build/.config.vsh.yaml b/target/nextflow/bowtie2/bowtie2_build/.config.vsh.yaml index 94446582..e43470bf 100644 --- a/target/nextflow/bowtie2/bowtie2_build/.config.vsh.yaml +++ b/target/nextflow/bowtie2/bowtie2_build/.config.vsh.yaml @@ -206,6 +206,7 @@ scope: target: "public" requirements: commands: + - "bowtie2-build" - "ps" keywords: - "Alignment" @@ -306,7 +307,7 @@ build_info: output: "target/nextflow/bowtie2/bowtie2_build" executable: "target/nextflow/bowtie2/bowtie2_build/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -328,138 +329,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bowtie2/bowtie2_build/main.nf b/target/nextflow/bowtie2/bowtie2_build/main.nf index 21a3af99..10396bef 100644 --- a/target/nextflow/bowtie2/bowtie2_build/main.nf +++ b/target/nextflow/bowtie2/bowtie2_build/main.nf @@ -3297,6 +3297,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bowtie2-build", "ps" ] }, @@ -3417,7 +3418,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bowtie2/bowtie2_build", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3429,225 +3430,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bowtie2/bowtie2_inspect/.config.vsh.yaml b/target/nextflow/bowtie2/bowtie2_inspect/.config.vsh.yaml index 3221bab3..40404854 100644 --- a/target/nextflow/bowtie2/bowtie2_inspect/.config.vsh.yaml +++ b/target/nextflow/bowtie2/bowtie2_inspect/.config.vsh.yaml @@ -117,6 +117,7 @@ scope: target: "public" requirements: commands: + - "bowtie2-inspect" - "ps" keywords: - "Alignment" @@ -218,7 +219,7 @@ build_info: output: "target/nextflow/bowtie2/bowtie2_inspect" executable: "target/nextflow/bowtie2/bowtie2_inspect/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -240,138 +241,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bowtie2/bowtie2_inspect/main.nf b/target/nextflow/bowtie2/bowtie2_inspect/main.nf index 0d78674c..69a96db0 100644 --- a/target/nextflow/bowtie2/bowtie2_inspect/main.nf +++ b/target/nextflow/bowtie2/bowtie2_inspect/main.nf @@ -3193,6 +3193,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bowtie2-inspect", "ps" ] }, @@ -3314,7 +3315,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bowtie2/bowtie2_inspect", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3326,225 +3327,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml b/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml index 74f8db6e..aae92f19 100644 --- a/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml +++ b/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml @@ -161,7 +161,7 @@ build_info: output: "target/nextflow/busco/busco_download_datasets" executable: "target/nextflow/busco/busco_download_datasets/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -183,138 +183,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/busco/busco_download_datasets/main.nf b/target/nextflow/busco/busco_download_datasets/main.nf index 825cd9f6..7ce00067 100644 --- a/target/nextflow/busco/busco_download_datasets/main.nf +++ b/target/nextflow/busco/busco_download_datasets/main.nf @@ -3241,7 +3241,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/busco/busco_download_datasets", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3253,225 +3253,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml b/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml index c66c7897..d8d9113f 100644 --- a/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml +++ b/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml @@ -148,7 +148,7 @@ build_info: output: "target/nextflow/busco/busco_list_datasets" executable: "target/nextflow/busco/busco_list_datasets/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -170,138 +170,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/busco/busco_list_datasets/main.nf b/target/nextflow/busco/busco_list_datasets/main.nf index 67e71174..acaced7b 100644 --- a/target/nextflow/busco/busco_list_datasets/main.nf +++ b/target/nextflow/busco/busco_list_datasets/main.nf @@ -3227,7 +3227,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/busco/busco_list_datasets", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3239,225 +3239,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/busco/busco_run/.config.vsh.yaml b/target/nextflow/busco/busco_run/.config.vsh.yaml index 38700fef..1e772fbc 100644 --- a/target/nextflow/busco/busco_run/.config.vsh.yaml +++ b/target/nextflow/busco/busco_run/.config.vsh.yaml @@ -426,7 +426,7 @@ build_info: output: "target/nextflow/busco/busco_run" executable: "target/nextflow/busco/busco_run/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -448,138 +448,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/busco/busco_run/main.nf b/target/nextflow/busco/busco_run/main.nf index 4d82097c..1a9dbb9d 100644 --- a/target/nextflow/busco/busco_run/main.nf +++ b/target/nextflow/busco/busco_run/main.nf @@ -3539,7 +3539,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/busco/busco_run", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3551,225 +3551,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bwa/bwa_aln/.config.vsh.yaml b/target/nextflow/bwa/bwa_aln/.config.vsh.yaml index 3f9cf2da..419dde96 100644 --- a/target/nextflow/bwa/bwa_aln/.config.vsh.yaml +++ b/target/nextflow/bwa/bwa_aln/.config.vsh.yaml @@ -326,6 +326,7 @@ scope: target: "public" requirements: commands: + - "bwa" - "ps" keywords: - "alignment" @@ -425,7 +426,7 @@ build_info: output: "target/nextflow/bwa/bwa_aln" executable: "target/nextflow/bwa/bwa_aln/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -447,138 +448,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bwa/bwa_aln/main.nf b/target/nextflow/bwa/bwa_aln/main.nf index f9b46959..328b6c4c 100644 --- a/target/nextflow/bwa/bwa_aln/main.nf +++ b/target/nextflow/bwa/bwa_aln/main.nf @@ -3469,6 +3469,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bwa", "ps" ] }, @@ -3587,7 +3588,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bwa/bwa_aln", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3599,225 +3600,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bwa/bwa_index/.config.vsh.yaml b/target/nextflow/bwa/bwa_index/.config.vsh.yaml index 82facb2d..9094e6ad 100644 --- a/target/nextflow/bwa/bwa_index/.config.vsh.yaml +++ b/target/nextflow/bwa/bwa_index/.config.vsh.yaml @@ -122,6 +122,7 @@ scope: target: "public" requirements: commands: + - "bwa" - "ps" keywords: - "alignment" @@ -220,7 +221,7 @@ build_info: output: "target/nextflow/bwa/bwa_index" executable: "target/nextflow/bwa/bwa_index/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -242,138 +243,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bwa/bwa_index/main.nf b/target/nextflow/bwa/bwa_index/main.nf index 6ff962b8..dffd2be6 100644 --- a/target/nextflow/bwa/bwa_index/main.nf +++ b/target/nextflow/bwa/bwa_index/main.nf @@ -3206,6 +3206,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bwa", "ps" ] }, @@ -3323,7 +3324,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bwa/bwa_index", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3335,225 +3336,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bwa/bwa_mem/.config.vsh.yaml b/target/nextflow/bwa/bwa_mem/.config.vsh.yaml index bebefaec..11f84b82 100644 --- a/target/nextflow/bwa/bwa_mem/.config.vsh.yaml +++ b/target/nextflow/bwa/bwa_mem/.config.vsh.yaml @@ -488,6 +488,7 @@ scope: target: "public" requirements: commands: + - "bwa" - "ps" keywords: - "alignment" @@ -586,7 +587,7 @@ build_info: output: "target/nextflow/bwa/bwa_mem" executable: "target/nextflow/bwa/bwa_mem/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -608,138 +609,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bwa/bwa_mem/main.nf b/target/nextflow/bwa/bwa_mem/main.nf index 858b97bb..0e385688 100644 --- a/target/nextflow/bwa/bwa_mem/main.nf +++ b/target/nextflow/bwa/bwa_mem/main.nf @@ -3661,6 +3661,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bwa", "ps" ] }, @@ -3778,7 +3779,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bwa/bwa_mem", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3790,225 +3791,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bwa/bwa_sampe/.config.vsh.yaml b/target/nextflow/bwa/bwa_sampe/.config.vsh.yaml index 3ccde10b..64b7fe67 100644 --- a/target/nextflow/bwa/bwa_sampe/.config.vsh.yaml +++ b/target/nextflow/bwa/bwa_sampe/.config.vsh.yaml @@ -227,6 +227,7 @@ scope: target: "public" requirements: commands: + - "bwa" - "ps" keywords: - "alignment" @@ -326,7 +327,7 @@ build_info: output: "target/nextflow/bwa/bwa_sampe" executable: "target/nextflow/bwa/bwa_sampe/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -348,138 +349,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bwa/bwa_sampe/main.nf b/target/nextflow/bwa/bwa_sampe/main.nf index c2a7ba06..8fb5922d 100644 --- a/target/nextflow/bwa/bwa_sampe/main.nf +++ b/target/nextflow/bwa/bwa_sampe/main.nf @@ -3341,6 +3341,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bwa", "ps" ] }, @@ -3459,7 +3460,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bwa/bwa_sampe", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3471,225 +3472,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bwa/bwa_samse/.config.vsh.yaml b/target/nextflow/bwa/bwa_samse/.config.vsh.yaml index 4ab14154..19e35734 100644 --- a/target/nextflow/bwa/bwa_samse/.config.vsh.yaml +++ b/target/nextflow/bwa/bwa_samse/.config.vsh.yaml @@ -132,6 +132,7 @@ scope: target: "public" requirements: commands: + - "bwa" - "ps" keywords: - "alignment" @@ -231,7 +232,7 @@ build_info: output: "target/nextflow/bwa/bwa_samse" executable: "target/nextflow/bwa/bwa_samse/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -253,138 +254,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bwa/bwa_samse/main.nf b/target/nextflow/bwa/bwa_samse/main.nf index 321a2ef7..2f1b9769 100644 --- a/target/nextflow/bwa/bwa_samse/main.nf +++ b/target/nextflow/bwa/bwa_samse/main.nf @@ -3221,6 +3221,7 @@ meta = [ }, "requirements" : { "commands" : [ + "bwa", "ps" ] }, @@ -3339,7 +3340,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bwa/bwa_samse", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3351,225 +3352,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/cellranger/cellranger_count/.config.vsh.yaml b/target/nextflow/cellranger/cellranger_count/.config.vsh.yaml index c4382b69..dd82ea0c 100644 --- a/target/nextflow/cellranger/cellranger_count/.config.vsh.yaml +++ b/target/nextflow/cellranger/cellranger_count/.config.vsh.yaml @@ -266,6 +266,7 @@ scope: target: "public" requirements: commands: + - "cellranger" - "ps" keywords: - "cellranger" @@ -373,7 +374,7 @@ build_info: output: "target/nextflow/cellranger/cellranger_count" executable: "target/nextflow/cellranger/cellranger_count/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -395,138 +396,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/cellranger/cellranger_count/main.nf b/target/nextflow/cellranger/cellranger_count/main.nf index 2124d160..b0d738ae 100644 --- a/target/nextflow/cellranger/cellranger_count/main.nf +++ b/target/nextflow/cellranger/cellranger_count/main.nf @@ -3343,6 +3343,7 @@ meta = [ }, "requirements" : { "commands" : [ + "cellranger", "ps" ] }, @@ -3473,7 +3474,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/cellranger/cellranger_count", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3485,225 +3486,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/cellranger/cellranger_mkref/.config.vsh.yaml b/target/nextflow/cellranger/cellranger_mkref/.config.vsh.yaml index 69f71e8a..371db012 100644 --- a/target/nextflow/cellranger/cellranger_mkref/.config.vsh.yaml +++ b/target/nextflow/cellranger/cellranger_mkref/.config.vsh.yaml @@ -75,6 +75,10 @@ scope: target: "public" requirements: commands: + - "cellranger" + - "pigz" + - "unpigz" + - "tar" - "ps" keywords: - "cellranger" @@ -193,7 +197,7 @@ build_info: output: "target/nextflow/cellranger/cellranger_mkref" executable: "target/nextflow/cellranger/cellranger_mkref/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -215,138 +219,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/cellranger/cellranger_mkref/main.nf b/target/nextflow/cellranger/cellranger_mkref/main.nf index bf9e313b..f24055ab 100644 --- a/target/nextflow/cellranger/cellranger_mkref/main.nf +++ b/target/nextflow/cellranger/cellranger_mkref/main.nf @@ -3134,6 +3134,10 @@ meta = [ }, "requirements" : { "commands" : [ + "cellranger", + "pigz", + "unpigz", + "tar", "ps" ] }, @@ -3281,7 +3285,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/cellranger/cellranger_mkref", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3293,225 +3297,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/cutadapt/.config.vsh.yaml b/target/nextflow/cutadapt/.config.vsh.yaml index 6d24428d..1cc057df 100644 --- a/target/nextflow/cutadapt/.config.vsh.yaml +++ b/target/nextflow/cutadapt/.config.vsh.yaml @@ -743,7 +743,7 @@ build_info: output: "target/nextflow/cutadapt" executable: "target/nextflow/cutadapt/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -765,138 +765,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/cutadapt/main.nf b/target/nextflow/cutadapt/main.nf index b7c6c97e..70d59d92 100644 --- a/target/nextflow/cutadapt/main.nf +++ b/target/nextflow/cutadapt/main.nf @@ -3849,7 +3849,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/cutadapt", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3861,225 +3861,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/falco/.config.vsh.yaml b/target/nextflow/falco/.config.vsh.yaml index f5f0961f..3f84a4eb 100644 --- a/target/nextflow/falco/.config.vsh.yaml +++ b/target/nextflow/falco/.config.vsh.yaml @@ -42,7 +42,7 @@ argument_groups: description: "Specifies a non-default file which contains \nthe list of contaminants\ \ to screen \noverrepresented sequences against. The file \nmust contain sets\ \ of named contaminants in \nthe form name[tab]sequence. Lines prefixed \nwith\ - \ a hash will be ignored. Default: \nhttps://github.com/smithlabcode/falco/blob/v1.2.2/Configuration/contaminant_list.txt\n" + \ a hash will be ignored. Default: \nhttps://github.com/smithlabcode/falco/blob/v1.2.5/Configuration/contaminant_list.txt\n" info: null must_exist: true create_parent: true @@ -55,7 +55,7 @@ argument_groups: description: "Specifies a non-default file which contains \nthe list of adapter\ \ sequences which will be \nexplicity searched against the library. The \nfile\ \ must contain sets of named adapters in \nthe form name[tab]sequence. Lines\ - \ prefixed \nwith a hash will be ignored. Default:\nhttps://github.com/smithlabcode/falco/blob/v1.2.2/Configuration/adapter_list.txt\n" + \ prefixed \nwith a hash will be ignored. Default:\nhttps://github.com/smithlabcode/falco/blob/v1.2.5/Configuration/adapter_list.txt\n" info: null must_exist: true create_parent: true @@ -69,7 +69,7 @@ argument_groups: \ which will be used to \ndetermine the warn/error limits for the \nvarious\ \ modules. This file can also be used \nto selectively remove some modules from\ \ the \noutput all together. The format needs to \nmirror the default limits.txt\ - \ file found in \nthe Configuration folder. Default: \nhttps://github.com/smithlabcode/falco/blob/v1.2.2/Configuration/limits.txt\n" + \ file found in \nthe Configuration folder. Default: \nhttps://github.com/smithlabcode/falco/blob/v1.2.5/Configuration/limits.txt\n" info: null must_exist: true create_parent: true @@ -108,6 +108,12 @@ argument_groups: \ be \ntested by swapping A/T and C/G\n" info: null direction: "input" + - type: "boolean_true" + name: "--allow_empty_input" + description: "Allow empty input files and generate empty output files without\ + \ an error state.\n" + info: null + direction: "input" - name: "Output arguments" arguments: - type: "file" @@ -201,6 +207,8 @@ test_resources: - type: "bash_script" path: "test.sh" is_executable: true +- type: "file" + path: "test_helpers.sh" info: null status: "enabled" scope: @@ -208,6 +216,7 @@ scope: target: "public" requirements: commands: + - "falco" - "ps" keywords: - "qc" @@ -288,24 +297,11 @@ runners: engines: - type: "docker" id: "docker" - image: "debian:trixie-slim" + image: "quay.io/biocontainers/falco:1.2.5--h077b44d_0" target_registry: "images.viash-hub.com" target_tag: "main" namespace_separator: "/" setup: - - type: "apt" - packages: - - "wget" - - "build-essential" - - "g++" - - "zlib1g-dev" - - "procps" - interactive: false - - type: "docker" - run: - - "wget https://github.com/smithlabcode/falco/releases/download/v1.2.2/falco-1.2.2.tar.gz\ - \ -O /tmp/falco.tar.gz && \\\ncd /tmp && \\\ntar xvf falco.tar.gz && \\\ncd\ - \ falco-1.2.2 && \\\n./configure && \\\nmake all && \\\nmake install\n" - type: "docker" run: - "echo \"falco: \\\"$(falco -v | sed -n 's/^falco //p')\\\"\" > /var/software_versions.txt\n" @@ -320,7 +316,7 @@ build_info: output: "target/nextflow/falco" executable: "target/nextflow/falco/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -342,138 +338,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/falco/main.nf b/target/nextflow/falco/main.nf index 3ed298d2..e5ac7b53 100644 --- a/target/nextflow/falco/main.nf +++ b/target/nextflow/falco/main.nf @@ -3089,7 +3089,7 @@ meta = [ { "type" : "file", "name" : "--contaminents", - "description" : "Specifies a non-default file which contains \nthe list of contaminants to screen \noverrepresented sequences against. The file \nmust contain sets of named contaminants in \nthe form name[tab]sequence. Lines prefixed \nwith a hash will be ignored. Default: \nhttps://github.com/smithlabcode/falco/blob/v1.2.2/Configuration/contaminant_list.txt\n", + "description" : "Specifies a non-default file which contains \nthe list of contaminants to screen \noverrepresented sequences against. The file \nmust contain sets of named contaminants in \nthe form name[tab]sequence. Lines prefixed \nwith a hash will be ignored. Default: \nhttps://github.com/smithlabcode/falco/blob/v1.2.5/Configuration/contaminant_list.txt\n", "must_exist" : true, "create_parent" : true, "required" : false, @@ -3100,7 +3100,7 @@ meta = [ { "type" : "file", "name" : "--adapters", - "description" : "Specifies a non-default file which contains \nthe list of adapter sequences which will be \nexplicity searched against the library. The \nfile must contain sets of named adapters in \nthe form name[tab]sequence. Lines prefixed \nwith a hash will be ignored. Default:\nhttps://github.com/smithlabcode/falco/blob/v1.2.2/Configuration/adapter_list.txt\n", + "description" : "Specifies a non-default file which contains \nthe list of adapter sequences which will be \nexplicity searched against the library. The \nfile must contain sets of named adapters in \nthe form name[tab]sequence. Lines prefixed \nwith a hash will be ignored. Default:\nhttps://github.com/smithlabcode/falco/blob/v1.2.5/Configuration/adapter_list.txt\n", "must_exist" : true, "create_parent" : true, "required" : false, @@ -3111,7 +3111,7 @@ meta = [ { "type" : "file", "name" : "--limits", - "description" : "Specifies a non-default file which contains \na set of criteria which will be used to \ndetermine the warn/error limits for the \nvarious modules. This file can also be used \nto selectively remove some modules from the \noutput all together. The format needs to \nmirror the default limits.txt file found in \nthe Configuration folder. Default: \nhttps://github.com/smithlabcode/falco/blob/v1.2.2/Configuration/limits.txt\n", + "description" : "Specifies a non-default file which contains \na set of criteria which will be used to \ndetermine the warn/error limits for the \nvarious modules. This file can also be used \nto selectively remove some modules from the \noutput all together. The format needs to \nmirror the default limits.txt file found in \nthe Configuration folder. Default: \nhttps://github.com/smithlabcode/falco/blob/v1.2.5/Configuration/limits.txt\n", "must_exist" : true, "create_parent" : true, "required" : false, @@ -3151,6 +3151,12 @@ meta = [ ], "description" : "[Falco only] The input is a \nreverse-complement. All modules will be \ntested by swapping A/T and C/G\n", "direction" : "input" + }, + { + "type" : "boolean_true", + "name" : "--allow_empty_input", + "description" : "Allow empty input files and generate empty output files without an error state.\n", + "direction" : "input" } ] }, @@ -3254,6 +3260,10 @@ meta = [ "type" : "bash_script", "path" : "test.sh", "is_executable" : true + }, + { + "type" : "file", + "path" : "/src/_utils/test_helpers.sh" } ], "status" : "enabled", @@ -3263,6 +3273,7 @@ meta = [ }, "requirements" : { "commands" : [ + "falco", "ps" ] }, @@ -3359,28 +3370,11 @@ meta = [ { "type" : "docker", "id" : "docker", - "image" : "debian:trixie-slim", + "image" : "quay.io/biocontainers/falco:1.2.5--h077b44d_0", "target_registry" : "images.viash-hub.com", "target_tag" : "main", "namespace_separator" : "/", "setup" : [ - { - "type" : "apt", - "packages" : [ - "wget", - "build-essential", - "g++", - "zlib1g-dev", - "procps" - ], - "interactive" : false - }, - { - "type" : "docker", - "run" : [ - "wget https://github.com/smithlabcode/falco/releases/download/v1.2.2/falco-1.2.2.tar.gz -O /tmp/falco.tar.gz && \\\\\ncd /tmp && \\\\\ntar xvf falco.tar.gz && \\\\\ncd falco-1.2.2 && \\\\\n./configure && \\\\\nmake all && \\\\\nmake install\n" - ] - }, { "type" : "docker", "run" : [ @@ -3400,7 +3394,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/falco", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3412,225 +3406,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", @@ -3665,6 +3445,7 @@ $( if [ ! -z ${VIASH_PAR_LIMITS+x} ]; then echo "${VIASH_PAR_LIMITS}" | sed "s#' $( if [ ! -z ${VIASH_PAR_SUBSAMPLE+x} ]; then echo "${VIASH_PAR_SUBSAMPLE}" | sed "s#'#'\\"'\\"'#g;s#.*#par_subsample='&'#" ; else echo "# par_subsample="; fi ) $( if [ ! -z ${VIASH_PAR_BISULFITE+x} ]; then echo "${VIASH_PAR_BISULFITE}" | sed "s#'#'\\"'\\"'#g;s#.*#par_bisulfite='&'#" ; else echo "# par_bisulfite="; fi ) $( if [ ! -z ${VIASH_PAR_REVERSE_COMPLEMENT+x} ]; then echo "${VIASH_PAR_REVERSE_COMPLEMENT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_reverse_complement='&'#" ; else echo "# par_reverse_complement="; fi ) +$( if [ ! -z ${VIASH_PAR_ALLOW_EMPTY_INPUT+x} ]; then echo "${VIASH_PAR_ALLOW_EMPTY_INPUT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_allow_empty_input='&'#" ; else echo "# par_allow_empty_input="; fi ) $( if [ ! -z ${VIASH_PAR_OUTDIR+x} ]; then echo "${VIASH_PAR_OUTDIR}" | sed "s#'#'\\"'\\"'#g;s#.*#par_outdir='&'#" ; else echo "# par_outdir="; fi ) $( if [ ! -z ${VIASH_PAR_FORMAT+x} ]; then echo "${VIASH_PAR_FORMAT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_format='&'#" ; else echo "# par_format="; fi ) $( if [ ! -z ${VIASH_PAR_DATA_FILENAME+x} ]; then echo "${VIASH_PAR_DATA_FILENAME}" | sed "s#'#'\\"'\\"'#g;s#.*#par_data_filename='&'#" ; else echo "# par_data_filename="; fi ) @@ -3697,6 +3478,8 @@ set -eo pipefail [[ "\\$par_nogroup" == "false" ]] && unset par_nogroup [[ "\\$par_bisulfite" == "false" ]] && unset par_bisulfite [[ "\\$par_reverse_complement" == "false" ]] && unset par_reverse_complement +[[ "\\$par_allow_empty_input" == "false" ]] && unset par_allow_empty_input + IFS=";" read -ra input <<< \\$par_input @@ -3707,6 +3490,7 @@ IFS=";" read -ra input <<< \\$par_input \\${par_limits:+--limits "\\$par_limits"} \\\\ \\${par_subsample:+-subsample \\$par_subsample} \\\\ \\${par_bisulfite:+-bisulfite} \\\\ + \\${par_allow_empty_input:+-allow-empty-input} \\\\ \\${par_reverse_complement:+-reverse-complement} \\\\ \\${par_outdir:+--outdir "\\$par_outdir"} \\\\ \\${par_format:+--format "\\$par_format"} \\\\ diff --git a/target/nextflow/falco/nextflow_schema.json b/target/nextflow/falco/nextflow_schema.json index d9520b4e..363637b5 100644 --- a/target/nextflow/falco/nextflow_schema.json +++ b/target/nextflow/falco/nextflow_schema.json @@ -66,6 +66,12 @@ "description": "[Falco only] The input is a \nreverse-complement", "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", "default": false + }, + "allow_empty_input": { + "type": "boolean", + "description": "Allow empty input files and generate empty output files without an error state.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false } } }, diff --git a/target/nextflow/fastp/.config.vsh.yaml b/target/nextflow/fastp/.config.vsh.yaml index 3ac2bfbe..20eeef80 100644 --- a/target/nextflow/fastp/.config.vsh.yaml +++ b/target/nextflow/fastp/.config.vsh.yaml @@ -1086,7 +1086,7 @@ build_info: output: "target/nextflow/fastp" executable: "target/nextflow/fastp/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -1108,138 +1108,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/fastp/main.nf b/target/nextflow/fastp/main.nf index 9fd1b48f..e04940f1 100644 --- a/target/nextflow/fastp/main.nf +++ b/target/nextflow/fastp/main.nf @@ -4253,7 +4253,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/fastp", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -4265,225 +4265,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/fastqc/.config.vsh.yaml b/target/nextflow/fastqc/.config.vsh.yaml index 73625361..5c6d3a92 100644 --- a/target/nextflow/fastqc/.config.vsh.yaml +++ b/target/nextflow/fastqc/.config.vsh.yaml @@ -351,7 +351,7 @@ build_info: output: "target/nextflow/fastqc" executable: "target/nextflow/fastqc/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -373,138 +373,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/fastqc/main.nf b/target/nextflow/fastqc/main.nf index 7371fe14..ebc09d21 100644 --- a/target/nextflow/fastqc/main.nf +++ b/target/nextflow/fastqc/main.nf @@ -3419,7 +3419,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/fastqc", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3431,225 +3431,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/featurecounts/.config.vsh.yaml b/target/nextflow/featurecounts/.config.vsh.yaml index 337954cf..ee5aa0fb 100644 --- a/target/nextflow/featurecounts/.config.vsh.yaml +++ b/target/nextflow/featurecounts/.config.vsh.yaml @@ -543,6 +543,7 @@ scope: target: "public" requirements: commands: + - "featureCounts" - "ps" keywords: - "Read counting" @@ -643,7 +644,7 @@ build_info: output: "target/nextflow/featurecounts" executable: "target/nextflow/featurecounts/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -665,138 +666,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/featurecounts/main.nf b/target/nextflow/featurecounts/main.nf index 40d3b918..9b35fccf 100644 --- a/target/nextflow/featurecounts/main.nf +++ b/target/nextflow/featurecounts/main.nf @@ -3651,6 +3651,7 @@ meta = [ }, "requirements" : { "commands" : [ + "featureCounts", "ps" ] }, @@ -3771,7 +3772,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/featurecounts", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3783,225 +3784,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/fq/fq_filter/.config.vsh.yaml b/target/nextflow/fq/fq_filter/.config.vsh.yaml index 3d5ed9e6..0db94e03 100644 --- a/target/nextflow/fq/fq_filter/.config.vsh.yaml +++ b/target/nextflow/fq/fq_filter/.config.vsh.yaml @@ -81,6 +81,7 @@ scope: target: "public" requirements: commands: + - "fq" - "ps" keywords: - "fastq" @@ -178,7 +179,7 @@ build_info: output: "target/nextflow/fq/fq_filter" executable: "target/nextflow/fq/fq_filter/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -200,138 +201,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/fq/fq_filter/main.nf b/target/nextflow/fq/fq_filter/main.nf index 8c1d9b9c..6b74e1de 100644 --- a/target/nextflow/fq/fq_filter/main.nf +++ b/target/nextflow/fq/fq_filter/main.nf @@ -3146,6 +3146,7 @@ meta = [ }, "requirements" : { "commands" : [ + "fq", "ps" ] }, @@ -3262,7 +3263,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/fq/fq_filter", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3274,225 +3275,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/fq/fq_generate/.config.vsh.yaml b/target/nextflow/fq/fq_generate/.config.vsh.yaml index ae74a0e9..7683a9f8 100644 --- a/target/nextflow/fq/fq_generate/.config.vsh.yaml +++ b/target/nextflow/fq/fq_generate/.config.vsh.yaml @@ -104,6 +104,7 @@ scope: target: "public" requirements: commands: + - "fq" - "ps" keywords: - "FASTQ" @@ -202,7 +203,7 @@ build_info: output: "target/nextflow/fq/fq_generate" executable: "target/nextflow/fq/fq_generate/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -224,138 +225,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/fq/fq_generate/main.nf b/target/nextflow/fq/fq_generate/main.nf index 80140a06..e8e967b8 100644 --- a/target/nextflow/fq/fq_generate/main.nf +++ b/target/nextflow/fq/fq_generate/main.nf @@ -3179,6 +3179,7 @@ meta = [ }, "requirements" : { "commands" : [ + "fq", "ps" ] }, @@ -3296,7 +3297,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/fq/fq_generate", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3308,225 +3309,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/fq/fq_lint/.config.vsh.yaml b/target/nextflow/fq/fq_lint/.config.vsh.yaml index 69dd2eb6..7836f4a7 100644 --- a/target/nextflow/fq/fq_lint/.config.vsh.yaml +++ b/target/nextflow/fq/fq_lint/.config.vsh.yaml @@ -131,6 +131,7 @@ scope: target: "public" requirements: commands: + - "fq" - "ps" keywords: - "fastq" @@ -229,7 +230,7 @@ build_info: output: "target/nextflow/fq/fq_lint" executable: "target/nextflow/fq/fq_lint/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -251,138 +252,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/fq/fq_lint/main.nf b/target/nextflow/fq/fq_lint/main.nf index 9bb12e40..8c90dbd3 100644 --- a/target/nextflow/fq/fq_lint/main.nf +++ b/target/nextflow/fq/fq_lint/main.nf @@ -3210,6 +3210,7 @@ meta = [ }, "requirements" : { "commands" : [ + "fq", "ps" ] }, @@ -3327,7 +3328,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/fq/fq_lint", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3339,225 +3340,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/fq/fq_subsample/.config.vsh.yaml b/target/nextflow/fq/fq_subsample/.config.vsh.yaml index 89510b3b..fbd250d6 100644 --- a/target/nextflow/fq/fq_subsample/.config.vsh.yaml +++ b/target/nextflow/fq/fq_subsample/.config.vsh.yaml @@ -117,6 +117,7 @@ scope: target: "public" requirements: commands: + - "fq" - "ps" keywords: - "fastq" @@ -214,7 +215,7 @@ build_info: output: "target/nextflow/fq/fq_subsample" executable: "target/nextflow/fq/fq_subsample/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -236,138 +237,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/fq/fq_subsample/main.nf b/target/nextflow/fq/fq_subsample/main.nf index f1ee791b..f6d13b7a 100644 --- a/target/nextflow/fq/fq_subsample/main.nf +++ b/target/nextflow/fq/fq_subsample/main.nf @@ -3188,6 +3188,7 @@ meta = [ }, "requirements" : { "commands" : [ + "fq", "ps" ] }, @@ -3304,7 +3305,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/fq/fq_subsample", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3316,225 +3317,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/gffread/.config.vsh.yaml b/target/nextflow/gffread/.config.vsh.yaml index ec848850..32ca4e96 100644 --- a/target/nextflow/gffread/.config.vsh.yaml +++ b/target/nextflow/gffread/.config.vsh.yaml @@ -683,7 +683,7 @@ build_info: output: "target/nextflow/gffread" executable: "target/nextflow/gffread/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -705,138 +705,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/gffread/main.nf b/target/nextflow/gffread/main.nf index c5f242b8..f5392cd5 100644 --- a/target/nextflow/gffread/main.nf +++ b/target/nextflow/gffread/main.nf @@ -3828,7 +3828,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/gffread", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3840,225 +3840,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml b/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml index ff3271c1..3c1b7bb0 100644 --- a/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml +++ b/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml @@ -221,7 +221,7 @@ build_info: output: "target/nextflow/kallisto/kallisto_index" executable: "target/nextflow/kallisto/kallisto_index/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -243,138 +243,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/kallisto/kallisto_index/main.nf b/target/nextflow/kallisto/kallisto_index/main.nf index 08cb6c2d..084aa003 100644 --- a/target/nextflow/kallisto/kallisto_index/main.nf +++ b/target/nextflow/kallisto/kallisto_index/main.nf @@ -3301,7 +3301,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/kallisto/kallisto_index", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3313,225 +3313,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml b/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml index 2762cf16..2e292a2a 100644 --- a/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml +++ b/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml @@ -249,7 +249,7 @@ build_info: output: "target/nextflow/kallisto/kallisto_quant" executable: "target/nextflow/kallisto/kallisto_quant/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -271,138 +271,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/kallisto/kallisto_quant/main.nf b/target/nextflow/kallisto/kallisto_quant/main.nf index 24dea3d2..e9f717d4 100644 --- a/target/nextflow/kallisto/kallisto_quant/main.nf +++ b/target/nextflow/kallisto/kallisto_quant/main.nf @@ -3335,7 +3335,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/kallisto/kallisto_quant", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3347,225 +3347,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml b/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml index 4a817e57..a8e80d17 100644 --- a/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml +++ b/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml @@ -400,6 +400,7 @@ scope: target: "public" requirements: commands: + - "lofreq" - "ps" keywords: - "variant calling" @@ -502,7 +503,7 @@ build_info: output: "target/nextflow/lofreq/lofreq_call" executable: "target/nextflow/lofreq/lofreq_call/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -524,138 +525,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/lofreq/lofreq_call/main.nf b/target/nextflow/lofreq/lofreq_call/main.nf index 47576438..250d1248 100644 --- a/target/nextflow/lofreq/lofreq_call/main.nf +++ b/target/nextflow/lofreq/lofreq_call/main.nf @@ -3509,6 +3509,7 @@ meta = [ }, "requirements" : { "commands" : [ + "lofreq", "ps" ] }, @@ -3631,7 +3632,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/lofreq/lofreq_call", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3643,225 +3644,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml b/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml index 9f0f743d..8d643b01 100644 --- a/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml +++ b/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml @@ -106,6 +106,7 @@ scope: target: "public" requirements: commands: + - "lofreq" - "ps" keywords: - "bam" @@ -210,7 +211,7 @@ build_info: output: "target/nextflow/lofreq/lofreq_indelqual" executable: "target/nextflow/lofreq/lofreq_indelqual/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -232,138 +233,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/lofreq/lofreq_indelqual/main.nf b/target/nextflow/lofreq/lofreq_indelqual/main.nf index 1c11bbe7..7f830b36 100644 --- a/target/nextflow/lofreq/lofreq_indelqual/main.nf +++ b/target/nextflow/lofreq/lofreq_indelqual/main.nf @@ -3170,6 +3170,7 @@ meta = [ }, "requirements" : { "commands" : [ + "lofreq", "ps" ] }, @@ -3294,7 +3295,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/lofreq/lofreq_indelqual", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3306,225 +3307,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/multiqc/.config.vsh.yaml b/target/nextflow/multiqc/.config.vsh.yaml index 693384d8..edf4a001 100644 --- a/target/nextflow/multiqc/.config.vsh.yaml +++ b/target/nextflow/multiqc/.config.vsh.yaml @@ -459,7 +459,7 @@ build_info: output: "target/nextflow/multiqc" executable: "target/nextflow/multiqc/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -481,138 +481,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/multiqc/main.nf b/target/nextflow/multiqc/main.nf index d115ffd8..db53dbec 100644 --- a/target/nextflow/multiqc/main.nf +++ b/target/nextflow/multiqc/main.nf @@ -3596,7 +3596,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/multiqc", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3608,225 +3608,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/nanoplot/.config.vsh.yaml b/target/nextflow/nanoplot/.config.vsh.yaml index 7abdc609..5cc546d3 100644 --- a/target/nextflow/nanoplot/.config.vsh.yaml +++ b/target/nextflow/nanoplot/.config.vsh.yaml @@ -495,7 +495,7 @@ build_info: output: "target/nextflow/nanoplot" executable: "target/nextflow/nanoplot/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -517,138 +517,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/nanoplot/main.nf b/target/nextflow/nanoplot/main.nf index 2df766aa..947326af 100644 --- a/target/nextflow/nanoplot/main.nf +++ b/target/nextflow/nanoplot/main.nf @@ -3627,7 +3627,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/nanoplot", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3639,225 +3639,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/pear/.config.vsh.yaml b/target/nextflow/pear/.config.vsh.yaml index f00e0f8b..ec473f95 100644 --- a/target/nextflow/pear/.config.vsh.yaml +++ b/target/nextflow/pear/.config.vsh.yaml @@ -292,6 +292,8 @@ scope: target: "public" requirements: commands: + - "pear" + - "gzip" - "ps" keywords: - "pair-end" @@ -393,7 +395,7 @@ build_info: output: "target/nextflow/pear" executable: "target/nextflow/pear/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -415,138 +417,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/pear/main.nf b/target/nextflow/pear/main.nf index 964f80c7..400a7c2e 100644 --- a/target/nextflow/pear/main.nf +++ b/target/nextflow/pear/main.nf @@ -3355,6 +3355,8 @@ meta = [ }, "requirements" : { "commands" : [ + "pear", + "gzip", "ps" ] }, @@ -3476,7 +3478,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/pear", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3488,225 +3490,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/qualimap/qualimap_rnaseq/.config.vsh.yaml b/target/nextflow/qualimap/qualimap_rnaseq/.config.vsh.yaml index ed7b4b0f..f4e41fcc 100644 --- a/target/nextflow/qualimap/qualimap_rnaseq/.config.vsh.yaml +++ b/target/nextflow/qualimap/qualimap_rnaseq/.config.vsh.yaml @@ -267,7 +267,7 @@ build_info: output: "target/nextflow/qualimap/qualimap_rnaseq" executable: "target/nextflow/qualimap/qualimap_rnaseq/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -289,138 +289,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/qualimap/qualimap_rnaseq/main.nf b/target/nextflow/qualimap/qualimap_rnaseq/main.nf index 45dba5aa..818b0d7e 100644 --- a/target/nextflow/qualimap/qualimap_rnaseq/main.nf +++ b/target/nextflow/qualimap/qualimap_rnaseq/main.nf @@ -3359,7 +3359,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/qualimap/qualimap_rnaseq", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3371,225 +3371,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml b/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml index 6887d0dc..14d3a5b0 100644 --- a/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml +++ b/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml @@ -855,7 +855,7 @@ build_info: output: "target/nextflow/rsem/rsem_calculate_expression" executable: "target/nextflow/rsem/rsem_calculate_expression/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -877,138 +877,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/rsem/rsem_calculate_expression/main.nf b/target/nextflow/rsem/rsem_calculate_expression/main.nf index 1307e852..14762755 100644 --- a/target/nextflow/rsem/rsem_calculate_expression/main.nf +++ b/target/nextflow/rsem/rsem_calculate_expression/main.nf @@ -3891,7 +3891,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/rsem/rsem_calculate_expression", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3903,225 +3903,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml b/target/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml index 2ba40d35..88bd9b3b 100644 --- a/target/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml +++ b/target/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml @@ -268,6 +268,7 @@ scope: target: "public" requirements: commands: + - "rsem-prepare-reference" - "ps" keywords: - "Transcriptome" @@ -414,7 +415,7 @@ build_info: output: "target/nextflow/rsem/rsem_prepare_reference" executable: "target/nextflow/rsem/rsem_prepare_reference/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -436,138 +437,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/rsem/rsem_prepare_reference/main.nf b/target/nextflow/rsem/rsem_prepare_reference/main.nf index 99bd37ef..5010ec84 100644 --- a/target/nextflow/rsem/rsem_prepare_reference/main.nf +++ b/target/nextflow/rsem/rsem_prepare_reference/main.nf @@ -3309,6 +3309,7 @@ meta = [ }, "requirements" : { "commands" : [ + "rsem-prepare-reference", "ps" ] }, @@ -3467,7 +3468,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/rsem/rsem_prepare_reference", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3479,225 +3480,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml index 1c876021..cd0f3d37 100644 --- a/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml @@ -173,7 +173,7 @@ build_info: output: "target/nextflow/rseqc/rseqc_bamstat" executable: "target/nextflow/rseqc/rseqc_bamstat/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -195,138 +195,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/rseqc/rseqc_bamstat/main.nf b/target/nextflow/rseqc/rseqc_bamstat/main.nf index 31214931..8192d745 100644 --- a/target/nextflow/rseqc/rseqc_bamstat/main.nf +++ b/target/nextflow/rseqc/rseqc_bamstat/main.nf @@ -3258,7 +3258,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/rseqc/rseqc_bamstat", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3270,225 +3270,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml index cef4c8d9..91881678 100644 --- a/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml @@ -199,7 +199,7 @@ build_info: output: "target/nextflow/rseqc/rseqc_inferexperiment" executable: "target/nextflow/rseqc/rseqc_inferexperiment/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -221,138 +221,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/rseqc/rseqc_inferexperiment/main.nf b/target/nextflow/rseqc/rseqc_inferexperiment/main.nf index 5da0c438..e0dd7004 100644 --- a/target/nextflow/rseqc/rseqc_inferexperiment/main.nf +++ b/target/nextflow/rseqc/rseqc_inferexperiment/main.nf @@ -3291,7 +3291,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/rseqc/rseqc_inferexperiment", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3303,225 +3303,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/rseqc/rseqc_inner_distance/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_inner_distance/.config.vsh.yaml index 680e3e78..0394b7cf 100644 --- a/target/nextflow/rseqc/rseqc_inner_distance/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_inner_distance/.config.vsh.yaml @@ -292,7 +292,7 @@ build_info: output: "target/nextflow/rseqc/rseqc_inner_distance" executable: "target/nextflow/rseqc/rseqc_inner_distance/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -314,138 +314,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/rseqc/rseqc_inner_distance/main.nf b/target/nextflow/rseqc/rseqc_inner_distance/main.nf index 273eb691..a1359e8d 100644 --- a/target/nextflow/rseqc/rseqc_inner_distance/main.nf +++ b/target/nextflow/rseqc/rseqc_inner_distance/main.nf @@ -3391,7 +3391,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/rseqc/rseqc_inner_distance", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3403,225 +3403,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/salmon/salmon_index/.config.vsh.yaml b/target/nextflow/salmon/salmon_index/.config.vsh.yaml index 3bbbe9eb..2fba881c 100644 --- a/target/nextflow/salmon/salmon_index/.config.vsh.yaml +++ b/target/nextflow/salmon/salmon_index/.config.vsh.yaml @@ -176,6 +176,7 @@ scope: target: "public" requirements: commands: + - "salmon" - "ps" keywords: - "Transcriptome" @@ -275,7 +276,7 @@ build_info: output: "target/nextflow/salmon/salmon_index" executable: "target/nextflow/salmon/salmon_index/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -297,138 +298,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/salmon/salmon_index/main.nf b/target/nextflow/salmon/salmon_index/main.nf index 027971a0..c1c3cf7e 100644 --- a/target/nextflow/salmon/salmon_index/main.nf +++ b/target/nextflow/salmon/salmon_index/main.nf @@ -3231,6 +3231,7 @@ meta = [ }, "requirements" : { "commands" : [ + "salmon", "ps" ] }, @@ -3351,7 +3352,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/salmon/salmon_index", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3363,225 +3364,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/salmon/salmon_quant/.config.vsh.yaml b/target/nextflow/salmon/salmon_quant/.config.vsh.yaml index 5493e482..fd46807a 100644 --- a/target/nextflow/salmon/salmon_quant/.config.vsh.yaml +++ b/target/nextflow/salmon/salmon_quant/.config.vsh.yaml @@ -1072,6 +1072,7 @@ scope: target: "public" requirements: commands: + - "salmon" - "ps" keywords: - "Transcriptome" @@ -1171,7 +1172,7 @@ build_info: output: "target/nextflow/salmon/salmon_quant" executable: "target/nextflow/salmon/salmon_quant/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -1193,138 +1194,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/salmon/salmon_quant/main.nf b/target/nextflow/salmon/salmon_quant/main.nf index 7f0073f6..6cfcef3a 100644 --- a/target/nextflow/salmon/salmon_quant/main.nf +++ b/target/nextflow/salmon/salmon_quant/main.nf @@ -4066,6 +4066,7 @@ meta = [ }, "requirements" : { "commands" : [ + "salmon", "ps" ] }, @@ -4186,7 +4187,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/salmon/salmon_quant", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -4198,225 +4199,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/samtools/samtools_collate/.config.vsh.yaml b/target/nextflow/samtools/samtools_collate/.config.vsh.yaml index c74daad4..9961d795 100644 --- a/target/nextflow/samtools/samtools_collate/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_collate/.config.vsh.yaml @@ -262,7 +262,7 @@ build_info: output: "target/nextflow/samtools/samtools_collate" executable: "target/nextflow/samtools/samtools_collate/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -284,138 +284,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/samtools/samtools_collate/main.nf b/target/nextflow/samtools/samtools_collate/main.nf index 595e559c..5fb8d45b 100644 --- a/target/nextflow/samtools/samtools_collate/main.nf +++ b/target/nextflow/samtools/samtools_collate/main.nf @@ -3362,7 +3362,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_collate", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3374,225 +3374,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml b/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml index 55ab47a9..8fc9944d 100644 --- a/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml @@ -241,7 +241,7 @@ build_info: output: "target/nextflow/samtools/samtools_faidx" executable: "target/nextflow/samtools/samtools_faidx/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -263,138 +263,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/samtools/samtools_faidx/main.nf b/target/nextflow/samtools/samtools_faidx/main.nf index 53b52253..9b04edf6 100644 --- a/target/nextflow/samtools/samtools_faidx/main.nf +++ b/target/nextflow/samtools/samtools_faidx/main.nf @@ -3334,7 +3334,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_faidx", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3346,225 +3346,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/samtools/samtools_fasta/.config.vsh.yaml b/target/nextflow/samtools/samtools_fasta/.config.vsh.yaml index 202db283..ec078a91 100644 --- a/target/nextflow/samtools/samtools_fasta/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_fasta/.config.vsh.yaml @@ -431,7 +431,7 @@ build_info: output: "target/nextflow/samtools/samtools_fasta" executable: "target/nextflow/samtools/samtools_fasta/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -453,138 +453,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/samtools/samtools_fasta/main.nf b/target/nextflow/samtools/samtools_fasta/main.nf index 76c13bfd..42a01178 100644 --- a/target/nextflow/samtools/samtools_fasta/main.nf +++ b/target/nextflow/samtools/samtools_fasta/main.nf @@ -3526,7 +3526,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_fasta", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3538,225 +3538,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml b/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml index 957bd903..24a05b55 100644 --- a/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml @@ -431,7 +431,7 @@ build_info: output: "target/nextflow/samtools/samtools_fastq" executable: "target/nextflow/samtools/samtools_fastq/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -453,138 +453,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/samtools/samtools_fastq/main.nf b/target/nextflow/samtools/samtools_fastq/main.nf index 31d41574..a41f3acd 100644 --- a/target/nextflow/samtools/samtools_fastq/main.nf +++ b/target/nextflow/samtools/samtools_fastq/main.nf @@ -3526,7 +3526,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_fastq", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3538,225 +3538,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml b/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml index 9b7fe6cf..ad281be3 100644 --- a/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml @@ -171,7 +171,7 @@ build_info: output: "target/nextflow/samtools/samtools_flagstat" executable: "target/nextflow/samtools/samtools_flagstat/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -193,138 +193,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/samtools/samtools_flagstat/main.nf b/target/nextflow/samtools/samtools_flagstat/main.nf index f42cb8d5..f4738a7d 100644 --- a/target/nextflow/samtools/samtools_flagstat/main.nf +++ b/target/nextflow/samtools/samtools_flagstat/main.nf @@ -3250,7 +3250,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_flagstat", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3262,225 +3262,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml b/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml index 46c0aba0..c47f4f50 100644 --- a/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml @@ -181,7 +181,7 @@ build_info: output: "target/nextflow/samtools/samtools_idxstats" executable: "target/nextflow/samtools/samtools_idxstats/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -203,138 +203,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/samtools/samtools_idxstats/main.nf b/target/nextflow/samtools/samtools_idxstats/main.nf index 412f41d5..6f7bbada 100644 --- a/target/nextflow/samtools/samtools_idxstats/main.nf +++ b/target/nextflow/samtools/samtools_idxstats/main.nf @@ -3262,7 +3262,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_idxstats", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3274,225 +3274,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/samtools/samtools_index/.config.vsh.yaml b/target/nextflow/samtools/samtools_index/.config.vsh.yaml index 7fdceab9..f954932c 100644 --- a/target/nextflow/samtools/samtools_index/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_index/.config.vsh.yaml @@ -187,7 +187,7 @@ build_info: output: "target/nextflow/samtools/samtools_index" executable: "target/nextflow/samtools/samtools_index/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -209,138 +209,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/samtools/samtools_index/main.nf b/target/nextflow/samtools/samtools_index/main.nf index e665b12c..9226c96b 100644 --- a/target/nextflow/samtools/samtools_index/main.nf +++ b/target/nextflow/samtools/samtools_index/main.nf @@ -3275,7 +3275,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_index", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3287,225 +3287,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/samtools/samtools_sort/.config.vsh.yaml b/target/nextflow/samtools/samtools_sort/.config.vsh.yaml index 3b72d5ff..5217b774 100644 --- a/target/nextflow/samtools/samtools_sort/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_sort/.config.vsh.yaml @@ -330,7 +330,7 @@ build_info: output: "target/nextflow/samtools/samtools_sort" executable: "target/nextflow/samtools/samtools_sort/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -352,138 +352,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/samtools/samtools_sort/main.nf b/target/nextflow/samtools/samtools_sort/main.nf index 8dee44b0..6604a62e 100644 --- a/target/nextflow/samtools/samtools_sort/main.nf +++ b/target/nextflow/samtools/samtools_sort/main.nf @@ -3447,7 +3447,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_sort", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3459,225 +3459,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/samtools/samtools_stats/.config.vsh.yaml b/target/nextflow/samtools/samtools_stats/.config.vsh.yaml index a1c4d216..65a18352 100644 --- a/target/nextflow/samtools/samtools_stats/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_stats/.config.vsh.yaml @@ -399,7 +399,7 @@ build_info: output: "target/nextflow/samtools/samtools_stats" executable: "target/nextflow/samtools/samtools_stats/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -421,138 +421,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/samtools/samtools_stats/main.nf b/target/nextflow/samtools/samtools_stats/main.nf index aef40a0c..70623382 100644 --- a/target/nextflow/samtools/samtools_stats/main.nf +++ b/target/nextflow/samtools/samtools_stats/main.nf @@ -3517,7 +3517,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_stats", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3529,225 +3529,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/samtools/samtools_view/.config.vsh.yaml b/target/nextflow/samtools/samtools_view/.config.vsh.yaml index d7218f3c..ce9669ce 100644 --- a/target/nextflow/samtools/samtools_view/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_view/.config.vsh.yaml @@ -663,7 +663,7 @@ build_info: output: "target/nextflow/samtools/samtools_view" executable: "target/nextflow/samtools/samtools_view/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -685,138 +685,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/samtools/samtools_view/main.nf b/target/nextflow/samtools/samtools_view/main.nf index 2df540a6..5fcec3ff 100644 --- a/target/nextflow/samtools/samtools_view/main.nf +++ b/target/nextflow/samtools/samtools_view/main.nf @@ -3698,7 +3698,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_view", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3710,225 +3710,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/seqtk/seqtk_sample/.config.vsh.yaml b/target/nextflow/seqtk/seqtk_sample/.config.vsh.yaml index 756fd5fb..16640c96 100644 --- a/target/nextflow/seqtk/seqtk_sample/.config.vsh.yaml +++ b/target/nextflow/seqtk/seqtk_sample/.config.vsh.yaml @@ -176,7 +176,7 @@ build_info: output: "target/nextflow/seqtk/seqtk_sample" executable: "target/nextflow/seqtk/seqtk_sample/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -198,138 +198,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/seqtk/seqtk_sample/main.nf b/target/nextflow/seqtk/seqtk_sample/main.nf index 077eb55c..7b366d4f 100644 --- a/target/nextflow/seqtk/seqtk_sample/main.nf +++ b/target/nextflow/seqtk/seqtk_sample/main.nf @@ -3260,7 +3260,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/seqtk/seqtk_sample", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3272,225 +3272,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/seqtk/seqtk_subseq/.config.vsh.yaml b/target/nextflow/seqtk/seqtk_subseq/.config.vsh.yaml index 5212be16..76f716ee 100644 --- a/target/nextflow/seqtk/seqtk_subseq/.config.vsh.yaml +++ b/target/nextflow/seqtk/seqtk_subseq/.config.vsh.yaml @@ -195,7 +195,7 @@ build_info: output: "target/nextflow/seqtk/seqtk_subseq" executable: "target/nextflow/seqtk/seqtk_subseq/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -217,138 +217,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/seqtk/seqtk_subseq/main.nf b/target/nextflow/seqtk/seqtk_subseq/main.nf index 61114c66..29abdb3d 100644 --- a/target/nextflow/seqtk/seqtk_subseq/main.nf +++ b/target/nextflow/seqtk/seqtk_subseq/main.nf @@ -3283,7 +3283,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/seqtk/seqtk_subseq", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3295,225 +3295,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/sgdemux/.config.vsh.yaml b/target/nextflow/sgdemux/.config.vsh.yaml index b3bbe2cd..17f4f0b2 100644 --- a/target/nextflow/sgdemux/.config.vsh.yaml +++ b/target/nextflow/sgdemux/.config.vsh.yaml @@ -333,6 +333,7 @@ scope: target: "public" requirements: commands: + - "sgdemux" - "ps" keywords: - "demultiplex" @@ -432,7 +433,7 @@ build_info: output: "target/nextflow/sgdemux" executable: "target/nextflow/sgdemux/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -454,138 +455,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/sgdemux/main.nf b/target/nextflow/sgdemux/main.nf index c28b6572..e3b22736 100644 --- a/target/nextflow/sgdemux/main.nf +++ b/target/nextflow/sgdemux/main.nf @@ -3413,6 +3413,7 @@ meta = [ }, "requirements" : { "commands" : [ + "sgdemux", "ps" ] }, @@ -3533,7 +3534,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/sgdemux", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3545,225 +3546,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/snpeff/.config.vsh.yaml b/target/nextflow/snpeff/snpeff_ann/.config.vsh.yaml similarity index 84% rename from target/nextflow/snpeff/.config.vsh.yaml rename to target/nextflow/snpeff/snpeff_ann/.config.vsh.yaml index 3a817ff6..cf071c7c 100644 --- a/target/nextflow/snpeff/.config.vsh.yaml +++ b/target/nextflow/snpeff/snpeff_ann/.config.vsh.yaml @@ -1,4 +1,5 @@ -name: "snpeff" +name: "snpeff_ann" +namespace: "snpeff" version: "main" argument_groups: - name: "Inputs" @@ -20,7 +21,7 @@ argument_groups: description: "Reference genome version." info: null example: - - "GRCh37.75" + - "GRCh38.86" required: true direction: "input" multiple: false @@ -512,6 +513,8 @@ resources: - type: "bash_script" path: "script.sh" is_executable: true +- type: "file" + path: "config.patch" description: "Genetic variant annotation, and functional effect prediction toolbox.\ \ \nIt annotates and predicts the effects of genetic variants on genes and \nproteins\ \ (such as amino acid changes).\n" @@ -611,11 +614,21 @@ runners: engines: - type: "docker" id: "docker" - image: "quay.io/staphb/snpeff:5.2a" + image: "quay.io/staphb/snpeff:5.2f" target_registry: "images.viash-hub.com" target_tag: "main" namespace_separator: "/" setup: + - type: "docker" + copy: + - "config.patch /opt/config.patch" + - type: "apt" + packages: + - "git" + interactive: false + - type: "docker" + run: + - "bash -c \"pushd /snpEff && git apply /opt/config.patch && popd\"\n" - type: "docker" run: - "version=$(snpEff -version) && \\\nversion_trimmed=$(echo \"$version\" | awk\ @@ -625,13 +638,13 @@ engines: - type: "native" id: "native" build_info: - config: "src/snpeff/config.vsh.yaml" + config: "src/snpeff/snpeff_ann/config.vsh.yaml" runner: "nextflow" engine: "docker|native" - output: "target/nextflow/snpeff" - executable: "target/nextflow/snpeff/main.nf" + output: "target/nextflow/snpeff/snpeff_ann" + executable: "target/nextflow/snpeff/snpeff_ann/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -653,138 +666,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/snpeff/snpeff_ann/config.patch b/target/nextflow/snpeff/snpeff_ann/config.patch new file mode 100644 index 00000000..1f2970f2 --- /dev/null +++ b/target/nextflow/snpeff/snpeff_ann/config.patch @@ -0,0 +1,40 @@ +diff --git a/snpEff.config b/snpEff.config +index 3aa2710f..c5ff6926 100644 +--- a/snpEff.config ++++ b/snpEff.config +@@ -24,22 +24,29 @@ data.dir = ./data/ + # Database repository: A URL to the server where you can download databases (command: 'snpEff download dbName') + #--- + +-# Old SourceForge databases +-# database.repository = http://downloads.sourceforge.net/project/snpeff/databases ++# AstraZeneca S3 bucket (ODSP: Oncology Data Science & AI) ++database.repository = https://snpeff.odsp.astrazeneca.com/databases + +-# Secondary Azure blob storage using SAS-Token (Shared Access Signature) ++# Deprecated (2025-08): Azure blob storage (primary) ++#database.repository = https://snpeff.blob.core.windows.net/databases/ ++ ++# Deprecated (2025-08): Azure blob storage (secondary) using SAS-Token (Shared Access Signature) + #database.repository = "https://datasetsnpeff.blob.core.windows.net/dataset" + #database.repositoryKey = "?sv=2019-10-10&st=2020-09-01T00%3A00%3A00Z&se=2050-09-01T00%3A00%3A00Z&si=prod&sr=c&sig=isafOa9tGnYBAvsXFUMDGMTbsG2z%2FShaihzp7JE5dHw%3D" + +-# Primary Azure blob storage +-database.repository = https://snpeff.blob.core.windows.net/databases/ ++# Deprecated (2018-03): SourceForge databases ++#database.repository = http://downloads.sourceforge.net/project/snpeff/databases + + #--- + # Latest version numbers. Check here if there is an update. + #--- +-#versions.url = https://pcingola.github.io/SnpEff/versions.txt ++ ++# Deprecated (2025): Azure versions.txt + versions.url = https://snpeff.blob.core.windows.net/databases/versions.txt + ++# Deprecated (2018): GitHub vertsions.txt ++#versions.url = https://pcingola.github.io/SnpEff/versions.txt ++ + #------------------------------------------------------------------------------- + # Third party databases + #------------------------------------------------------------------------------- diff --git a/target/nextflow/snpeff/main.nf b/target/nextflow/snpeff/snpeff_ann/main.nf similarity index 96% rename from target/nextflow/snpeff/main.nf rename to target/nextflow/snpeff/snpeff_ann/main.nf index 9d7047d7..e9e20f70 100644 --- a/target/nextflow/snpeff/main.nf +++ b/target/nextflow/snpeff/snpeff_ann/main.nf @@ -1,4 +1,4 @@ -// snpeff main +// snpeff_ann main // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3030,7 +3030,8 @@ nextflow.enable.dsl=2 meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ - "name" : "snpeff", + "name" : "snpeff_ann", + "namespace" : "snpeff", "version" : "main", "argument_groups" : [ { @@ -3055,7 +3056,7 @@ meta = [ "name" : "--genome_version", "description" : "Reference genome version.", "example" : [ - "GRCh37.75" + "GRCh38.86" ], "required" : true, "direction" : "input", @@ -3641,6 +3642,10 @@ meta = [ "type" : "bash_script", "path" : "script.sh", "is_executable" : true + }, + { + "type" : "file", + "path" : "config.patch" } ], "description" : "Genetic variant annotation, and functional effect prediction toolbox. \nIt annotates and predicts the effects of genetic variants on genes and \nproteins (such as amino acid changes).\n", @@ -3761,11 +3766,30 @@ meta = [ { "type" : "docker", "id" : "docker", - "image" : "quay.io/staphb/snpeff:5.2a", + "image" : "quay.io/staphb/snpeff:5.2f", "target_registry" : "images.viash-hub.com", "target_tag" : "main", "namespace_separator" : "/", "setup" : [ + { + "type" : "docker", + "copy" : [ + "config.patch /opt/config.patch" + ] + }, + { + "type" : "apt", + "packages" : [ + "git" + ], + "interactive" : false + }, + { + "type" : "docker", + "run" : [ + "bash -c \\"pushd /snpEff && git apply /opt/config.patch && popd\\"\n" + ] + }, { "type" : "docker", "run" : [ @@ -3780,12 +3804,12 @@ meta = [ } ], "build_info" : { - "config" : "/workdir/root/repo/src/snpeff/config.vsh.yaml", + "config" : "/workdir/root/repo/src/snpeff/snpeff_ann/config.vsh.yaml", "runner" : "nextflow", "engine" : "docker|native", - "output" : "target/nextflow/snpeff", + "output" : "target/nextflow/snpeff/snpeff_ann", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3797,225 +3821,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", @@ -4186,7 +3996,7 @@ done # Run SnpEff -snpEff \\\\ +snpEff ann \\\\ \\${par_chr:+-chr "\\$par_chr"} \\\\ \\${par_classic:+-classic} \\\\ \\${par_csv_stats:+-csvStats "\\$par_csv_stats"} \\\\ @@ -4657,7 +4467,7 @@ meta["defaults"] = [ directives: readJsonBlob('''{ "container" : { "registry" : "images.viash-hub.com", - "image" : "vsh/biobox/snpeff", + "image" : "vsh/biobox/snpeff/snpeff_ann", "tag" : "main" }, "tag" : "$id" diff --git a/target/nextflow/snpeff/nextflow.config b/target/nextflow/snpeff/snpeff_ann/nextflow.config similarity index 99% rename from target/nextflow/snpeff/nextflow.config rename to target/nextflow/snpeff/snpeff_ann/nextflow.config index fdb4e533..328cf754 100644 --- a/target/nextflow/snpeff/nextflow.config +++ b/target/nextflow/snpeff/snpeff_ann/nextflow.config @@ -1,5 +1,5 @@ manifest { - name = 'snpeff' + name = 'snpeff/snpeff_ann' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' version = 'main' diff --git a/target/nextflow/snpeff/nextflow_schema.json b/target/nextflow/snpeff/snpeff_ann/nextflow_schema.json similarity index 99% rename from target/nextflow/snpeff/nextflow_schema.json rename to target/nextflow/snpeff/snpeff_ann/nextflow_schema.json index cd654f4f..f3289601 100644 --- a/target/nextflow/snpeff/nextflow_schema.json +++ b/target/nextflow/snpeff/snpeff_ann/nextflow_schema.json @@ -1,6 +1,6 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "title": "snpeff", + "title": "snpeff_ann", "description": "Genetic variant annotation, and functional effect prediction toolbox. \nIt annotates and predicts the effects of genetic variants on genes and \nproteins (such as amino acid changes).\n", "type": "object", "$defs": { @@ -19,7 +19,7 @@ "genome_version": { "type": "string", "description": "Reference genome version.", - "help_text": "Type: `string`, multiple: `False`, required, example: `\"GRCh37.75\"`. " + "help_text": "Type: `string`, multiple: `False`, required, example: `\"GRCh38.86\"`. " } } }, diff --git a/target/nextflow/sortmerna/.config.vsh.yaml b/target/nextflow/sortmerna/.config.vsh.yaml index 10e040f2..5e2217e1 100644 --- a/target/nextflow/sortmerna/.config.vsh.yaml +++ b/target/nextflow/sortmerna/.config.vsh.yaml @@ -597,7 +597,7 @@ build_info: output: "target/nextflow/sortmerna" executable: "target/nextflow/sortmerna/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -619,138 +619,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/sortmerna/main.nf b/target/nextflow/sortmerna/main.nf index 9e68933e..47878c72 100644 --- a/target/nextflow/sortmerna/main.nf +++ b/target/nextflow/sortmerna/main.nf @@ -3690,7 +3690,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/sortmerna", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3702,225 +3702,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/star/star_align_reads/.config.vsh.yaml b/target/nextflow/star/star_align_reads/.config.vsh.yaml index 2cac2790..3ebdaf5a 100644 --- a/target/nextflow/star/star_align_reads/.config.vsh.yaml +++ b/target/nextflow/star/star_align_reads/.config.vsh.yaml @@ -2545,6 +2545,11 @@ scope: target: "public" requirements: commands: + - "STAR" + - "python" + - "ps" + - "zcat" + - "bzcat" - "ps" keywords: - "align" @@ -2666,7 +2671,7 @@ build_info: output: "target/nextflow/star/star_align_reads" executable: "target/nextflow/star/star_align_reads/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -2688,138 +2693,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/star/star_align_reads/main.nf b/target/nextflow/star/star_align_reads/main.nf index cd8b35b9..2ac2406f 100644 --- a/target/nextflow/star/star_align_reads/main.nf +++ b/target/nextflow/star/star_align_reads/main.nf @@ -6026,6 +6026,11 @@ meta = [ }, "requirements" : { "commands" : [ + "STAR", + "python", + "ps", + "zcat", + "bzcat", "ps" ] }, @@ -6173,7 +6178,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/star/star_align_reads", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -6185,225 +6190,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/star/star_genome_generate/.config.vsh.yaml b/target/nextflow/star/star_genome_generate/.config.vsh.yaml index bced2bf9..431e44f4 100644 --- a/target/nextflow/star/star_genome_generate/.config.vsh.yaml +++ b/target/nextflow/star/star_genome_generate/.config.vsh.yaml @@ -221,6 +221,7 @@ scope: target: "public" requirements: commands: + - "STAR" - "ps" keywords: - "genome" @@ -331,7 +332,7 @@ build_info: output: "target/nextflow/star/star_genome_generate" executable: "target/nextflow/star/star_genome_generate/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -353,138 +354,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/star/star_genome_generate/main.nf b/target/nextflow/star/star_genome_generate/main.nf index 8bd70d04..159d7e06 100644 --- a/target/nextflow/star/star_genome_generate/main.nf +++ b/target/nextflow/star/star_genome_generate/main.nf @@ -3287,6 +3287,7 @@ meta = [ }, "requirements" : { "commands" : [ + "STAR", "ps" ] }, @@ -3417,7 +3418,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/star/star_genome_generate", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3429,225 +3430,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/trimgalore/.config.vsh.yaml b/target/nextflow/trimgalore/.config.vsh.yaml index 8b4faad2..572b0ce2 100644 --- a/target/nextflow/trimgalore/.config.vsh.yaml +++ b/target/nextflow/trimgalore/.config.vsh.yaml @@ -668,6 +668,7 @@ scope: target: "public" requirements: commands: + - "trim_galore" - "ps" keywords: - "trimming" @@ -768,7 +769,7 @@ build_info: output: "target/nextflow/trimgalore" executable: "target/nextflow/trimgalore/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -790,138 +791,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/trimgalore/main.nf b/target/nextflow/trimgalore/main.nf index 9a8409fe..40fbde8a 100644 --- a/target/nextflow/trimgalore/main.nf +++ b/target/nextflow/trimgalore/main.nf @@ -3662,6 +3662,7 @@ meta = [ }, "requirements" : { "commands" : [ + "trim_galore", "ps" ] }, @@ -3782,7 +3783,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/trimgalore", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3794,225 +3795,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/umi_tools/umi_tools_dedup/.config.vsh.yaml b/target/nextflow/umi_tools/umi_tools_dedup/.config.vsh.yaml index c4b3e47d..9580b035 100644 --- a/target/nextflow/umi_tools/umi_tools_dedup/.config.vsh.yaml +++ b/target/nextflow/umi_tools/umi_tools_dedup/.config.vsh.yaml @@ -609,7 +609,7 @@ build_info: output: "target/nextflow/umi_tools/umi_tools_dedup" executable: "target/nextflow/umi_tools/umi_tools_dedup/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -631,138 +631,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/umi_tools/umi_tools_dedup/main.nf b/target/nextflow/umi_tools/umi_tools_dedup/main.nf index 87b0136b..4fad0017 100644 --- a/target/nextflow/umi_tools/umi_tools_dedup/main.nf +++ b/target/nextflow/umi_tools/umi_tools_dedup/main.nf @@ -3709,7 +3709,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/umi_tools/umi_tools_dedup", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3721,225 +3721,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml b/target/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml index 6528222b..4948e3d5 100644 --- a/target/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml +++ b/target/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml @@ -437,7 +437,7 @@ build_info: output: "target/nextflow/umi_tools/umi_tools_extract" executable: "target/nextflow/umi_tools/umi_tools_extract/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -459,138 +459,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/umi_tools/umi_tools_extract/main.nf b/target/nextflow/umi_tools/umi_tools_extract/main.nf index 82b22900..899f8c5a 100644 --- a/target/nextflow/umi_tools/umi_tools_extract/main.nf +++ b/target/nextflow/umi_tools/umi_tools_extract/main.nf @@ -3529,7 +3529,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/umi_tools/umi_tools_extract", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3541,225 +3541,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/umi_tools/umi_tools_prepareforrsem/.config.vsh.yaml b/target/nextflow/umi_tools/umi_tools_prepareforrsem/.config.vsh.yaml index ad4e63e1..86475d8b 100644 --- a/target/nextflow/umi_tools/umi_tools_prepareforrsem/.config.vsh.yaml +++ b/target/nextflow/umi_tools/umi_tools_prepareforrsem/.config.vsh.yaml @@ -259,7 +259,7 @@ build_info: output: "target/nextflow/umi_tools/umi_tools_prepareforrsem" executable: "target/nextflow/umi_tools/umi_tools_prepareforrsem/main.nf" viash_version: "0.9.4" - git_commit: "7158daa5f609274a6d98fd196a7e84e302717216" + git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" @@ -281,138 +281,10 @@ package_config: source: "src" target: "target" config_mods: - - ".requirements.commands := ['ps']\n" + - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" - authors: - - name: "Robrecht Cannoodt" - roles: - - "author" - - "maintainer" - info: - links: - email: "robrecht@data-intuitive.com" - github: "rcannood" - orcid: "0000-0003-3641-729X" - linkedin: "robrechtcannoodt" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Science Engineer" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Angela Oliveira Pisco" - roles: - - "author" - info: - role: "Contributor" - links: - github: "aopisco" - orcid: "0000-0003-0142-2355" - linkedin: "aopisco" - organizations: - - name: "Insitro" - href: "https://insitro.com" - role: "Director of Computational Biology" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Core Member" - - name: "Dorien Roosen" - roles: - - "author" - info: - links: - email: "dorien@data-intuitive.com" - github: "dorien-er" - linkedin: "dorien-roosen" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Dries Schaumont" - roles: - - "author" - info: - links: - email: "dries@data-intuitive.com" - github: "DriesSchaumont" - orcid: "0000-0002-4389-0440" - linkedin: "dries-schaumont" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist" - - name: "Emma Rousseau" - roles: - - "author" - info: - links: - github: "emmarousseau" - linkedin: "emmarousseau1" - - name: "Jakub Majercik" - roles: - - "author" - info: - links: - email: "jakub@data-intuitive.com" - github: "jakubmajercik" - linkedin: "jakubmajercik" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatics Engineer" - - name: "Kai Waldrant" - roles: - - "author" - info: - links: - github: "KaiWaldrant" - orcid: "0009-0003-8555-1361" - linkedin: "kaiwaldrant" - - name: "Leïla Paquay" - roles: - - "author" - info: - links: - github: "Leila011" - linkedin: "leilapaquay" - - name: "Sai Nirmayi Yasa" - roles: - - "author" - info: - links: - github: "sainirmayi" - linkedin: "sai-nirmayi-yasa" - - name: "Theodoro Gasperin Terra Camargo" - roles: - - "author" - info: - links: - email: "theodorogtc@gmail.com" - github: "tgaspe" - linkedin: "theodoro-gasperin-terra-camargo" - - name: "Toni Verbeiren" - roles: - - "author" - info: - links: - github: "tverbeiren" - linkedin: "verbeiren" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Data Scientist and CEO" - - name: "Weiwei Schultz" - roles: - - "author" - info: - links: - linkedin: "weiwei-schultz" - organizations: - - name: "Janssen R&D US" - role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/umi_tools/umi_tools_prepareforrsem/main.nf b/target/nextflow/umi_tools/umi_tools_prepareforrsem/main.nf index d11cb99e..fde5387d 100644 --- a/target/nextflow/umi_tools/umi_tools_prepareforrsem/main.nf +++ b/target/nextflow/umi_tools/umi_tools_prepareforrsem/main.nf @@ -3351,7 +3351,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/umi_tools/umi_tools_prepareforrsem", "viash_version" : "0.9.4", - "git_commit" : "7158daa5f609274a6d98fd196a7e84e302717216", + "git_commit" : "9991e9a4f5ddd5085a4e2becf962950b1daf594b", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3363,225 +3363,11 @@ meta = [ "source" : "src", "target" : "target", "config_mods" : [ - ".requirements.commands := ['ps']\n", + ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], - "authors" : [ - { - "name" : "Robrecht Cannoodt", - "roles" : [ - "author", - "maintainer" - ], - "info" : { - "links" : { - "email" : "robrecht@data-intuitive.com", - "github" : "rcannood", - "orcid" : "0000-0003-3641-729X", - "linkedin" : "robrechtcannoodt" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Science Engineer" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Angela Oliveira Pisco", - "roles" : [ - "author" - ], - "info" : { - "role" : "Contributor", - "links" : { - "github" : "aopisco", - "orcid" : "0000-0003-0142-2355", - "linkedin" : "aopisco" - }, - "organizations" : [ - { - "name" : "Insitro", - "href" : "https://insitro.com", - "role" : "Director of Computational Biology" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Core Member" - } - ] - } - }, - { - "name" : "Dorien Roosen", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dorien@data-intuitive.com", - "github" : "dorien-er", - "linkedin" : "dorien-roosen" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Dries Schaumont", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "dries@data-intuitive.com", - "github" : "DriesSchaumont", - "orcid" : "0000-0002-4389-0440", - "linkedin" : "dries-schaumont" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist" - } - ] - } - }, - { - "name" : "Emma Rousseau", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "emmarousseau", - "linkedin" : "emmarousseau1" - } - } - }, - { - "name" : "Jakub Majercik", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "jakub@data-intuitive.com", - "github" : "jakubmajercik", - "linkedin" : "jakubmajercik" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatics Engineer" - } - ] - } - }, - { - "name" : "Kai Waldrant", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "KaiWaldrant", - "orcid" : "0009-0003-8555-1361", - "linkedin" : "kaiwaldrant" - } - } - }, - { - "name" : "Leïla Paquay", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "Leila011", - "linkedin" : "leilapaquay" - } - } - }, - { - "name" : "Sai Nirmayi Yasa", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "sainirmayi", - "linkedin" : "sai-nirmayi-yasa" - } - } - }, - { - "name" : "Theodoro Gasperin Terra Camargo", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "email" : "theodorogtc@gmail.com", - "github" : "tgaspe", - "linkedin" : "theodoro-gasperin-terra-camargo" - } - } - }, - { - "name" : "Toni Verbeiren", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "github" : "tverbeiren", - "linkedin" : "verbeiren" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Data Scientist and CEO" - } - ] - } - }, - { - "name" : "Weiwei Schultz", - "roles" : [ - "author" - ], - "info" : { - "links" : { - "linkedin" : "weiwei-schultz" - }, - "organizations" : [ - { - "name" : "Janssen R&D US", - "role" : "Associate Director Data Sciences" - } - ] - } - } - ], "keywords" : [ "bioinformatics", "modules",