From ae3fef8eecae7526b54b4ae0c72c0c5b00e4e45d Mon Sep 17 00:00:00 2001 From: CI Date: Mon, 1 Jul 2024 20:19:17 +0000 Subject: [PATCH] Build branch main with version main (ec69d9a) Build pipeline: viash-hub.biobox.main-t2txs Source commit: https://github.com/viash-hub/biobox/commit/ec69d9af7a59c2618a49bef7d0bf9afc743ca065 Source message: FEAT: update busco to 5.7.1 (#72) * FEAT: update busco to 5.7.1 * Typo --- CHANGELOG.md | 9 + .../busco_download_datasets/config.vsh.yaml | 2 +- src/busco/busco_list_datasets/config.vsh.yaml | 2 +- src/busco/busco_run/config.vsh.yaml | 6 +- src/busco/busco_run/help.txt | 9 +- src/busco/busco_run/script.sh | 1 + src/cutadapt/config.vsh.yaml | 18 + src/cutadapt/script.sh | 31 +- src/cutadapt/test.sh | 5 + target/executable/arriba/.config.vsh.yaml | 2 +- target/executable/arriba/arriba | 4 +- .../executable/bcl_convert/.config.vsh.yaml | 2 +- target/executable/bcl_convert/bcl_convert | 4 +- .../bedtools_getfasta/.config.vsh.yaml | 2 +- .../bedtools_getfasta/bedtools_getfasta | 4 +- .../busco_download_datasets/.config.vsh.yaml | 4 +- .../busco_download_datasets | 6 +- .../busco_list_datasets/.config.vsh.yaml | 4 +- .../busco_list_datasets/busco_list_datasets | 6 +- .../busco/busco_run/.config.vsh.yaml | 9 +- target/executable/busco/busco_run/busco_run | 26 +- target/executable/cutadapt/.config.vsh.yaml | 22 +- target/executable/cutadapt/cutadapt | 75 +- target/executable/falco/.config.vsh.yaml | 2 +- target/executable/falco/falco | 4 +- target/executable/fastp/.config.vsh.yaml | 2 +- target/executable/fastp/fastp | 4 +- .../executable/featurecounts/.config.vsh.yaml | 2 +- target/executable/featurecounts/featurecounts | 4 +- target/executable/gffread/.config.vsh.yaml | 2 +- target/executable/gffread/gffread | 4 +- .../lofreq/lofreq_call/.config.vsh.yaml | 2 +- .../executable/lofreq/lofreq_call/lofreq_call | 4 +- .../lofreq/lofreq_indelqual/.config.vsh.yaml | 2 +- .../lofreq/lofreq_indelqual/lofreq_indelqual | 4 +- target/executable/multiqc/.config.vsh.yaml | 2 +- target/executable/multiqc/multiqc | 4 +- target/executable/pear/.config.vsh.yaml | 2 +- target/executable/pear/pear | 4 +- .../salmon/salmon_index/.config.vsh.yaml | 2 +- .../salmon/salmon_index/salmon_index | 4 +- .../salmon/salmon_quant/.config.vsh.yaml | 2 +- .../salmon/salmon_quant/salmon_quant | 4 +- .../samtools_collate/.config.vsh.yaml | 2 +- .../samtools_collate/samtools_collate | 4 +- .../samtools/samtools_faidx/.config.vsh.yaml | 2 +- .../samtools/samtools_faidx/samtools_faidx | 4 +- .../samtools/samtools_fastq/.config.vsh.yaml | 2 +- .../samtools/samtools_fastq/samtools_fastq | 4 +- .../samtools_flagstat/.config.vsh.yaml | 2 +- .../samtools_flagstat/samtools_flagstat | 4 +- .../samtools_idxstats/.config.vsh.yaml | 2 +- .../samtools_idxstats/samtools_idxstats | 4 +- .../samtools/samtools_index/.config.vsh.yaml | 2 +- .../samtools/samtools_index/samtools_index | 4 +- .../samtools/samtools_sort/.config.vsh.yaml | 2 +- .../samtools/samtools_sort/samtools_sort | 4 +- .../samtools/samtools_stats/.config.vsh.yaml | 2 +- .../samtools/samtools_stats/samtools_stats | 4 +- .../samtools/samtools_view/.config.vsh.yaml | 2 +- .../samtools/samtools_view/samtools_view | 4 +- .../star/star_align_reads/.config.vsh.yaml | 2 +- .../star/star_align_reads/star_align_reads | 4 +- .../star_genome_generate/.config.vsh.yaml | 2 +- .../star_genome_generate/star_genome_generate | 4 +- target/nextflow/arriba/.config.vsh.yaml | 2 +- target/nextflow/arriba/main.nf | 2 +- target/nextflow/bcl_convert/.config.vsh.yaml | 2 +- target/nextflow/bcl_convert/main.nf | 2 +- .../bedtools_getfasta/.config.vsh.yaml | 2 +- .../bedtools/bedtools_getfasta/main.nf | 2 +- .../busco_download_datasets/.config.vsh.yaml | 4 +- .../busco/busco_download_datasets/main.nf | 4 +- .../nextflow_schema.json | 95 -- .../busco_list_datasets/.config.vsh.yaml | 4 +- .../busco/busco_list_datasets/main.nf | 4 +- .../nextflow/busco/busco_run/.config.vsh.yaml | 9 +- target/nextflow/busco/busco_run/main.nf | 12 +- .../busco/busco_run/nextflow_schema.json | 471 +++++++ target/nextflow/cutadapt/.config.vsh.yaml | 22 +- target/nextflow/cutadapt/main.nf | 53 +- target/nextflow/cutadapt/nextflow_schema.json | 26 + target/nextflow/falco/.config.vsh.yaml | 2 +- target/nextflow/falco/main.nf | 2 +- target/nextflow/fastp/.config.vsh.yaml | 2 +- target/nextflow/fastp/main.nf | 2 +- .../nextflow/featurecounts/.config.vsh.yaml | 2 +- target/nextflow/featurecounts/main.nf | 2 +- target/nextflow/gffread/.config.vsh.yaml | 2 +- target/nextflow/gffread/main.nf | 2 +- .../lofreq/lofreq_call/.config.vsh.yaml | 2 +- target/nextflow/lofreq/lofreq_call/main.nf | 2 +- .../lofreq/lofreq_indelqual/.config.vsh.yaml | 2 +- .../nextflow/lofreq/lofreq_indelqual/main.nf | 2 +- target/nextflow/multiqc/.config.vsh.yaml | 2 +- target/nextflow/multiqc/main.nf | 2 +- target/nextflow/pear/.config.vsh.yaml | 2 +- target/nextflow/pear/main.nf | 2 +- .../salmon/salmon_index/.config.vsh.yaml | 2 +- target/nextflow/salmon/salmon_index/main.nf | 2 +- .../salmon/salmon_quant/.config.vsh.yaml | 2 +- target/nextflow/salmon/salmon_quant/main.nf | 2 +- .../salmon/salmon_quant/nextflow_schema.json | 1119 +++++++++++++++++ .../samtools_collate/.config.vsh.yaml | 2 +- .../samtools/samtools_collate/main.nf | 2 +- .../samtools/samtools_faidx/.config.vsh.yaml | 2 +- .../nextflow/samtools/samtools_faidx/main.nf | 2 +- .../samtools/samtools_fastq/.config.vsh.yaml | 2 +- .../nextflow/samtools/samtools_fastq/main.nf | 2 +- .../samtools_flagstat/.config.vsh.yaml | 2 +- .../samtools/samtools_flagstat/main.nf | 2 +- .../samtools_idxstats/.config.vsh.yaml | 2 +- .../samtools/samtools_idxstats/main.nf | 2 +- .../samtools/samtools_index/.config.vsh.yaml | 2 +- .../nextflow/samtools/samtools_index/main.nf | 2 +- .../samtools/samtools_sort/.config.vsh.yaml | 2 +- .../nextflow/samtools/samtools_sort/main.nf | 2 +- .../samtools/samtools_stats/.config.vsh.yaml | 2 +- .../nextflow/samtools/samtools_stats/main.nf | 2 +- .../samtools/samtools_view/.config.vsh.yaml | 2 +- .../nextflow/samtools/samtools_view/main.nf | 2 +- .../star/star_align_reads/.config.vsh.yaml | 2 +- target/nextflow/star/star_align_reads/main.nf | 2 +- .../star_genome_generate/.config.vsh.yaml | 2 +- .../star/star_genome_generate/main.nf | 2 +- 125 files changed, 2030 insertions(+), 268 deletions(-) delete mode 100644 target/nextflow/busco/busco_download_datasets/nextflow_schema.json create mode 100644 target/nextflow/busco/busco_run/nextflow_schema.json create mode 100644 target/nextflow/salmon/salmon_quant/nextflow_schema.json diff --git a/CHANGELOG.md b/CHANGELOG.md index bfe2b1b6..3a036fba 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,6 +4,14 @@ * `pear`: fix component not exiting with the correct exitcode when PEAR fails. +* `cutadapt`: fix `--par_quality_cutoff_r2` argument. + +* `cutadapt`: demultiplexing is now disabled by default. It can be re-enabled by using `demultiplex_mode`. + +## MINOR CHANGES + +* `busco` components: update BUSCO to `5.7.1`. + # biobox 0.1.0 ## BREAKING CHANGES @@ -12,6 +20,7 @@ Viash 0.9.0 in order to avoid issues with the current default separator `:` unintentionally splitting up certain file paths. + ## NEW FEATURES * `arriba`: Detect gene fusions from RNA-seq data (PR #1). diff --git a/src/busco/busco_download_datasets/config.vsh.yaml b/src/busco/busco_download_datasets/config.vsh.yaml index 04d76dd6..5297af2e 100644 --- a/src/busco/busco_download_datasets/config.vsh.yaml +++ b/src/busco/busco_download_datasets/config.vsh.yaml @@ -37,7 +37,7 @@ test_resources: path: test.sh engines: - type: docker - image: quay.io/biocontainers/busco:5.6.1--pyhdfd78af_0 + image: quay.io/biocontainers/busco:5.7.1--pyhdfd78af_0 setup: - type: docker run: | diff --git a/src/busco/busco_list_datasets/config.vsh.yaml b/src/busco/busco_list_datasets/config.vsh.yaml index 6ada7c84..cac34cc6 100644 --- a/src/busco/busco_list_datasets/config.vsh.yaml +++ b/src/busco/busco_list_datasets/config.vsh.yaml @@ -29,7 +29,7 @@ test_resources: path: test.sh engines: - type: docker - image: quay.io/biocontainers/busco:5.6.1--pyhdfd78af_0 + image: quay.io/biocontainers/busco:5.7.1--pyhdfd78af_0 setup: - type: docker run: | diff --git a/src/busco/busco_run/config.vsh.yaml b/src/busco/busco_run/config.vsh.yaml index d79f03f5..23ee95fb 100644 --- a/src/busco/busco_run/config.vsh.yaml +++ b/src/busco/busco_run/config.vsh.yaml @@ -181,6 +181,10 @@ argument_groups: - name: MetaEuk Settings arguments: + - name: --metaeuk + type: boolean_true + description: | + Use Metaeuk gene predictor. - name: --metaeuk_parameters type: string description: | @@ -204,7 +208,7 @@ test_resources: path: test_data engines: - type: docker - image: quay.io/biocontainers/busco:5.6.1--pyhdfd78af_0 + image: quay.io/biocontainers/busco:5.7.1--pyhdfd78af_0 setup: - type: docker run: | diff --git a/src/busco/busco_run/help.txt b/src/busco/busco_run/help.txt index 2cacec4d..6d83f9be 100644 --- a/src/busco/busco_run/help.txt +++ b/src/busco/busco_run/help.txt @@ -2,7 +2,9 @@ busco -h ``` -Welcome to BUSCO 5.6.1: the Benchmarking Universal Single-Copy Ortholog assessment tool. +usage: busco -i [SEQUENCE_FILE] -l [LINEAGE] -o [OUTPUT_NAME] -m [MODE] [OTHER OPTIONS] + +Welcome to BUSCO 5.7.1: the Benchmarking Universal Single-Copy Ortholog assessment tool. For more detailed usage information, please review the README file provided with this distribution and the BUSCO user guide. Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO optional arguments: @@ -18,7 +20,7 @@ optional arguments: -l LINEAGE, --lineage_dataset LINEAGE Specify the name of the BUSCO lineage to be used. --augustus Use augustus gene predictor for eukaryote runs - --augustus_parameters --PARAM1=VALUE1,--PARAM2=VALUE2 + --augustus_parameters "--PARAM1=VALUE1,--PARAM2=VALUE2" Pass additional arguments to Augustus. All arguments should be contained within a single string with no white space, with each argument separated by a comma. --augustus_species AUGUSTUS_SPECIES Specify a species for Augustus training. @@ -42,11 +44,12 @@ optional arguments: --limit N How many candidate regions (contig or transcript) to consider per BUSCO (default: 3) --list-datasets Print the list of available BUSCO datasets --long Optimization Augustus self-training mode (Default: Off); adds considerably to the run time, but can improve results for some non-model organisms + --metaeuk Use Metaeuk gene predictor --metaeuk_parameters "--PARAM1=VALUE1,--PARAM2=VALUE2" Pass additional arguments to Metaeuk for the first run. All arguments should be contained within a single string with no white space, with each argument separated by a comma. --metaeuk_rerun_parameters "--PARAM1=VALUE1,--PARAM2=VALUE2" Pass additional arguments to Metaeuk for the second run. All arguments should be contained within a single string with no white space, with each argument separated by a comma. - --miniprot Use miniprot gene predictor + --miniprot Use Miniprot gene predictor --skip_bbtools Skip BBTools for assembly statistics --offline To indicate that BUSCO cannot attempt to download files --opt-out-run-stats Opt out of data collection. Information on the data collected is available in the user guide. diff --git a/src/busco/busco_run/script.sh b/src/busco/busco_run/script.sh index 5b562f83..a0ef24de 100644 --- a/src/busco/busco_run/script.sh +++ b/src/busco/busco_run/script.sh @@ -39,6 +39,7 @@ busco \ ${par_force:+--force} \ ${par_limit:+--limit "$par_limit"} \ ${par_long:+--long} \ + ${par_metaeuk:+--metaeuk} \ ${par_metaeuk_parameters:+--metaeuk_parameters "$par_metaeuk_parameters"} \ ${par_metaeuk_rerun_parameters:+--metaeuk_rerun_parameters "$par_metaeuk_rerun_parameters"} \ ${par_miniprot:+--miniprot} \ diff --git a/src/cutadapt/config.vsh.yaml b/src/cutadapt/config.vsh.yaml index a62f0aa9..b315d0ce 100644 --- a/src/cutadapt/config.vsh.yaml +++ b/src/cutadapt/config.vsh.yaml @@ -240,6 +240,24 @@ argument_groups: Check both the read and its reverse complement for adapter matches. If match is on reverse-complemented version, output that one. + + #################################################################### + - name: "Demultiplexing options" + arguments: + - name: "--demultiplex_mode" + type: string + choices: ["single", "unique_dual", "combinatorial_dual"] + required: false + description: | + Enable demultiplexing and set the mode for it. + With mode 'unique_dual', adapters from the first and second read are used, + and the indexes from the reads are only used in pairs. This implies + --pair_adapters. + Enabling mode 'combinatorial_dual' allows all combinations of the sets of indexes + on R1 and R2. It is necessary to write each read pair to an output + file depending on the adapters found on both R1 and R2. + Mode 'single', uses indexes or barcodes located at the 5' + end of the R1 read (single). #################################################################### - name: Read modifications diff --git a/src/cutadapt/script.sh b/src/cutadapt/script.sh index 5e1f9e30..20c92724 100644 --- a/src/cutadapt/script.sh +++ b/src/cutadapt/script.sh @@ -127,7 +127,7 @@ mod_args=$(echo \ ${par_cut_r2:+--cut_r2 "${par_cut_r2}"} \ ${par_nextseq_trim:+--nextseq-trim "${par_nextseq_trim}"} \ ${par_quality_cutoff:+--quality-cutoff "${par_quality_cutoff}"} \ - ${par_quality_cutoff_r2:+--quality-cutoff_r2 "${par_quality_cutoff_r2}"} \ + ${par_quality_cutoff_r2:+-Q "${par_quality_cutoff_r2}"} \ ${par_quality_base:+--quality-base "${par_quality_base}"} \ ${par_poly_a:+--poly-a} \ ${par_length:+--length "${par_length}"} \ @@ -196,14 +196,35 @@ else ext="fasta" fi -if [ $mode = "se" ]; then +demultiplex_mode="$par_demultiplex_mode" +if [[ $mode == "se" ]]; then + if [[ "$demultiplex_mode" == "unique_dual" ]] || [[ "$demultiplex_mode" == "combinatorial_dual" ]]; then + echo "Demultiplexing dual indexes is not possible with single-end data." + exit 1 + fi + prefix="trimmed_" + if [[ ! -z "$demultiplex_mode" ]]; then + prefix="{name}_" + fi output_args=$(echo \ - --output "$output_dir/{name}_001.$ext" \ + --output "$output_dir/${prefix}001.$ext" \ ) else + demultiplex_indicator_r1='{name}_' + demultiplex_indicator_r2=$demultiplex_indicator_r1 + if [[ "$demultiplex_mode" == "combinatorial_dual" ]]; then + demultiplex_indicator_r1='{name1}_{name2}_' + demultiplex_indicator_r2='{name1}_{name2}_' + fi + prefix_r1="trimmed_" + prefix_r2="trimmed_" + if [[ ! -z "$demultiplex_mode" ]]; then + prefix_r1=$demultiplex_indicator_r1 + prefix_r2=$demultiplex_indicator_r2 + fi output_args=$(echo \ - --output "$output_dir/{name}_R1_001.$ext" \ - --paired-output "$output_dir/{name}_R2_001.$ext" \ + --output "$output_dir/${prefix_r1}R1_001.$ext" \ + --paired-output "$output_dir/${prefix_r2}R2_001.$ext" \ ) fi diff --git a/src/cutadapt/test.sh b/src/cutadapt/test.sh index eff997d7..1d6d9c18 100644 --- a/src/cutadapt/test.sh +++ b/src/cutadapt/test.sh @@ -1,6 +1,7 @@ #!/bin/bash set -e +set -eo pipefail ############################################# # helper functions @@ -57,6 +58,7 @@ EOF --adapter ADAPTER \ --input example.fa \ --fasta \ + --demultiplex_mode single \ --no_match_adapter_wildcards \ --json @@ -101,6 +103,7 @@ EOF --output "out_test1/*.fasta" \ --adapter ADAPTER \ --input example.fa \ + --demultiplex_mode single \ --fasta \ --no_match_adapter_wildcards \ --json @@ -160,6 +163,7 @@ EOF --adapter AAAAA \ --adapter_fasta adapters1.fasta \ --adapter_fasta adapters2.fasta \ + --demultiplex_mode single \ --input example.fa \ --fasta \ --json @@ -224,6 +228,7 @@ EOF --input example_R1.fastq \ --input_r2 example_R2.fastq \ --quality_cutoff 20 \ + --demultiplex_mode unique_dual \ --json \ ---cpus 1 diff --git a/target/executable/arriba/.config.vsh.yaml b/target/executable/arriba/.config.vsh.yaml index c32764e0..cc5b0174 100644 --- a/target/executable/arriba/.config.vsh.yaml +++ b/target/executable/arriba/.config.vsh.yaml @@ -688,7 +688,7 @@ build_info: output: "target/executable/arriba" executable: "target/executable/arriba/arriba" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/arriba/arriba b/target/executable/arriba/arriba index 18d3b95d..b9a3ef38 100755 --- a/target/executable/arriba/arriba +++ b/target/executable/arriba/arriba @@ -749,9 +749,9 @@ ENTRYPOINT [] RUN arriba -h | grep 'Version:' 2>&1 | sed 's/Version:\s\(.*\)/arriba: "\1"/' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component arriba" -LABEL org.opencontainers.image.created="2024-07-01T10:12:56Z" +LABEL org.opencontainers.image.created="2024-07-01T20:00:37Z" LABEL org.opencontainers.image.source="https://github.com/suhrig/arriba" -LABEL org.opencontainers.image.revision="3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" +LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bcl_convert/.config.vsh.yaml b/target/executable/bcl_convert/.config.vsh.yaml index c807fc6e..f31e851c 100644 --- a/target/executable/bcl_convert/.config.vsh.yaml +++ b/target/executable/bcl_convert/.config.vsh.yaml @@ -386,7 +386,7 @@ build_info: output: "target/executable/bcl_convert" executable: "target/executable/bcl_convert/bcl_convert" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/bcl_convert/bcl_convert b/target/executable/bcl_convert/bcl_convert index d41fe407..dc93b646 100755 --- a/target/executable/bcl_convert/bcl_convert +++ b/target/executable/bcl_convert/bcl_convert @@ -593,9 +593,9 @@ rm /tmp/bcl-convert.rpm RUN echo "bcl-convert: \"$(bcl-convert -V 2>&1 >/dev/null | sed -n '/Version/ s/^bcl-convert\ Version //p')\"" > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component bcl_convert" -LABEL org.opencontainers.image.created="2024-07-01T10:12:54Z" +LABEL org.opencontainers.image.created="2024-07-01T20:00:36Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox" -LABEL org.opencontainers.image.revision="3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" +LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml b/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml index 3ec34c5c..b435433b 100644 --- a/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml @@ -217,7 +217,7 @@ build_info: output: "target/executable/bedtools/bedtools_getfasta" executable: "target/executable/bedtools/bedtools_getfasta/bedtools_getfasta" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta b/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta index 7ba8fb3c..e057c8c9 100755 --- a/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta +++ b/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta @@ -521,9 +521,9 @@ RUN apt-get update && \ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_getfasta" -LABEL org.opencontainers.image.created="2024-07-01T10:12:54Z" +LABEL org.opencontainers.image.created="2024-07-01T20:00:35Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" +LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/busco/busco_download_datasets/.config.vsh.yaml b/target/executable/busco/busco_download_datasets/.config.vsh.yaml index 6984d0c4..95d1bbf1 100644 --- a/target/executable/busco/busco_download_datasets/.config.vsh.yaml +++ b/target/executable/busco/busco_download_datasets/.config.vsh.yaml @@ -125,7 +125,7 @@ runners: engines: - type: "docker" id: "docker" - image: "quay.io/biocontainers/busco:5.6.1--pyhdfd78af_0" + image: "quay.io/biocontainers/busco:5.7.1--pyhdfd78af_0" target_registry: "images.viash-hub.com" target_tag: "main" namespace_separator: "/" @@ -144,7 +144,7 @@ build_info: output: "target/executable/busco/busco_download_datasets" executable: "target/executable/busco/busco_download_datasets/busco_download_datasets" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/busco/busco_download_datasets/busco_download_datasets b/target/executable/busco/busco_download_datasets/busco_download_datasets index 5565d8aa..6d51c9b7 100755 --- a/target/executable/busco/busco_download_datasets/busco_download_datasets +++ b/target/executable/busco/busco_download_datasets/busco_download_datasets @@ -465,14 +465,14 @@ function ViashDockerfile { if [[ "$engine_id" == "docker" ]]; then cat << 'VIASHDOCKER' -FROM quay.io/biocontainers/busco:5.6.1--pyhdfd78af_0 +FROM quay.io/biocontainers/busco:5.7.1--pyhdfd78af_0 ENTRYPOINT [] RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component busco busco_download_datasets" -LABEL org.opencontainers.image.created="2024-07-01T10:12:49Z" +LABEL org.opencontainers.image.created="2024-07-01T20:00:30Z" LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco" -LABEL org.opencontainers.image.revision="3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" +LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065" 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 058f4756..8d652280 100644 --- a/target/executable/busco/busco_list_datasets/.config.vsh.yaml +++ b/target/executable/busco/busco_list_datasets/.config.vsh.yaml @@ -112,7 +112,7 @@ runners: engines: - type: "docker" id: "docker" - image: "quay.io/biocontainers/busco:5.6.1--pyhdfd78af_0" + image: "quay.io/biocontainers/busco:5.7.1--pyhdfd78af_0" target_registry: "images.viash-hub.com" target_tag: "main" namespace_separator: "/" @@ -131,7 +131,7 @@ build_info: output: "target/executable/busco/busco_list_datasets" executable: "target/executable/busco/busco_list_datasets/busco_list_datasets" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/busco/busco_list_datasets/busco_list_datasets b/target/executable/busco/busco_list_datasets/busco_list_datasets index e1f8ba4f..9b3bd2fc 100755 --- a/target/executable/busco/busco_list_datasets/busco_list_datasets +++ b/target/executable/busco/busco_list_datasets/busco_list_datasets @@ -455,14 +455,14 @@ function ViashDockerfile { if [[ "$engine_id" == "docker" ]]; then cat << 'VIASHDOCKER' -FROM quay.io/biocontainers/busco:5.6.1--pyhdfd78af_0 +FROM quay.io/biocontainers/busco:5.7.1--pyhdfd78af_0 ENTRYPOINT [] RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component busco busco_list_datasets" -LABEL org.opencontainers.image.created="2024-07-01T10:12:49Z" +LABEL org.opencontainers.image.created="2024-07-01T20:00:31Z" LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco" -LABEL org.opencontainers.image.revision="3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" +LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065" 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 a9757177..66c003b1 100644 --- a/target/executable/busco/busco_run/.config.vsh.yaml +++ b/target/executable/busco/busco_run/.config.vsh.yaml @@ -263,6 +263,11 @@ argument_groups: direction: "input" - name: "MetaEuk Settings" arguments: + - type: "boolean_true" + name: "--metaeuk" + description: "Use Metaeuk gene predictor.\n" + info: null + direction: "input" - type: "string" name: "--metaeuk_parameters" description: "Pass additional arguments to Metaeuk for the first run (see Metaeuk\ @@ -385,7 +390,7 @@ runners: engines: - type: "docker" id: "docker" - image: "quay.io/biocontainers/busco:5.6.1--pyhdfd78af_0" + image: "quay.io/biocontainers/busco:5.7.1--pyhdfd78af_0" target_registry: "images.viash-hub.com" target_tag: "main" namespace_separator: "/" @@ -404,7 +409,7 @@ build_info: output: "target/executable/busco/busco_run" executable: "target/executable/busco/busco_run/busco_run" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/busco/busco_run/busco_run b/target/executable/busco/busco_run/busco_run index 089b9f56..31084cbb 100755 --- a/target/executable/busco/busco_run/busco_run +++ b/target/executable/busco/busco_run/busco_run @@ -329,6 +329,10 @@ function ViashHelp { echo " Use Miniprot gene predictor." echo "" echo "MetaEuk Settings:" + echo " --metaeuk" + echo " type: boolean_true" + echo " Use Metaeuk gene predictor." + echo "" echo " --metaeuk_parameters" echo " type: string" echo " example: --max-overlap=15,--min-exon-aa=15" @@ -618,14 +622,14 @@ function ViashDockerfile { if [[ "$engine_id" == "docker" ]]; then cat << 'VIASHDOCKER' -FROM quay.io/biocontainers/busco:5.6.1--pyhdfd78af_0 +FROM quay.io/biocontainers/busco:5.7.1--pyhdfd78af_0 ENTRYPOINT [] RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component busco busco_run" -LABEL org.opencontainers.image.created="2024-07-01T10:12:50Z" +LABEL org.opencontainers.image.created="2024-07-01T20:00:31Z" LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco" -LABEL org.opencontainers.image.revision="3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" +LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -989,6 +993,11 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_MINIPROT=true shift 1 ;; + --metaeuk) + [ -n "$VIASH_PAR_METAEUK" ] && ViashError Bad arguments for option \'--metaeuk\': \'$VIASH_PAR_METAEUK\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_METAEUK=true + shift 1 + ;; --metaeuk_parameters) [ -n "$VIASH_PAR_METAEUK_PARAMETERS" ] && ViashError Bad arguments for option \'--metaeuk_parameters\': \'$VIASH_PAR_METAEUK_PARAMETERS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 VIASH_PAR_METAEUK_PARAMETERS="$2" @@ -1234,6 +1243,9 @@ fi if [ -z ${VIASH_PAR_MINIPROT+x} ]; then VIASH_PAR_MINIPROT="false" fi +if [ -z ${VIASH_PAR_METAEUK+x} ]; then + VIASH_PAR_METAEUK="false" +fi # check whether required files exist if [ ! -z "$VIASH_PAR_INPUT" ] && [ ! -e "$VIASH_PAR_INPUT" ]; then @@ -1326,6 +1338,12 @@ if [[ -n "$VIASH_PAR_MINIPROT" ]]; then exit 1 fi fi +if [[ -n "$VIASH_PAR_METAEUK" ]]; then + if ! [[ "$VIASH_PAR_METAEUK" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then + ViashError '--metaeuk' 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. @@ -1566,6 +1584,7 @@ $( if [ ! -z ${VIASH_PAR_LIMIT+x} ]; then echo "${VIASH_PAR_LIMIT}" | sed "s#'#' $( if [ ! -z ${VIASH_PAR_SCAFFOLD_COMPOSITION+x} ]; then echo "${VIASH_PAR_SCAFFOLD_COMPOSITION}" | sed "s#'#'\"'\"'#g;s#.*#par_scaffold_composition='&'#" ; else echo "# par_scaffold_composition="; fi ) $( if [ ! -z ${VIASH_PAR_E_VALUE+x} ]; then echo "${VIASH_PAR_E_VALUE}" | sed "s#'#'\"'\"'#g;s#.*#par_e_value='&'#" ; else echo "# par_e_value="; fi ) $( if [ ! -z ${VIASH_PAR_MINIPROT+x} ]; then echo "${VIASH_PAR_MINIPROT}" | sed "s#'#'\"'\"'#g;s#.*#par_miniprot='&'#" ; else echo "# par_miniprot="; fi ) +$( if [ ! -z ${VIASH_PAR_METAEUK+x} ]; then echo "${VIASH_PAR_METAEUK}" | sed "s#'#'\"'\"'#g;s#.*#par_metaeuk='&'#" ; else echo "# par_metaeuk="; fi ) $( if [ ! -z ${VIASH_PAR_METAEUK_PARAMETERS+x} ]; then echo "${VIASH_PAR_METAEUK_PARAMETERS}" | sed "s#'#'\"'\"'#g;s#.*#par_metaeuk_parameters='&'#" ; else echo "# par_metaeuk_parameters="; fi ) $( if [ ! -z ${VIASH_PAR_METAEUK_RERUN_PARAMETERS+x} ]; then echo "${VIASH_PAR_METAEUK_RERUN_PARAMETERS}" | sed "s#'#'\"'\"'#g;s#.*#par_metaeuk_rerun_parameters='&'#" ; else echo "# par_metaeuk_rerun_parameters="; fi ) $( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "${VIASH_META_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_name='&'#" ; else echo "# meta_name="; fi ) @@ -1625,6 +1644,7 @@ busco \\ \${par_force:+--force} \\ \${par_limit:+--limit "\$par_limit"} \\ \${par_long:+--long} \\ + \${par_metaeuk:+--metaeuk} \\ \${par_metaeuk_parameters:+--metaeuk_parameters "\$par_metaeuk_parameters"} \\ \${par_metaeuk_rerun_parameters:+--metaeuk_rerun_parameters "\$par_metaeuk_rerun_parameters"} \\ \${par_miniprot:+--miniprot} \\ diff --git a/target/executable/cutadapt/.config.vsh.yaml b/target/executable/cutadapt/.config.vsh.yaml index 4e3ac4fd..65139947 100644 --- a/target/executable/cutadapt/.config.vsh.yaml +++ b/target/executable/cutadapt/.config.vsh.yaml @@ -305,6 +305,26 @@ argument_groups: \ If match is on reverse-complemented version,\noutput that one.\n" info: null direction: "input" +- name: "Demultiplexing options" + arguments: + - type: "string" + name: "--demultiplex_mode" + description: "Enable demultiplexing and set the mode for it.\nWith mode 'unique_dual',\ + \ adapters from the first and second read are used,\nand the indexes from the\ + \ reads are only used in pairs. This implies\n--pair_adapters.\nEnabling mode\ + \ 'combinatorial_dual' allows all combinations of the sets of indexes\non R1\ + \ and R2. It is necessary to write each read pair to an output\nfile depending\ + \ on the adapters found on both R1 and R2.\nMode 'single', uses indexes or barcodes\ + \ located at the 5'\nend of the R1 read (single). \n" + info: null + required: false + choices: + - "single" + - "unique_dual" + - "combinatorial_dual" + direction: "input" + multiple: false + multiple_sep: ";" - name: "Read modifications" arguments: - type: "integer" @@ -707,7 +727,7 @@ build_info: output: "target/executable/cutadapt" executable: "target/executable/cutadapt/cutadapt" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/cutadapt/cutadapt b/target/executable/cutadapt/cutadapt index 5be89fdd..4c246b77 100755 --- a/target/executable/cutadapt/cutadapt +++ b/target/executable/cutadapt/cutadapt @@ -357,6 +357,22 @@ function ViashHelp { echo " matches. If match is on reverse-complemented version," echo " output that one." echo "" + echo "Demultiplexing options:" + echo " --demultiplex_mode" + echo " type: string" + echo " choices: [ single, unique_dual, combinatorial_dual ]" + echo " Enable demultiplexing and set the mode for it." + echo " With mode 'unique_dual', adapters from the first and second read are" + echo " used," + echo " and the indexes from the reads are only used in pairs. This implies" + echo " --pair_adapters." + echo " Enabling mode 'combinatorial_dual' allows all combinations of the sets" + echo " of indexes" + echo " on R1 and R2. It is necessary to write each read pair to an output" + echo " file depending on the adapters found on both R1 and R2." + echo " Mode 'single', uses indexes or barcodes located at the 5'" + echo " end of the R1 read (single)." + echo "" echo "Read modifications:" echo " -u, --cut" echo " type: integer, multiple values allowed" @@ -810,9 +826,9 @@ RUN pip install --upgrade pip && \ RUN cutadapt --version | sed 's/\(.*\)/cutadapt: "\1"/' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component cutadapt" -LABEL org.opencontainers.image.created="2024-07-01T10:12:46Z" +LABEL org.opencontainers.image.created="2024-07-01T20:00:27Z" LABEL org.opencontainers.image.source="https://github.com/marcelm/cutadapt" -LABEL org.opencontainers.image.revision="3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" +LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -1303,6 +1319,17 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_REVCOMP=true shift 1 ;; + --demultiplex_mode) + [ -n "$VIASH_PAR_DEMULTIPLEX_MODE" ] && ViashError Bad arguments for option \'--demultiplex_mode\': \'$VIASH_PAR_DEMULTIPLEX_MODE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_DEMULTIPLEX_MODE="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --demultiplex_mode. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --demultiplex_mode=*) + [ -n "$VIASH_PAR_DEMULTIPLEX_MODE" ] && ViashError Bad arguments for option \'--demultiplex_mode=*\': \'$VIASH_PAR_DEMULTIPLEX_MODE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_DEMULTIPLEX_MODE=$(ViashRemoveFlags "$1") + shift 1 + ;; --cut) if [ -z "$VIASH_PAR_CUT" ]; then VIASH_PAR_CUT="$2" @@ -2202,6 +2229,18 @@ if [ ! -z "$VIASH_PAR_ACTION" ]; then unset IFS fi +if [ ! -z "$VIASH_PAR_DEMULTIPLEX_MODE" ]; then + VIASH_PAR_DEMULTIPLEX_MODE_CHOICES=("single;unique_dual;combinatorial_dual") + IFS=';' + set -f + if ! [[ ";${VIASH_PAR_DEMULTIPLEX_MODE_CHOICES[*]};" =~ ";$VIASH_PAR_DEMULTIPLEX_MODE;" ]]; then + ViashError '--demultiplex_mode' specified value of \'$VIASH_PAR_DEMULTIPLEX_MODE\' 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_REPORT" ]; then VIASH_PAR_REPORT_CHOICES=("full;minimal") IFS=';' @@ -2378,6 +2417,7 @@ $( if [ ! -z ${VIASH_PAR_MATCH_READ_WILDCARDS+x} ]; then echo "${VIASH_PAR_MATCH $( if [ ! -z ${VIASH_PAR_NO_MATCH_ADAPTER_WILDCARDS+x} ]; then echo "${VIASH_PAR_NO_MATCH_ADAPTER_WILDCARDS}" | sed "s#'#'\"'\"'#g;s#.*#par_no_match_adapter_wildcards='&'#" ; else echo "# par_no_match_adapter_wildcards="; fi ) $( if [ ! -z ${VIASH_PAR_ACTION+x} ]; then echo "${VIASH_PAR_ACTION}" | sed "s#'#'\"'\"'#g;s#.*#par_action='&'#" ; else echo "# par_action="; fi ) $( if [ ! -z ${VIASH_PAR_REVCOMP+x} ]; then echo "${VIASH_PAR_REVCOMP}" | sed "s#'#'\"'\"'#g;s#.*#par_revcomp='&'#" ; else echo "# par_revcomp="; fi ) +$( if [ ! -z ${VIASH_PAR_DEMULTIPLEX_MODE+x} ]; then echo "${VIASH_PAR_DEMULTIPLEX_MODE}" | sed "s#'#'\"'\"'#g;s#.*#par_demultiplex_mode='&'#" ; else echo "# par_demultiplex_mode="; fi ) $( if [ ! -z ${VIASH_PAR_CUT+x} ]; then echo "${VIASH_PAR_CUT}" | sed "s#'#'\"'\"'#g;s#.*#par_cut='&'#" ; else echo "# par_cut="; fi ) $( if [ ! -z ${VIASH_PAR_CUT_R2+x} ]; then echo "${VIASH_PAR_CUT_R2}" | sed "s#'#'\"'\"'#g;s#.*#par_cut_r2='&'#" ; else echo "# par_cut_r2="; fi ) $( if [ ! -z ${VIASH_PAR_NEXTSEQ_TRIM+x} ]; then echo "${VIASH_PAR_NEXTSEQ_TRIM}" | sed "s#'#'\"'\"'#g;s#.*#par_nextseq_trim='&'#" ; else echo "# par_nextseq_trim="; fi ) @@ -2545,7 +2585,7 @@ mod_args=\$(echo \\ \${par_cut_r2:+--cut_r2 "\${par_cut_r2}"} \\ \${par_nextseq_trim:+--nextseq-trim "\${par_nextseq_trim}"} \\ \${par_quality_cutoff:+--quality-cutoff "\${par_quality_cutoff}"} \\ - \${par_quality_cutoff_r2:+--quality-cutoff_r2 "\${par_quality_cutoff_r2}"} \\ + \${par_quality_cutoff_r2:+-Q "\${par_quality_cutoff_r2}"} \\ \${par_quality_base:+--quality-base "\${par_quality_base}"} \\ \${par_poly_a:+--poly-a} \\ \${par_length:+--length "\${par_length}"} \\ @@ -2614,14 +2654,35 @@ else ext="fasta" fi -if [ \$mode = "se" ]; then +demultiplex_mode="\$par_demultiplex_mode" +if [[ \$mode == "se" ]]; then + if [[ "\$demultiplex_mode" == "unique_dual" ]] || [[ "\$demultiplex_mode" == "combinatorial_dual" ]]; then + echo "Demultiplexing dual indexes is not possible with single-end data." + exit 1 + fi + prefix="trimmed_" + if [[ ! -z "\$demultiplex_mode" ]]; then + prefix="{name}_" + fi output_args=\$(echo \\ - --output "\$output_dir/{name}_001.\$ext" \\ + --output "\$output_dir/\${prefix}001.\$ext" \\ ) else + demultiplex_indicator_r1='{name}_' + demultiplex_indicator_r2=\$demultiplex_indicator_r1 + if [[ "\$demultiplex_mode" == "combinatorial_dual" ]]; then + demultiplex_indicator_r1='{name1}_{name2}_' + demultiplex_indicator_r2='{name1}_{name2}_' + fi + prefix_r1="trimmed_" + prefix_r2="trimmed_" + if [[ ! -z "\$demultiplex_mode" ]]; then + prefix_r1=\$demultiplex_indicator_r1 + prefix_r2=\$demultiplex_indicator_r2 + fi output_args=\$(echo \\ - --output "\$output_dir/{name}_R1_001.\$ext" \\ - --paired-output "\$output_dir/{name}_R2_001.\$ext" \\ + --output "\$output_dir/\${prefix_r1}R1_001.\$ext" \\ + --paired-output "\$output_dir/\${prefix_r2}R2_001.\$ext" \\ ) fi diff --git a/target/executable/falco/.config.vsh.yaml b/target/executable/falco/.config.vsh.yaml index 036f9922..dbc6eaeb 100644 --- a/target/executable/falco/.config.vsh.yaml +++ b/target/executable/falco/.config.vsh.yaml @@ -304,7 +304,7 @@ build_info: output: "target/executable/falco" executable: "target/executable/falco/falco" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/falco/falco b/target/executable/falco/falco index b885064b..0270e7df 100755 --- a/target/executable/falco/falco +++ b/target/executable/falco/falco @@ -584,9 +584,9 @@ make install RUN echo "falco: \"$(falco -v | sed -n 's/^falco //p')\"" > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component falco" -LABEL org.opencontainers.image.created="2024-07-01T10:12:46Z" +LABEL org.opencontainers.image.created="2024-07-01T20:00:27Z" LABEL org.opencontainers.image.source="https://github.com/smithlabcode/falco" -LABEL org.opencontainers.image.revision="3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" +LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/fastp/.config.vsh.yaml b/target/executable/fastp/.config.vsh.yaml index 4fbbf896..9cdb4ad7 100644 --- a/target/executable/fastp/.config.vsh.yaml +++ b/target/executable/fastp/.config.vsh.yaml @@ -1065,7 +1065,7 @@ build_info: output: "target/executable/fastp" executable: "target/executable/fastp/fastp" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/fastp/fastp b/target/executable/fastp/fastp index 523ca18e..e410d13e 100755 --- a/target/executable/fastp/fastp +++ b/target/executable/fastp/fastp @@ -1023,9 +1023,9 @@ ENTRYPOINT [] RUN fastp --version 2>&1 | sed 's# #: "#;s#$#"#' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component fastp" -LABEL org.opencontainers.image.created="2024-07-01T10:12:47Z" +LABEL org.opencontainers.image.created="2024-07-01T20:00:28Z" LABEL org.opencontainers.image.source="https://github.com/OpenGene/fastp" -LABEL org.opencontainers.image.revision="3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" +LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/featurecounts/.config.vsh.yaml b/target/executable/featurecounts/.config.vsh.yaml index c5f7489b..c0444d60 100644 --- a/target/executable/featurecounts/.config.vsh.yaml +++ b/target/executable/featurecounts/.config.vsh.yaml @@ -631,7 +631,7 @@ build_info: output: "target/executable/featurecounts" executable: "target/executable/featurecounts/featurecounts" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/featurecounts/featurecounts b/target/executable/featurecounts/featurecounts index 8ac30721..0ba9404f 100755 --- a/target/executable/featurecounts/featurecounts +++ b/target/executable/featurecounts/featurecounts @@ -749,9 +749,9 @@ ENTRYPOINT [] RUN featureCounts -v 2>&1 | sed 's/featureCounts v\([0-9.]*\)/featureCounts: \1/' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component featurecounts" -LABEL org.opencontainers.image.created="2024-07-01T10:12:56Z" +LABEL org.opencontainers.image.created="2024-07-01T20:00:37Z" LABEL org.opencontainers.image.source="https://github.com/ShiLab-Bioinformatics/subread" -LABEL org.opencontainers.image.revision="3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" +LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/gffread/.config.vsh.yaml b/target/executable/gffread/.config.vsh.yaml index cf64a227..57c08f95 100644 --- a/target/executable/gffread/.config.vsh.yaml +++ b/target/executable/gffread/.config.vsh.yaml @@ -671,7 +671,7 @@ build_info: output: "target/executable/gffread" executable: "target/executable/gffread/gffread" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/gffread/gffread b/target/executable/gffread/gffread index 57abbe80..bd9accd0 100755 --- a/target/executable/gffread/gffread +++ b/target/executable/gffread/gffread @@ -802,9 +802,9 @@ ENTRYPOINT [] RUN echo "gffread: \"$(gffread --version 2>&1)\"" > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component gffread" -LABEL org.opencontainers.image.created="2024-07-01T10:12:47Z" +LABEL org.opencontainers.image.created="2024-07-01T20:00:28Z" LABEL org.opencontainers.image.source="https://github.com/gpertea/gffread" -LABEL org.opencontainers.image.revision="3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" +LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/lofreq/lofreq_call/.config.vsh.yaml b/target/executable/lofreq/lofreq_call/.config.vsh.yaml index 4eb7396b..4b3894a3 100644 --- a/target/executable/lofreq/lofreq_call/.config.vsh.yaml +++ b/target/executable/lofreq/lofreq_call/.config.vsh.yaml @@ -489,7 +489,7 @@ build_info: output: "target/executable/lofreq/lofreq_call" executable: "target/executable/lofreq/lofreq_call/lofreq_call" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/lofreq/lofreq_call/lofreq_call b/target/executable/lofreq/lofreq_call/lofreq_call index ca9b81c4..05f6eab6 100755 --- a/target/executable/lofreq/lofreq_call/lofreq_call +++ b/target/executable/lofreq/lofreq_call/lofreq_call @@ -651,9 +651,9 @@ RUN version=$(lofreq version | grep 'version' | sed 's/version: //') && \ echo "lofreq: $version" > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component lofreq lofreq_call" -LABEL org.opencontainers.image.created="2024-07-01T10:12:50Z" +LABEL org.opencontainers.image.created="2024-07-01T20:00:32Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox" -LABEL org.opencontainers.image.revision="3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" +LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml b/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml index 35d7f7bc..971b824c 100644 --- a/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml +++ b/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml @@ -197,7 +197,7 @@ build_info: output: "target/executable/lofreq/lofreq_indelqual" executable: "target/executable/lofreq/lofreq_indelqual/lofreq_indelqual" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual b/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual index 39098c07..40858291 100755 --- a/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual +++ b/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual @@ -496,9 +496,9 @@ RUN version=$(lofreq version | grep 'version' | sed 's/version: //') && \ echo "lofreq: $version" > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component lofreq lofreq_indelqual" -LABEL org.opencontainers.image.created="2024-07-01T10:12:50Z" +LABEL org.opencontainers.image.created="2024-07-01T20:00:31Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox" -LABEL org.opencontainers.image.revision="3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" +LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/multiqc/.config.vsh.yaml b/target/executable/multiqc/.config.vsh.yaml index e950c1fd..2efffe7c 100644 --- a/target/executable/multiqc/.config.vsh.yaml +++ b/target/executable/multiqc/.config.vsh.yaml @@ -438,7 +438,7 @@ build_info: output: "target/executable/multiqc" executable: "target/executable/multiqc/multiqc" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/multiqc/multiqc b/target/executable/multiqc/multiqc index 60f79c3c..89c88766 100755 --- a/target/executable/multiqc/multiqc +++ b/target/executable/multiqc/multiqc @@ -632,9 +632,9 @@ ENTRYPOINT [] RUN multiqc --version | sed 's/multiqc, version\s\(.*\)/multiqc: "\1"/' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component multiqc" -LABEL org.opencontainers.image.created="2024-07-01T10:12:45Z" +LABEL org.opencontainers.image.created="2024-07-01T20:00:27Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox" -LABEL org.opencontainers.image.revision="3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" +LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/pear/.config.vsh.yaml b/target/executable/pear/.config.vsh.yaml index d2d63460..7a91ad37 100644 --- a/target/executable/pear/.config.vsh.yaml +++ b/target/executable/pear/.config.vsh.yaml @@ -380,7 +380,7 @@ build_info: output: "target/executable/pear" executable: "target/executable/pear/pear" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/pear/pear b/target/executable/pear/pear index d44d6c8e..cf8fed5b 100755 --- a/target/executable/pear/pear +++ b/target/executable/pear/pear @@ -592,9 +592,9 @@ RUN version=$(pear -h | grep 'PEAR v' | sed 's/PEAR v//' | sed 's/ .*//') && \ echo "pear: $version" > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component pear" -LABEL org.opencontainers.image.created="2024-07-01T10:12:54Z" +LABEL org.opencontainers.image.created="2024-07-01T20:00:35Z" LABEL org.opencontainers.image.source="https://github.com/tseemann/PEAR" -LABEL org.opencontainers.image.revision="3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" +LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065" 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 e30a10ac..1ac21053 100644 --- a/target/executable/salmon/salmon_index/.config.vsh.yaml +++ b/target/executable/salmon/salmon_index/.config.vsh.yaml @@ -263,7 +263,7 @@ build_info: output: "target/executable/salmon/salmon_index" executable: "target/executable/salmon/salmon_index/salmon_index" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/salmon/salmon_index/salmon_index b/target/executable/salmon/salmon_index/salmon_index index 19fadd83..355ffd00 100755 --- a/target/executable/salmon/salmon_index/salmon_index +++ b/target/executable/salmon/salmon_index/salmon_index @@ -541,9 +541,9 @@ ENTRYPOINT [] RUN salmon index -v 2>&1 | sed 's/salmon \([0-9.]*\)/salmon: \1/' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component salmon salmon_index" -LABEL org.opencontainers.image.created="2024-07-01T10:12:55Z" +LABEL org.opencontainers.image.created="2024-07-01T20:00:36Z" LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon" -LABEL org.opencontainers.image.revision="3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" +LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/salmon/salmon_quant/.config.vsh.yaml b/target/executable/salmon/salmon_quant/.config.vsh.yaml index 934c3fa5..cc6a5f2b 100644 --- a/target/executable/salmon/salmon_quant/.config.vsh.yaml +++ b/target/executable/salmon/salmon_quant/.config.vsh.yaml @@ -1159,7 +1159,7 @@ build_info: output: "target/executable/salmon/salmon_quant" executable: "target/executable/salmon/salmon_quant/salmon_quant" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/salmon/salmon_quant/salmon_quant b/target/executable/salmon/salmon_quant/salmon_quant index 0754f17a..4c2f4dfc 100755 --- a/target/executable/salmon/salmon_quant/salmon_quant +++ b/target/executable/salmon/salmon_quant/salmon_quant @@ -1163,9 +1163,9 @@ ENTRYPOINT [] RUN salmon index -v 2>&1 | sed 's/salmon \([0-9.]*\)/salmon: \1/' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component salmon salmon_quant" -LABEL org.opencontainers.image.created="2024-07-01T10:12:55Z" +LABEL org.opencontainers.image.created="2024-07-01T20:00:36Z" LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon" -LABEL org.opencontainers.image.revision="3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" +LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/samtools/samtools_collate/.config.vsh.yaml b/target/executable/samtools/samtools_collate/.config.vsh.yaml index 427a79f0..56838037 100644 --- a/target/executable/samtools/samtools_collate/.config.vsh.yaml +++ b/target/executable/samtools/samtools_collate/.config.vsh.yaml @@ -250,7 +250,7 @@ build_info: output: "target/executable/samtools/samtools_collate" executable: "target/executable/samtools/samtools_collate/samtools_collate" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/samtools/samtools_collate/samtools_collate b/target/executable/samtools/samtools_collate/samtools_collate index 145f8760..3f26004c 100755 --- a/target/executable/samtools/samtools_collate/samtools_collate +++ b/target/executable/samtools/samtools_collate/samtools_collate @@ -514,9 +514,9 @@ RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_collate" -LABEL org.opencontainers.image.created="2024-07-01T10:12:52Z" +LABEL org.opencontainers.image.created="2024-07-01T20:00:33Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" +LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065" 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 e98f3dd6..4eedfdb8 100644 --- a/target/executable/samtools/samtools_faidx/.config.vsh.yaml +++ b/target/executable/samtools/samtools_faidx/.config.vsh.yaml @@ -229,7 +229,7 @@ build_info: output: "target/executable/samtools/samtools_faidx" executable: "target/executable/samtools/samtools_faidx/samtools_faidx" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/samtools/samtools_faidx/samtools_faidx b/target/executable/samtools/samtools_faidx/samtools_faidx index df44cde1..e99bfb01 100755 --- a/target/executable/samtools/samtools_faidx/samtools_faidx +++ b/target/executable/samtools/samtools_faidx/samtools_faidx @@ -507,9 +507,9 @@ RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_faidx" -LABEL org.opencontainers.image.created="2024-07-01T10:12:53Z" +LABEL org.opencontainers.image.created="2024-07-01T20:00:34Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" +LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065" 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 ff123825..2ec62dc2 100644 --- a/target/executable/samtools/samtools_fastq/.config.vsh.yaml +++ b/target/executable/samtools/samtools_fastq/.config.vsh.yaml @@ -417,7 +417,7 @@ build_info: output: "target/executable/samtools/samtools_fastq" executable: "target/executable/samtools/samtools_fastq/samtools_fastq" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/samtools/samtools_fastq/samtools_fastq b/target/executable/samtools/samtools_fastq/samtools_fastq index 1c55d8cb..8fa30daf 100755 --- a/target/executable/samtools/samtools_fastq/samtools_fastq +++ b/target/executable/samtools/samtools_fastq/samtools_fastq @@ -620,9 +620,9 @@ RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_fastq" -LABEL org.opencontainers.image.created="2024-07-01T10:12:51Z" +LABEL org.opencontainers.image.created="2024-07-01T20:00:33Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" +LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065" 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 1a4089d4..fb3ba323 100644 --- a/target/executable/samtools/samtools_flagstat/.config.vsh.yaml +++ b/target/executable/samtools/samtools_flagstat/.config.vsh.yaml @@ -159,7 +159,7 @@ build_info: output: "target/executable/samtools/samtools_flagstat" executable: "target/executable/samtools/samtools_flagstat/samtools_flagstat" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/samtools/samtools_flagstat/samtools_flagstat b/target/executable/samtools/samtools_flagstat/samtools_flagstat index a9abf0de..e0ed8a16 100755 --- a/target/executable/samtools/samtools_flagstat/samtools_flagstat +++ b/target/executable/samtools/samtools_flagstat/samtools_flagstat @@ -469,9 +469,9 @@ RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_flagstat" -LABEL org.opencontainers.image.created="2024-07-01T10:12:53Z" +LABEL org.opencontainers.image.created="2024-07-01T20:00:34Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" +LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065" 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 b1cd4a32..ce30f840 100644 --- a/target/executable/samtools/samtools_idxstats/.config.vsh.yaml +++ b/target/executable/samtools/samtools_idxstats/.config.vsh.yaml @@ -169,7 +169,7 @@ build_info: output: "target/executable/samtools/samtools_idxstats" executable: "target/executable/samtools/samtools_idxstats/samtools_idxstats" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/samtools/samtools_idxstats/samtools_idxstats b/target/executable/samtools/samtools_idxstats/samtools_idxstats index 0b043e05..6f647e59 100755 --- a/target/executable/samtools/samtools_idxstats/samtools_idxstats +++ b/target/executable/samtools/samtools_idxstats/samtools_idxstats @@ -473,9 +473,9 @@ RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_idxstats" -LABEL org.opencontainers.image.created="2024-07-01T10:12:52Z" +LABEL org.opencontainers.image.created="2024-07-01T20:00:34Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" +LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065" 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 2f721d41..2b01d5de 100644 --- a/target/executable/samtools/samtools_index/.config.vsh.yaml +++ b/target/executable/samtools/samtools_index/.config.vsh.yaml @@ -175,7 +175,7 @@ build_info: output: "target/executable/samtools/samtools_index" executable: "target/executable/samtools/samtools_index/samtools_index" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/samtools/samtools_index/samtools_index b/target/executable/samtools/samtools_index/samtools_index index 3566211f..85d2b130 100755 --- a/target/executable/samtools/samtools_index/samtools_index +++ b/target/executable/samtools/samtools_index/samtools_index @@ -480,9 +480,9 @@ RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_index" -LABEL org.opencontainers.image.created="2024-07-01T10:12:51Z" +LABEL org.opencontainers.image.created="2024-07-01T20:00:32Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" +LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065" 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 95a04243..a68eeb70 100644 --- a/target/executable/samtools/samtools_sort/.config.vsh.yaml +++ b/target/executable/samtools/samtools_sort/.config.vsh.yaml @@ -318,7 +318,7 @@ build_info: output: "target/executable/samtools/samtools_sort" executable: "target/executable/samtools/samtools_sort/samtools_sort" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/samtools/samtools_sort/samtools_sort b/target/executable/samtools/samtools_sort/samtools_sort index 1cc70f8d..8c7beb4d 100755 --- a/target/executable/samtools/samtools_sort/samtools_sort +++ b/target/executable/samtools/samtools_sort/samtools_sort @@ -551,9 +551,9 @@ RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_sort" -LABEL org.opencontainers.image.created="2024-07-01T10:12:53Z" +LABEL org.opencontainers.image.created="2024-07-01T20:00:35Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" +LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065" 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 23eab3a6..6c6858a9 100644 --- a/target/executable/samtools/samtools_stats/.config.vsh.yaml +++ b/target/executable/samtools/samtools_stats/.config.vsh.yaml @@ -380,7 +380,7 @@ build_info: output: "target/executable/samtools/samtools_stats" executable: "target/executable/samtools/samtools_stats/samtools_stats" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/samtools/samtools_stats/samtools_stats b/target/executable/samtools/samtools_stats/samtools_stats index bd44818b..cecf716e 100755 --- a/target/executable/samtools/samtools_stats/samtools_stats +++ b/target/executable/samtools/samtools_stats/samtools_stats @@ -568,9 +568,9 @@ RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_stats" -LABEL org.opencontainers.image.created="2024-07-01T10:12:52Z" +LABEL org.opencontainers.image.created="2024-07-01T20:00:33Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" +LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065" 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 812006bb..d5ec6344 100644 --- a/target/executable/samtools/samtools_view/.config.vsh.yaml +++ b/target/executable/samtools/samtools_view/.config.vsh.yaml @@ -651,7 +651,7 @@ build_info: output: "target/executable/samtools/samtools_view" executable: "target/executable/samtools/samtools_view/samtools_view" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/samtools/samtools_view/samtools_view b/target/executable/samtools/samtools_view/samtools_view index 9521f3e5..f8b9c99a 100755 --- a/target/executable/samtools/samtools_view/samtools_view +++ b/target/executable/samtools/samtools_view/samtools_view @@ -820,9 +820,9 @@ RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_view" -LABEL org.opencontainers.image.created="2024-07-01T10:12:51Z" +LABEL org.opencontainers.image.created="2024-07-01T20:00:32Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" +LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065" 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 7abda748..203e68a3 100644 --- a/target/executable/star/star_align_reads/.config.vsh.yaml +++ b/target/executable/star/star_align_reads/.config.vsh.yaml @@ -2108,7 +2108,7 @@ build_info: output: "target/executable/star/star_align_reads" executable: "target/executable/star/star_align_reads/star_align_reads" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/star/star_align_reads/star_align_reads b/target/executable/star/star_align_reads/star_align_reads index 1bff55ae..c0df581d 100755 --- a/target/executable/star/star_align_reads/star_align_reads +++ b/target/executable/star/star_align_reads/star_align_reads @@ -1665,9 +1665,9 @@ RUN apt-get update && \ RUN STAR --version | sed 's#\(.*\)#star: "\1"#' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component star star_align_reads" -LABEL org.opencontainers.image.created="2024-07-01T10:12:48Z" +LABEL org.opencontainers.image.created="2024-07-01T20:00:29Z" LABEL org.opencontainers.image.source="https://github.com/alexdobin/STAR" -LABEL org.opencontainers.image.revision="3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" +LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/star/star_genome_generate/.config.vsh.yaml b/target/executable/star/star_genome_generate/.config.vsh.yaml index 931137ee..27d40ee9 100644 --- a/target/executable/star/star_genome_generate/.config.vsh.yaml +++ b/target/executable/star/star_genome_generate/.config.vsh.yaml @@ -319,7 +319,7 @@ build_info: output: "target/executable/star/star_genome_generate" executable: "target/executable/star/star_genome_generate/star_genome_generate" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/star/star_genome_generate/star_genome_generate b/target/executable/star/star_genome_generate/star_genome_generate index 894ca90e..fe4bae1b 100755 --- a/target/executable/star/star_genome_generate/star_genome_generate +++ b/target/executable/star/star_genome_generate/star_genome_generate @@ -572,9 +572,9 @@ RUN apt-get update && \ RUN STAR --version | sed 's#\(.*\)#star: "\1"#' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component star star_genome_generate" -LABEL org.opencontainers.image.created="2024-07-01T10:12:48Z" +LABEL org.opencontainers.image.created="2024-07-01T20:00:29Z" LABEL org.opencontainers.image.source="https://github.com/alexdobin/STAR" -LABEL org.opencontainers.image.revision="3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" +LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/nextflow/arriba/.config.vsh.yaml b/target/nextflow/arriba/.config.vsh.yaml index 4b55469e..092425b7 100644 --- a/target/nextflow/arriba/.config.vsh.yaml +++ b/target/nextflow/arriba/.config.vsh.yaml @@ -688,7 +688,7 @@ build_info: output: "target/nextflow/arriba" executable: "target/nextflow/arriba/main.nf" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/arriba/main.nf b/target/nextflow/arriba/main.nf index e7ab38cb..2a2aa485 100644 --- a/target/nextflow/arriba/main.nf +++ b/target/nextflow/arriba/main.nf @@ -3534,7 +3534,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/arriba", "viash_version" : "0.9.0-RC6", - "git_commit" : "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a", + "git_commit" : "ec69d9af7a59c2618a49bef7d0bf9afc743ca065", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/bcl_convert/.config.vsh.yaml b/target/nextflow/bcl_convert/.config.vsh.yaml index 796dffdb..e766bf68 100644 --- a/target/nextflow/bcl_convert/.config.vsh.yaml +++ b/target/nextflow/bcl_convert/.config.vsh.yaml @@ -386,7 +386,7 @@ build_info: output: "target/nextflow/bcl_convert" executable: "target/nextflow/bcl_convert/main.nf" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/bcl_convert/main.nf b/target/nextflow/bcl_convert/main.nf index 7eaeb215..5d63c030 100644 --- a/target/nextflow/bcl_convert/main.nf +++ b/target/nextflow/bcl_convert/main.nf @@ -3249,7 +3249,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bcl_convert", "viash_version" : "0.9.0-RC6", - "git_commit" : "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a", + "git_commit" : "ec69d9af7a59c2618a49bef7d0bf9afc743ca065", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml index 6ef58675..c327db82 100644 --- a/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml @@ -217,7 +217,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_getfasta" executable: "target/nextflow/bedtools/bedtools_getfasta/main.nf" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/bedtools/bedtools_getfasta/main.nf b/target/nextflow/bedtools/bedtools_getfasta/main.nf index 352aec3b..d1062d91 100644 --- a/target/nextflow/bedtools/bedtools_getfasta/main.nf +++ b/target/nextflow/bedtools/bedtools_getfasta/main.nf @@ -3033,7 +3033,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_getfasta", "viash_version" : "0.9.0-RC6", - "git_commit" : "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a", + "git_commit" : "ec69d9af7a59c2618a49bef7d0bf9afc743ca065", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml b/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml index 03aee5fa..322abf48 100644 --- a/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml +++ b/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml @@ -125,7 +125,7 @@ runners: engines: - type: "docker" id: "docker" - image: "quay.io/biocontainers/busco:5.6.1--pyhdfd78af_0" + image: "quay.io/biocontainers/busco:5.7.1--pyhdfd78af_0" target_registry: "images.viash-hub.com" target_tag: "main" namespace_separator: "/" @@ -144,7 +144,7 @@ build_info: output: "target/nextflow/busco/busco_download_datasets" executable: "target/nextflow/busco/busco_download_datasets/main.nf" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/busco/busco_download_datasets/main.nf b/target/nextflow/busco/busco_download_datasets/main.nf index f7243112..a088ef04 100644 --- a/target/nextflow/busco/busco_download_datasets/main.nf +++ b/target/nextflow/busco/busco_download_datasets/main.nf @@ -2935,7 +2935,7 @@ meta = [ { "type" : "docker", "id" : "docker", - "image" : "quay.io/biocontainers/busco:5.6.1--pyhdfd78af_0", + "image" : "quay.io/biocontainers/busco:5.7.1--pyhdfd78af_0", "target_registry" : "images.viash-hub.com", "target_tag" : "main", "namespace_separator" : "/", @@ -2959,7 +2959,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/busco/busco_download_datasets", "viash_version" : "0.9.0-RC6", - "git_commit" : "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a", + "git_commit" : "ec69d9af7a59c2618a49bef7d0bf9afc743ca065", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/busco/busco_download_datasets/nextflow_schema.json b/target/nextflow/busco/busco_download_datasets/nextflow_schema.json deleted file mode 100644 index 10f7d894..00000000 --- a/target/nextflow/busco/busco_download_datasets/nextflow_schema.json +++ /dev/null @@ -1,95 +0,0 @@ -{ -"$schema": "http://json-schema.org/draft-07/schema", -"title": "busco_download_datasets", -"description": "Downloads available busco datasets", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "download": { - "type": - "string", - "description": "Type: `string`, required, example: `stramenopiles_odb10`. Download dataset", - "help_text": "Type: `string`, required, example: `stramenopiles_odb10`. Download dataset. Possible values are a specific dataset name, \"all\", \"prokaryota\", \"eukaryota\", or \"virus\".\nThe full list of available datasets can be viewed [here](https://busco-data.ezlab.org/v5/data/lineages/) or by running the busco/busco_list_datasets component.\n" - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "download_path": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.download_path.download_path`, example: `busco_downloads`. Local filepath for storing BUSCO dataset downloads\n", - "help_text": "Type: `file`, default: `$id.$key.download_path.download_path`, example: `busco_downloads`. Local filepath for storing BUSCO dataset downloads\n" - , - "default": "$id.$key.download_path.download_path" - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" - }, - - { - "$ref": "#/definitions/outputs" - }, - - { - "$ref": "#/definitions/nextflow input-output arguments" - } -] -} diff --git a/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml b/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml index 43fe2062..4862527c 100644 --- a/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml +++ b/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml @@ -112,7 +112,7 @@ runners: engines: - type: "docker" id: "docker" - image: "quay.io/biocontainers/busco:5.6.1--pyhdfd78af_0" + image: "quay.io/biocontainers/busco:5.7.1--pyhdfd78af_0" target_registry: "images.viash-hub.com" target_tag: "main" namespace_separator: "/" @@ -131,7 +131,7 @@ build_info: output: "target/nextflow/busco/busco_list_datasets" executable: "target/nextflow/busco/busco_list_datasets/main.nf" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/busco/busco_list_datasets/main.nf b/target/nextflow/busco/busco_list_datasets/main.nf index 4b980c25..43c360f3 100644 --- a/target/nextflow/busco/busco_list_datasets/main.nf +++ b/target/nextflow/busco/busco_list_datasets/main.nf @@ -2921,7 +2921,7 @@ meta = [ { "type" : "docker", "id" : "docker", - "image" : "quay.io/biocontainers/busco:5.6.1--pyhdfd78af_0", + "image" : "quay.io/biocontainers/busco:5.7.1--pyhdfd78af_0", "target_registry" : "images.viash-hub.com", "target_tag" : "main", "namespace_separator" : "/", @@ -2945,7 +2945,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/busco/busco_list_datasets", "viash_version" : "0.9.0-RC6", - "git_commit" : "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a", + "git_commit" : "ec69d9af7a59c2618a49bef7d0bf9afc743ca065", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/busco/busco_run/.config.vsh.yaml b/target/nextflow/busco/busco_run/.config.vsh.yaml index a9476fd6..309b7303 100644 --- a/target/nextflow/busco/busco_run/.config.vsh.yaml +++ b/target/nextflow/busco/busco_run/.config.vsh.yaml @@ -263,6 +263,11 @@ argument_groups: direction: "input" - name: "MetaEuk Settings" arguments: + - type: "boolean_true" + name: "--metaeuk" + description: "Use Metaeuk gene predictor.\n" + info: null + direction: "input" - type: "string" name: "--metaeuk_parameters" description: "Pass additional arguments to Metaeuk for the first run (see Metaeuk\ @@ -385,7 +390,7 @@ runners: engines: - type: "docker" id: "docker" - image: "quay.io/biocontainers/busco:5.6.1--pyhdfd78af_0" + image: "quay.io/biocontainers/busco:5.7.1--pyhdfd78af_0" target_registry: "images.viash-hub.com" target_tag: "main" namespace_separator: "/" @@ -404,7 +409,7 @@ build_info: output: "target/nextflow/busco/busco_run" executable: "target/nextflow/busco/busco_run/main.nf" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/busco/busco_run/main.nf b/target/nextflow/busco/busco_run/main.nf index 8ac5bf5f..e723bb91 100644 --- a/target/nextflow/busco/busco_run/main.nf +++ b/target/nextflow/busco/busco_run/main.nf @@ -3082,6 +3082,12 @@ meta = [ { "name" : "MetaEuk Settings", "arguments" : [ + { + "type" : "boolean_true", + "name" : "--metaeuk", + "description" : "Use Metaeuk gene predictor.\n", + "direction" : "input" + }, { "type" : "string", "name" : "--metaeuk_parameters", @@ -3227,7 +3233,7 @@ meta = [ { "type" : "docker", "id" : "docker", - "image" : "quay.io/biocontainers/busco:5.6.1--pyhdfd78af_0", + "image" : "quay.io/biocontainers/busco:5.7.1--pyhdfd78af_0", "target_registry" : "images.viash-hub.com", "target_tag" : "main", "namespace_separator" : "/", @@ -3251,7 +3257,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/busco/busco_run", "viash_version" : "0.9.0-RC6", - "git_commit" : "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a", + "git_commit" : "ec69d9af7a59c2618a49bef7d0bf9afc743ca065", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3320,6 +3326,7 @@ $( if [ ! -z ${VIASH_PAR_LIMIT+x} ]; then echo "${VIASH_PAR_LIMIT}" | sed "s#'#' $( if [ ! -z ${VIASH_PAR_SCAFFOLD_COMPOSITION+x} ]; then echo "${VIASH_PAR_SCAFFOLD_COMPOSITION}" | sed "s#'#'\\"'\\"'#g;s#.*#par_scaffold_composition='&'#" ; else echo "# par_scaffold_composition="; fi ) $( if [ ! -z ${VIASH_PAR_E_VALUE+x} ]; then echo "${VIASH_PAR_E_VALUE}" | sed "s#'#'\\"'\\"'#g;s#.*#par_e_value='&'#" ; else echo "# par_e_value="; fi ) $( if [ ! -z ${VIASH_PAR_MINIPROT+x} ]; then echo "${VIASH_PAR_MINIPROT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_miniprot='&'#" ; else echo "# par_miniprot="; fi ) +$( if [ ! -z ${VIASH_PAR_METAEUK+x} ]; then echo "${VIASH_PAR_METAEUK}" | sed "s#'#'\\"'\\"'#g;s#.*#par_metaeuk='&'#" ; else echo "# par_metaeuk="; fi ) $( if [ ! -z ${VIASH_PAR_METAEUK_PARAMETERS+x} ]; then echo "${VIASH_PAR_METAEUK_PARAMETERS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_metaeuk_parameters='&'#" ; else echo "# par_metaeuk_parameters="; fi ) $( if [ ! -z ${VIASH_PAR_METAEUK_RERUN_PARAMETERS+x} ]; then echo "${VIASH_PAR_METAEUK_RERUN_PARAMETERS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_metaeuk_rerun_parameters='&'#" ; else echo "# par_metaeuk_rerun_parameters="; fi ) $( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "${VIASH_META_NAME}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_name='&'#" ; else echo "# meta_name="; fi ) @@ -3379,6 +3386,7 @@ busco \\\\ \\${par_force:+--force} \\\\ \\${par_limit:+--limit "\\$par_limit"} \\\\ \\${par_long:+--long} \\\\ + \\${par_metaeuk:+--metaeuk} \\\\ \\${par_metaeuk_parameters:+--metaeuk_parameters "\\$par_metaeuk_parameters"} \\\\ \\${par_metaeuk_rerun_parameters:+--metaeuk_rerun_parameters "\\$par_metaeuk_rerun_parameters"} \\\\ \\${par_miniprot:+--miniprot} \\\\ diff --git a/target/nextflow/busco/busco_run/nextflow_schema.json b/target/nextflow/busco/busco_run/nextflow_schema.json new file mode 100644 index 00000000..64390d89 --- /dev/null +++ b/target/nextflow/busco/busco_run/nextflow_schema.json @@ -0,0 +1,471 @@ +{ +"$schema": "http://json-schema.org/draft-07/schema", +"title": "busco_run", +"description": "Assessment of genome assembly and annotation completeness with single copy orthologs", +"type": "object", +"definitions": { + + + + "inputs" : { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + + + "input": { + "type": + "string", + "description": "Type: `file`, required, example: `file.fasta`. Input sequence file in FASTA format", + "help_text": "Type: `file`, required, example: `file.fasta`. Input sequence file in FASTA format. Can be an assembled genome or transcriptome (DNA), or protein sequences from an annotated gene set. Also possible to use a path to a directory containing multiple input files.\n" + + } + + + , + "mode": { + "type": + "string", + "description": "Type: `string`, required, example: `proteins`, choices: ``genome`, `geno`, `transcriptome`, `tran`, `proteins`, `prot``. Specify which BUSCO analysis mode to run", + "help_text": "Type: `string`, required, example: `proteins`, choices: ``genome`, `geno`, `transcriptome`, `tran`, `proteins`, `prot``. Specify which BUSCO analysis mode to run. There are three valid modes:\n - geno or genome, for genome assemblies (DNA)\n - tran or transcriptome, for transcriptome assemblies (DNA)\n - prot or proteins, for annotated gene sets (protein)\n", + "enum": ["genome", "geno", "transcriptome", "tran", "proteins", "prot"] + + + } + + + , + "lineage_dataset": { + "type": + "string", + "description": "Type: `string`, example: `stramenopiles_odb10`. Specify a BUSCO lineage dataset that is most closely related to the assembly or gene set being assessed", + "help_text": "Type: `string`, example: `stramenopiles_odb10`. Specify a BUSCO lineage dataset that is most closely related to the assembly or gene set being assessed. \nThe full list of available datasets can be viewed [here](https://busco-data.ezlab.org/v5/data/lineages/) or by running the busco/busco_list_datasets component.\nWhen unsure, the \"--auto_lineage\" flag can be set to automatically find the optimal lineage path.\nBUSCO will automatically download the requested dataset if it is not already present in the download folder. \nYou can optionally provide a path to a local dataset instead of a name, e.g. path/to/dataset.\nDatasets can be downloaded using the busco/busco_download_dataset component.\n" + + } + + +} +}, + + + "outputs" : { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + + + "short_summary_json": { + "type": + "string", + "description": "Type: `file`, default: `$id.$key.short_summary_json.json`, example: `short_summary.json`. Output file for short summary in JSON format", + "help_text": "Type: `file`, default: `$id.$key.short_summary_json.json`, example: `short_summary.json`. Output file for short summary in JSON format.\n" + , + "default": "$id.$key.short_summary_json.json" + } + + + , + "short_summary_txt": { + "type": + "string", + "description": "Type: `file`, default: `$id.$key.short_summary_txt.txt`, example: `short_summary.txt`. Output file for short summary in TXT format", + "help_text": "Type: `file`, default: `$id.$key.short_summary_txt.txt`, example: `short_summary.txt`. Output file for short summary in TXT format.\n" + , + "default": "$id.$key.short_summary_txt.txt" + } + + + , + "full_table": { + "type": + "string", + "description": "Type: `file`, default: `$id.$key.full_table.tsv`, example: `full_table.tsv`. Full table output in TSV format", + "help_text": "Type: `file`, default: `$id.$key.full_table.tsv`, example: `full_table.tsv`. Full table output in TSV format.\n" + , + "default": "$id.$key.full_table.tsv" + } + + + , + "missing_busco_list": { + "type": + "string", + "description": "Type: `file`, default: `$id.$key.missing_busco_list.tsv`, example: `missing_busco_list.tsv`. Missing list output in TSV format", + "help_text": "Type: `file`, default: `$id.$key.missing_busco_list.tsv`, example: `missing_busco_list.tsv`. Missing list output in TSV format.\n" + , + "default": "$id.$key.missing_busco_list.tsv" + } + + + , + "output_dir": { + "type": + "string", + "description": "Type: `file`, default: `$id.$key.output_dir.output_dir`, example: `output_dir/`. The full output directory, if so desired", + "help_text": "Type: `file`, default: `$id.$key.output_dir.output_dir`, example: `output_dir/`. The full output directory, if so desired.\n" + , + "default": "$id.$key.output_dir.output_dir" + } + + +} +}, + + + "resource and run settings" : { + "title": "Resource and Run Settings", + "type": "object", + "description": "No description", + "properties": { + + + "force": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Force rewriting of existing files", + "help_text": "Type: `boolean_true`, default: `false`. Force rewriting of existing files. Must be used when output files with the provided name already exist.\n" + , + "default": "False" + } + + + , + "quiet": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Disable the info logs, displays only errors", + "help_text": "Type: `boolean_true`, default: `false`. Disable the info logs, displays only errors.\n" + , + "default": "False" + } + + + , + "restart": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Continue a run that had already partially completed", + "help_text": "Type: `boolean_true`, default: `false`. Continue a run that had already partially completed. Restarting skips calls to tools that have completed but performs all pre- and post-processing steps.\n" + , + "default": "False" + } + + + , + "tar": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Compress some subdirectories with many files to save space", + "help_text": "Type: `boolean_true`, default: `false`. Compress some subdirectories with many files to save space.\n" + , + "default": "False" + } + + +} +}, + + + "lineage dataset settings" : { + "title": "Lineage Dataset Settings", + "type": "object", + "description": "No description", + "properties": { + + + "auto_lineage": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Run auto-lineage pipelilne to automatically determine BUSCO lineage dataset that is most closely related to the assembly or gene set being assessed", + "help_text": "Type: `boolean_true`, default: `false`. Run auto-lineage pipelilne to automatically determine BUSCO lineage dataset that is most closely related to the assembly or gene set being assessed.\n" + , + "default": "False" + } + + + , + "auto_lineage_euk": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Run auto-placement just on eukaryota tree to find optimal lineage path", + "help_text": "Type: `boolean_true`, default: `false`. Run auto-placement just on eukaryota tree to find optimal lineage path.\n" + , + "default": "False" + } + + + , + "auto_lineage_prok": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Run auto_lineage just on prokaryota trees to find optimum lineage path", + "help_text": "Type: `boolean_true`, default: `false`. Run auto_lineage just on prokaryota trees to find optimum lineage path.\n" + , + "default": "False" + } + + + , + "datasets_version": { + "type": + "string", + "description": "Type: `string`, example: `odb10`. Specify the version of BUSCO datasets\n", + "help_text": "Type: `string`, example: `odb10`. Specify the version of BUSCO datasets\n" + + } + + +} +}, + + + "augustus settings" : { + "title": "Augustus Settings", + "type": "object", + "description": "No description", + "properties": { + + + "augustus": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Use augustus gene predictor for eukaryote runs", + "help_text": "Type: `boolean_true`, default: `false`. Use augustus gene predictor for eukaryote runs.\n" + , + "default": "False" + } + + + , + "augustus_parameters": { + "type": + "string", + "description": "Type: `string`, example: `--PARAM1=VALUE1,--PARAM2=VALUE2`. Additional parameters to be passed to Augustus (see Augustus documentation: https://github", + "help_text": "Type: `string`, example: `--PARAM1=VALUE1,--PARAM2=VALUE2`. Additional parameters to be passed to Augustus (see Augustus documentation: https://github.com/Gaius-Augustus/Augustus/blob/master/docs/RUNNING-AUGUSTUS.md).\nParameters should be contained within a single string, without whitespace and seperated by commas.\n" + + } + + + , + "augustus_species": { + "type": + "string", + "description": "Type: `string`. Specify the augustus species\n", + "help_text": "Type: `string`. Specify the augustus species\n" + + } + + + , + "long": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Optimize Augustus self-training mode", + "help_text": "Type: `boolean_true`, default: `false`. Optimize Augustus self-training mode. This adds considerably to the run time, but can improve results for some non-model organisms.\n" + , + "default": "False" + } + + +} +}, + + + "bbtools settings" : { + "title": "BBTools Settings", + "type": "object", + "description": "No description", + "properties": { + + + "contig_break": { + "type": + "integer", + "description": "Type: `integer`. Number of contiguous Ns to signify a break between contigs in BBTools analysis", + "help_text": "Type: `integer`. Number of contiguous Ns to signify a break between contigs in BBTools analysis.\n" + + } + + + , + "limit": { + "type": + "integer", + "description": "Type: `integer`. Number of candidate regions (contig or transcript) from the BLAST output to consider per BUSCO", + "help_text": "Type: `integer`. Number of candidate regions (contig or transcript) from the BLAST output to consider per BUSCO.\nThis option is only effective in pipelines using BLAST, i.e. the genome pipeline (see --augustus) or the prokaryota transcriptome pipeline.\n" + + } + + + , + "scaffold_composition": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Writes ACGTN content per scaffold to a file scaffold_composition", + "help_text": "Type: `boolean_true`, default: `false`. Writes ACGTN content per scaffold to a file scaffold_composition.txt.\n" + , + "default": "False" + } + + +} +}, + + + "blast settings" : { + "title": "BLAST Settings", + "type": "object", + "description": "No description", + "properties": { + + + "e_value": { + "type": + "number", + "description": "Type: `double`. E-value cutoff for BLAST searches", + "help_text": "Type: `double`. E-value cutoff for BLAST searches.\n" + + } + + +} +}, + + + "protein gene prediction settings" : { + "title": "Protein Gene Prediction settings", + "type": "object", + "description": "No description", + "properties": { + + + "miniprot": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Use Miniprot gene predictor", + "help_text": "Type: `boolean_true`, default: `false`. Use Miniprot gene predictor.\n" + , + "default": "False" + } + + +} +}, + + + "metaeuk settings" : { + "title": "MetaEuk Settings", + "type": "object", + "description": "No description", + "properties": { + + + "metaeuk": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Use Metaeuk gene predictor", + "help_text": "Type: `boolean_true`, default: `false`. Use Metaeuk gene predictor.\n" + , + "default": "False" + } + + + , + "metaeuk_parameters": { + "type": + "string", + "description": "Type: `string`, example: `--max-overlap=15,--min-exon-aa=15`. Pass additional arguments to Metaeuk for the first run (see Metaeuk documentation https://github", + "help_text": "Type: `string`, example: `--max-overlap=15,--min-exon-aa=15`. Pass additional arguments to Metaeuk for the first run (see Metaeuk documentation https://github.com/soedinglab/metaeuk).\nAll parameters should be contained within a single string with no white space, with each parameter separated by a comma.\n" + + } + + + , + "metaeuk_rerun_parameters": { + "type": + "string", + "description": "Type: `string`, example: `--max-overlap=15,--min-exon-aa=15`. Pass additional arguments to Metaeuk for the second run (see Metaeuk documentation https://github", + "help_text": "Type: `string`, example: `--max-overlap=15,--min-exon-aa=15`. Pass additional arguments to Metaeuk for the second run (see Metaeuk documentation https://github.com/soedinglab/metaeuk).\nAll parameters should be contained within a single string with no white space, with each parameter separated by a comma.\n" + + } + + +} +}, + + + "nextflow input-output arguments" : { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + + + "publish_dir": { + "type": + "string", + "description": "Type: `string`, required, example: `output/`. Path to an output directory", + "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." + + } + + + , + "param_list": { + "type": + "string", + "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", + "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", + "hidden": true + + } + + +} +} +}, +"allOf": [ + + { + "$ref": "#/definitions/inputs" + }, + + { + "$ref": "#/definitions/outputs" + }, + + { + "$ref": "#/definitions/resource and run settings" + }, + + { + "$ref": "#/definitions/lineage dataset settings" + }, + + { + "$ref": "#/definitions/augustus settings" + }, + + { + "$ref": "#/definitions/bbtools settings" + }, + + { + "$ref": "#/definitions/blast settings" + }, + + { + "$ref": "#/definitions/protein gene prediction settings" + }, + + { + "$ref": "#/definitions/metaeuk settings" + }, + + { + "$ref": "#/definitions/nextflow input-output arguments" + } +] +} diff --git a/target/nextflow/cutadapt/.config.vsh.yaml b/target/nextflow/cutadapt/.config.vsh.yaml index 832549f0..eafbd954 100644 --- a/target/nextflow/cutadapt/.config.vsh.yaml +++ b/target/nextflow/cutadapt/.config.vsh.yaml @@ -305,6 +305,26 @@ argument_groups: \ If match is on reverse-complemented version,\noutput that one.\n" info: null direction: "input" +- name: "Demultiplexing options" + arguments: + - type: "string" + name: "--demultiplex_mode" + description: "Enable demultiplexing and set the mode for it.\nWith mode 'unique_dual',\ + \ adapters from the first and second read are used,\nand the indexes from the\ + \ reads are only used in pairs. This implies\n--pair_adapters.\nEnabling mode\ + \ 'combinatorial_dual' allows all combinations of the sets of indexes\non R1\ + \ and R2. It is necessary to write each read pair to an output\nfile depending\ + \ on the adapters found on both R1 and R2.\nMode 'single', uses indexes or barcodes\ + \ located at the 5'\nend of the R1 read (single). \n" + info: null + required: false + choices: + - "single" + - "unique_dual" + - "combinatorial_dual" + direction: "input" + multiple: false + multiple_sep: ";" - name: "Read modifications" arguments: - type: "integer" @@ -707,7 +727,7 @@ build_info: output: "target/nextflow/cutadapt" executable: "target/nextflow/cutadapt/main.nf" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/cutadapt/main.nf b/target/nextflow/cutadapt/main.nf index 9a25a4d2..b5d67657 100644 --- a/target/nextflow/cutadapt/main.nf +++ b/target/nextflow/cutadapt/main.nf @@ -3089,6 +3089,25 @@ meta = [ } ] }, + { + "name" : "Demultiplexing options", + "arguments" : [ + { + "type" : "string", + "name" : "--demultiplex_mode", + "description" : "Enable demultiplexing and set the mode for it.\nWith mode 'unique_dual', adapters from the first and second read are used,\nand the indexes from the reads are only used in pairs. This implies\n--pair_adapters.\nEnabling mode 'combinatorial_dual' allows all combinations of the sets of indexes\non R1 and R2. It is necessary to write each read pair to an output\nfile depending on the adapters found on both R1 and R2.\nMode 'single', uses indexes or barcodes located at the 5'\nend of the R1 read (single). \n", + "required" : false, + "choices" : [ + "single", + "unique_dual", + "combinatorial_dual" + ], + "direction" : "input", + "multiple" : false, + "multiple_sep" : ";" + } + ] + }, { "name" : "Read modifications", "arguments" : [ @@ -3549,7 +3568,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/cutadapt", "viash_version" : "0.9.0-RC6", - "git_commit" : "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a", + "git_commit" : "ec69d9af7a59c2618a49bef7d0bf9afc743ca065", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3618,6 +3637,7 @@ $( if [ ! -z ${VIASH_PAR_MATCH_READ_WILDCARDS+x} ]; then echo "${VIASH_PAR_MATCH $( if [ ! -z ${VIASH_PAR_NO_MATCH_ADAPTER_WILDCARDS+x} ]; then echo "${VIASH_PAR_NO_MATCH_ADAPTER_WILDCARDS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_no_match_adapter_wildcards='&'#" ; else echo "# par_no_match_adapter_wildcards="; fi ) $( if [ ! -z ${VIASH_PAR_ACTION+x} ]; then echo "${VIASH_PAR_ACTION}" | sed "s#'#'\\"'\\"'#g;s#.*#par_action='&'#" ; else echo "# par_action="; fi ) $( if [ ! -z ${VIASH_PAR_REVCOMP+x} ]; then echo "${VIASH_PAR_REVCOMP}" | sed "s#'#'\\"'\\"'#g;s#.*#par_revcomp='&'#" ; else echo "# par_revcomp="; fi ) +$( if [ ! -z ${VIASH_PAR_DEMULTIPLEX_MODE+x} ]; then echo "${VIASH_PAR_DEMULTIPLEX_MODE}" | sed "s#'#'\\"'\\"'#g;s#.*#par_demultiplex_mode='&'#" ; else echo "# par_demultiplex_mode="; fi ) $( if [ ! -z ${VIASH_PAR_CUT+x} ]; then echo "${VIASH_PAR_CUT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_cut='&'#" ; else echo "# par_cut="; fi ) $( if [ ! -z ${VIASH_PAR_CUT_R2+x} ]; then echo "${VIASH_PAR_CUT_R2}" | sed "s#'#'\\"'\\"'#g;s#.*#par_cut_r2='&'#" ; else echo "# par_cut_r2="; fi ) $( if [ ! -z ${VIASH_PAR_NEXTSEQ_TRIM+x} ]; then echo "${VIASH_PAR_NEXTSEQ_TRIM}" | sed "s#'#'\\"'\\"'#g;s#.*#par_nextseq_trim='&'#" ; else echo "# par_nextseq_trim="; fi ) @@ -3785,7 +3805,7 @@ mod_args=\\$(echo \\\\ \\${par_cut_r2:+--cut_r2 "\\${par_cut_r2}"} \\\\ \\${par_nextseq_trim:+--nextseq-trim "\\${par_nextseq_trim}"} \\\\ \\${par_quality_cutoff:+--quality-cutoff "\\${par_quality_cutoff}"} \\\\ - \\${par_quality_cutoff_r2:+--quality-cutoff_r2 "\\${par_quality_cutoff_r2}"} \\\\ + \\${par_quality_cutoff_r2:+-Q "\\${par_quality_cutoff_r2}"} \\\\ \\${par_quality_base:+--quality-base "\\${par_quality_base}"} \\\\ \\${par_poly_a:+--poly-a} \\\\ \\${par_length:+--length "\\${par_length}"} \\\\ @@ -3854,14 +3874,35 @@ else ext="fasta" fi -if [ \\$mode = "se" ]; then +demultiplex_mode="\\$par_demultiplex_mode" +if [[ \\$mode == "se" ]]; then + if [[ "\\$demultiplex_mode" == "unique_dual" ]] || [[ "\\$demultiplex_mode" == "combinatorial_dual" ]]; then + echo "Demultiplexing dual indexes is not possible with single-end data." + exit 1 + fi + prefix="trimmed_" + if [[ ! -z "\\$demultiplex_mode" ]]; then + prefix="{name}_" + fi output_args=\\$(echo \\\\ - --output "\\$output_dir/{name}_001.\\$ext" \\\\ + --output "\\$output_dir/\\${prefix}001.\\$ext" \\\\ ) else + demultiplex_indicator_r1='{name}_' + demultiplex_indicator_r2=\\$demultiplex_indicator_r1 + if [[ "\\$demultiplex_mode" == "combinatorial_dual" ]]; then + demultiplex_indicator_r1='{name1}_{name2}_' + demultiplex_indicator_r2='{name1}_{name2}_' + fi + prefix_r1="trimmed_" + prefix_r2="trimmed_" + if [[ ! -z "\\$demultiplex_mode" ]]; then + prefix_r1=\\$demultiplex_indicator_r1 + prefix_r2=\\$demultiplex_indicator_r2 + fi output_args=\\$(echo \\\\ - --output "\\$output_dir/{name}_R1_001.\\$ext" \\\\ - --paired-output "\\$output_dir/{name}_R2_001.\\$ext" \\\\ + --output "\\$output_dir/\\${prefix_r1}R1_001.\\$ext" \\\\ + --paired-output "\\$output_dir/\\${prefix_r2}R2_001.\\$ext" \\\\ ) fi diff --git a/target/nextflow/cutadapt/nextflow_schema.json b/target/nextflow/cutadapt/nextflow_schema.json index 2438aca0..d5f821f0 100644 --- a/target/nextflow/cutadapt/nextflow_schema.json +++ b/target/nextflow/cutadapt/nextflow_schema.json @@ -323,6 +323,28 @@ } +} +}, + + + "demultiplexing options" : { + "title": "Demultiplexing options", + "type": "object", + "description": "No description", + "properties": { + + + "demultiplex_mode": { + "type": + "string", + "description": "Type: `string`, choices: ``single`, `unique_dual`, `combinatorial_dual``. Enable demultiplexing and set the mode for it", + "help_text": "Type: `string`, choices: ``single`, `unique_dual`, `combinatorial_dual``. Enable demultiplexing and set the mode for it.\nWith mode \u0027unique_dual\u0027, adapters from the first and second read are used,\nand the indexes from the reads are only used in pairs. This implies\n--pair_adapters.\nEnabling mode \u0027combinatorial_dual\u0027 allows all combinations of the sets of indexes\non R1 and R2. It is necessary to write each read pair to an output\nfile depending on the adapters found on both R1 and R2.\nMode \u0027single\u0027, uses indexes or barcodes located at the 5\u0027\nend of the R1 read (single). \n", + "enum": ["single", "unique_dual", "combinatorial_dual"] + + + } + + } }, @@ -726,6 +748,10 @@ "$ref": "#/definitions/input parameters" }, + { + "$ref": "#/definitions/demultiplexing options" + }, + { "$ref": "#/definitions/read modifications" }, diff --git a/target/nextflow/falco/.config.vsh.yaml b/target/nextflow/falco/.config.vsh.yaml index 129962ed..87a4685c 100644 --- a/target/nextflow/falco/.config.vsh.yaml +++ b/target/nextflow/falco/.config.vsh.yaml @@ -304,7 +304,7 @@ build_info: output: "target/nextflow/falco" executable: "target/nextflow/falco/main.nf" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/falco/main.nf b/target/nextflow/falco/main.nf index fe95cc01..8361a59a 100644 --- a/target/nextflow/falco/main.nf +++ b/target/nextflow/falco/main.nf @@ -3119,7 +3119,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/falco", "viash_version" : "0.9.0-RC6", - "git_commit" : "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a", + "git_commit" : "ec69d9af7a59c2618a49bef7d0bf9afc743ca065", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/fastp/.config.vsh.yaml b/target/nextflow/fastp/.config.vsh.yaml index b6ac437f..9f0080a7 100644 --- a/target/nextflow/fastp/.config.vsh.yaml +++ b/target/nextflow/fastp/.config.vsh.yaml @@ -1065,7 +1065,7 @@ build_info: output: "target/nextflow/fastp" executable: "target/nextflow/fastp/main.nf" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/fastp/main.nf b/target/nextflow/fastp/main.nf index cd9e7912..088f1b09 100644 --- a/target/nextflow/fastp/main.nf +++ b/target/nextflow/fastp/main.nf @@ -3965,7 +3965,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/fastp", "viash_version" : "0.9.0-RC6", - "git_commit" : "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a", + "git_commit" : "ec69d9af7a59c2618a49bef7d0bf9afc743ca065", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/featurecounts/.config.vsh.yaml b/target/nextflow/featurecounts/.config.vsh.yaml index 86fd62af..ed8be6e9 100644 --- a/target/nextflow/featurecounts/.config.vsh.yaml +++ b/target/nextflow/featurecounts/.config.vsh.yaml @@ -631,7 +631,7 @@ build_info: output: "target/nextflow/featurecounts" executable: "target/nextflow/featurecounts/main.nf" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/featurecounts/main.nf b/target/nextflow/featurecounts/main.nf index 6d24e616..9a21be59 100644 --- a/target/nextflow/featurecounts/main.nf +++ b/target/nextflow/featurecounts/main.nf @@ -3497,7 +3497,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/featurecounts", "viash_version" : "0.9.0-RC6", - "git_commit" : "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a", + "git_commit" : "ec69d9af7a59c2618a49bef7d0bf9afc743ca065", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/gffread/.config.vsh.yaml b/target/nextflow/gffread/.config.vsh.yaml index bc485951..b9266842 100644 --- a/target/nextflow/gffread/.config.vsh.yaml +++ b/target/nextflow/gffread/.config.vsh.yaml @@ -671,7 +671,7 @@ build_info: output: "target/nextflow/gffread" executable: "target/nextflow/gffread/main.nf" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/gffread/main.nf b/target/nextflow/gffread/main.nf index d9420399..d1b6f325 100644 --- a/target/nextflow/gffread/main.nf +++ b/target/nextflow/gffread/main.nf @@ -3554,7 +3554,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/gffread", "viash_version" : "0.9.0-RC6", - "git_commit" : "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a", + "git_commit" : "ec69d9af7a59c2618a49bef7d0bf9afc743ca065", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml b/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml index 2cb1a9ec..53b228ee 100644 --- a/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml +++ b/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml @@ -489,7 +489,7 @@ build_info: output: "target/nextflow/lofreq/lofreq_call" executable: "target/nextflow/lofreq/lofreq_call/main.nf" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/lofreq/lofreq_call/main.nf b/target/nextflow/lofreq/lofreq_call/main.nf index 0ce10650..fafa53d0 100644 --- a/target/nextflow/lofreq/lofreq_call/main.nf +++ b/target/nextflow/lofreq/lofreq_call/main.nf @@ -3356,7 +3356,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/lofreq/lofreq_call", "viash_version" : "0.9.0-RC6", - "git_commit" : "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a", + "git_commit" : "ec69d9af7a59c2618a49bef7d0bf9afc743ca065", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml b/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml index b6b2fc14..442eebb9 100644 --- a/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml +++ b/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml @@ -197,7 +197,7 @@ build_info: output: "target/nextflow/lofreq/lofreq_indelqual" executable: "target/nextflow/lofreq/lofreq_indelqual/main.nf" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/lofreq/lofreq_indelqual/main.nf b/target/nextflow/lofreq/lofreq_indelqual/main.nf index a04ab274..aed6f29a 100644 --- a/target/nextflow/lofreq/lofreq_indelqual/main.nf +++ b/target/nextflow/lofreq/lofreq_indelqual/main.nf @@ -3019,7 +3019,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/lofreq/lofreq_indelqual", "viash_version" : "0.9.0-RC6", - "git_commit" : "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a", + "git_commit" : "ec69d9af7a59c2618a49bef7d0bf9afc743ca065", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/multiqc/.config.vsh.yaml b/target/nextflow/multiqc/.config.vsh.yaml index a260c2a5..ee588470 100644 --- a/target/nextflow/multiqc/.config.vsh.yaml +++ b/target/nextflow/multiqc/.config.vsh.yaml @@ -438,7 +438,7 @@ build_info: output: "target/nextflow/multiqc" executable: "target/nextflow/multiqc/main.nf" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/multiqc/main.nf b/target/nextflow/multiqc/main.nf index c5bf0d67..2450df8f 100644 --- a/target/nextflow/multiqc/main.nf +++ b/target/nextflow/multiqc/main.nf @@ -3310,7 +3310,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/multiqc", "viash_version" : "0.9.0-RC6", - "git_commit" : "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a", + "git_commit" : "ec69d9af7a59c2618a49bef7d0bf9afc743ca065", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/pear/.config.vsh.yaml b/target/nextflow/pear/.config.vsh.yaml index de564430..cf3ca163 100644 --- a/target/nextflow/pear/.config.vsh.yaml +++ b/target/nextflow/pear/.config.vsh.yaml @@ -380,7 +380,7 @@ build_info: output: "target/nextflow/pear" executable: "target/nextflow/pear/main.nf" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/pear/main.nf b/target/nextflow/pear/main.nf index 047c8997..02afb1b5 100644 --- a/target/nextflow/pear/main.nf +++ b/target/nextflow/pear/main.nf @@ -3201,7 +3201,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/pear", "viash_version" : "0.9.0-RC6", - "git_commit" : "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a", + "git_commit" : "ec69d9af7a59c2618a49bef7d0bf9afc743ca065", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/salmon/salmon_index/.config.vsh.yaml b/target/nextflow/salmon/salmon_index/.config.vsh.yaml index 9a20c5fc..e8ee5f45 100644 --- a/target/nextflow/salmon/salmon_index/.config.vsh.yaml +++ b/target/nextflow/salmon/salmon_index/.config.vsh.yaml @@ -263,7 +263,7 @@ build_info: output: "target/nextflow/salmon/salmon_index" executable: "target/nextflow/salmon/salmon_index/main.nf" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/salmon/salmon_index/main.nf b/target/nextflow/salmon/salmon_index/main.nf index fb5deb37..5834c64d 100644 --- a/target/nextflow/salmon/salmon_index/main.nf +++ b/target/nextflow/salmon/salmon_index/main.nf @@ -3077,7 +3077,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/salmon/salmon_index", "viash_version" : "0.9.0-RC6", - "git_commit" : "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a", + "git_commit" : "ec69d9af7a59c2618a49bef7d0bf9afc743ca065", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/salmon/salmon_quant/.config.vsh.yaml b/target/nextflow/salmon/salmon_quant/.config.vsh.yaml index ce60d78f..b17290e3 100644 --- a/target/nextflow/salmon/salmon_quant/.config.vsh.yaml +++ b/target/nextflow/salmon/salmon_quant/.config.vsh.yaml @@ -1159,7 +1159,7 @@ build_info: output: "target/nextflow/salmon/salmon_quant" executable: "target/nextflow/salmon/salmon_quant/main.nf" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/salmon/salmon_quant/main.nf b/target/nextflow/salmon/salmon_quant/main.nf index 6c39719c..a6ad01ef 100644 --- a/target/nextflow/salmon/salmon_quant/main.nf +++ b/target/nextflow/salmon/salmon_quant/main.nf @@ -3912,7 +3912,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/salmon/salmon_quant", "viash_version" : "0.9.0-RC6", - "git_commit" : "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a", + "git_commit" : "ec69d9af7a59c2618a49bef7d0bf9afc743ca065", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/salmon/salmon_quant/nextflow_schema.json b/target/nextflow/salmon/salmon_quant/nextflow_schema.json new file mode 100644 index 00000000..80b21398 --- /dev/null +++ b/target/nextflow/salmon/salmon_quant/nextflow_schema.json @@ -0,0 +1,1119 @@ +{ +"$schema": "http://json-schema.org/draft-07/schema", +"title": "salmon_quant", +"description": "Salmon is a tool for wicked-fast transcript quantification from RNA-seq data. It can either make use of pre-computed alignments (in the form of a SAM/BAM file) to the transcripts rather than the raw reads, or can be run in the mapping-based mode. \n", +"type": "object", +"definitions": { + + + + "common input options" : { + "title": "Common input options", + "type": "object", + "description": "No description", + "properties": { + + + "lib_type": { + "type": + "string", + "description": "Type: `string`, default: `A`, choices: ``A`, `U`, `SF`, `SR`, `IU`, `IS`, `ISF`, `ISR`, `OU`, `OS`, `OSF`, `OSR`, `MU`, `MS`, `MSF`, `MSR``. Format string describing the library", + "help_text": "Type: `string`, default: `A`, choices: ``A`, `U`, `SF`, `SR`, `IU`, `IS`, `ISF`, `ISR`, `OU`, `OS`, `OSF`, `OSR`, `MU`, `MS`, `MSF`, `MSR``. Format string describing the library.\nThe library type string consists of three parts: \n1. Relative orientation of the reads: This part is only provided if the library is paired-end, THe possible options are\n I = inward\n O = outward\n M = matching\n2. Strandedness of the library: This part specifies whether the protocol is stranded or unstranded. The options are:\n S = stranded\n U = unstranded\n3. Directionality of the reads: If the library is stranded, the final part of the library string is used to specify the strand from which the read originates. The possible values are\n F = read 1 (or single-end read) comes from the forward strand\n R = read 1 (or single-end read) comes from the reverse strand\n", + "enum": ["A", "U", "SF", "SR", "IU", "IS", "ISF", "ISR", "OU", "OS", "OSF", "OSR", "MU", "MS", "MSF", "MSR"] + + , + "default": "A" + } + + +} +}, + + + "mapping input options" : { + "title": "Mapping input options", + "type": "object", + "description": "No description", + "properties": { + + + "index": { + "type": + "string", + "description": "Type: `file`, example: `transcriptome_index`. Salmon index", + "help_text": "Type: `file`, example: `transcriptome_index`. Salmon index.\n" + + } + + + , + "unmated_reads": { + "type": + "string", + "description": "Type: List of `file`, example: `sample.fq.gz`, multiple_sep: `\":\"`. List of files containing unmated reads of (e", + "help_text": "Type: List of `file`, example: `sample.fq.gz`, multiple_sep: `\":\"`. List of files containing unmated reads of (e.g. single-end reads).\n" + + } + + + , + "mates1": { + "type": + "string", + "description": "Type: List of `file`, example: `sample_1.fq.gz`, multiple_sep: `\":\"`. File containing the #1 mates", + "help_text": "Type: List of `file`, example: `sample_1.fq.gz`, multiple_sep: `\":\"`. File containing the #1 mates.\n" + + } + + + , + "mates2": { + "type": + "string", + "description": "Type: List of `file`, example: `sample_2.fq.gz`, multiple_sep: `\":\"`. File containing the #2 mates", + "help_text": "Type: List of `file`, example: `sample_2.fq.gz`, multiple_sep: `\":\"`. File containing the #2 mates.\n" + + } + + +} +}, + + + "alignment input options" : { + "title": "Alignment input options", + "type": "object", + "description": "No description", + "properties": { + + + "discard_orphans": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Discard orphan alignments in the input [for alignment-based mode only]", + "help_text": "Type: `boolean_true`, default: `false`. Discard orphan alignments in the input [for alignment-based mode only]. If this flag is passed, then only paired alignments will be considered toward quantification estimates. The default behavior is to consider orphan alignments if no valid paired mappings exist.\n" + , + "default": "False" + } + + + , + "alignments": { + "type": + "string", + "description": "Type: List of `file`, example: `sample.fq.gz`, multiple_sep: `\":\"`. Input alignment (BAM) file(s)", + "help_text": "Type: List of `file`, example: `sample.fq.gz`, multiple_sep: `\":\"`. Input alignment (BAM) file(s).\n" + + } + + + , + "eqclasses": { + "type": + "string", + "description": "Type: `file`. input salmon weighted equivalence class file", + "help_text": "Type: `file`. input salmon weighted equivalence class file.\n" + + } + + + , + "targets": { + "type": + "string", + "description": "Type: `file`, example: `transcripts.fasta`. FASTA format file containing target transcripts", + "help_text": "Type: `file`, example: `transcripts.fasta`. FASTA format file containing target transcripts.\n" + + } + + + , + "ont": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Use alignment model for Oxford Nanopore long reads\n", + "help_text": "Type: `boolean_true`, default: `false`. Use alignment model for Oxford Nanopore long reads\n" + , + "default": "False" + } + + +} +}, + + + "output" : { + "title": "Output", + "type": "object", + "description": "No description", + "properties": { + + + "output": { + "type": + "string", + "description": "Type: `file`, required, default: `$id.$key.output.output`, example: `quant_output`. Output quantification directory", + "help_text": "Type: `file`, required, default: `$id.$key.output.output`, example: `quant_output`. Output quantification directory.\n" + , + "default": "$id.$key.output.output" + } + + + , + "quant_results": { + "type": + "string", + "description": "Type: `file`, required, default: `$id.$key.quant_results.sf`, example: `quant.sf`. Salmon quantification file", + "help_text": "Type: `file`, required, default: `$id.$key.quant_results.sf`, example: `quant.sf`. Salmon quantification file.\n" + , + "default": "$id.$key.quant_results.sf" + } + + +} +}, + + + "basic options" : { + "title": "Basic options", + "type": "object", + "description": "No description", + "properties": { + + + "seq_bias": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Perform sequence-specific bias correction", + "help_text": "Type: `boolean_true`, default: `false`. Perform sequence-specific bias correction.\n" + , + "default": "False" + } + + + , + "gc_bias": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Perform fragment GC bias correction [beta for single-end reads]", + "help_text": "Type: `boolean_true`, default: `false`. Perform fragment GC bias correction [beta for single-end reads].\n" + , + "default": "False" + } + + + , + "pos_bias": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Perform positional bias correction", + "help_text": "Type: `boolean_true`, default: `false`. Perform positional bias correction.\n" + , + "default": "False" + } + + + , + "incompat_prior": { + "type": + "number", + "description": "Type: `double`, example: `0`. Set the prior probability that an alignment that disagrees with the specified library type (--lib_type) results from the true fragment origin", + "help_text": "Type: `double`, example: `0`. Set the prior probability that an alignment that disagrees with the specified library type (--lib_type) results from the true fragment origin. Setting this to 0 specifies that alignments that disagree with the library type should be \"impossible\", while setting it to 1 says that alignments that disagree with the library type are no less likely than those that do.\n" + + } + + + , + "gene_map": { + "type": + "string", + "description": "Type: `file`, example: `gene_map.gtf`. File containing a mapping of transcripts to genes", + "help_text": "Type: `file`, example: `gene_map.gtf`. File containing a mapping of transcripts to genes. If this file is provided salmon will output both quant.sf and quant.genes.sf files, where the latter contains aggregated gene-level abundance estimates. The transcript to gene mapping should be provided as either a GTF file, or a in a simple tab-delimited format where each line contains the name of a transcript and the gene to which it belongs separated by a tab. The extension of the file is used to determine how the file should be parsed. Files ending in \u0027.gtf\u0027, \u0027.gff\u0027 or \u0027.gff3\u0027 are assumed to be in GTF format; files with any other extension are assumed to be in the simple format. In GTF / GFF format, the \"transcript_id\" is assumed to contain the transcript identifier and the \"gene_id\" is assumed to contain the corresponding gene identifier.\n" + + } + + + , + "aux_target_file": { + "type": + "string", + "description": "Type: `file`, example: `auxilary_targets.txt`. A file containing a list of \"auxiliary\" targets", + "help_text": "Type: `file`, example: `auxilary_targets.txt`. A file containing a list of \"auxiliary\" targets. These are valid targets (i.e., not decoys) to which fragments are allowed to map and be assigned, and which will be quantified, but for which auxiliary models like sequence-specific and fragment-GC bias correction should not be applied.\n" + + } + + + , + "meta": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. If you\u0027re using Salmon on a metagenomic dataset, consider setting this flag to disable parts of the abundance estimation model that make less sense for metagenomic data", + "help_text": "Type: `boolean_true`, default: `false`. If you\u0027re using Salmon on a metagenomic dataset, consider setting this flag to disable parts of the abundance estimation model that make less sense for metagenomic data.\n" + , + "default": "False" + } + + + , + "score_exp": { + "type": + "number", + "description": "Type: `double`, example: `1`. The factor by which sub-optimal alignment scores are downweighted to produce a probability", + "help_text": "Type: `double`, example: `1`. The factor by which sub-optimal alignment scores are downweighted to produce a probability. If the best alignment score for the current read is S, and the score for a particular alignment is w, then the probability will be computed porportional to exp( - scoreExp * (S-w) ).\n" + + } + + +} +}, + + + "options specific to mapping mode" : { + "title": "Options specific to mapping mode", + "type": "object", + "description": "No description", + "properties": { + + + "discard_orphans_quasi": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nDiscard orphan mappings in selective-alignment mode", + "help_text": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nDiscard orphan mappings in selective-alignment mode. If this flag is passed then only paired mappings will be considered toward quantification estimates. The default behavior is to consider orphan mappings if no valid paired mappings exist. This flag is independent of the option to write the orphaned mappings to file (--writeOrphanLinks).\n" + , + "default": "False" + } + + + , + "consensus_slack": { + "type": + "number", + "description": "Type: `double`, example: `0.35`. [selective-alignment mode only] \nThe amount of slack allowed in the selective-alignment filtering mechanism", + "help_text": "Type: `double`, example: `0.35`. [selective-alignment mode only] \nThe amount of slack allowed in the selective-alignment filtering mechanism. If this is set to a fraction, X, greater than 0 (and in [0,1)), then uniMEM chains with scores below (100 * X)% of the best chain score for a read, and read pairs with a sum of chain scores below (100 * X)% of the best chain score for a read pair will be discounted as a mapping candidates. The default value of this option is 0.35.\n" + + } + + + , + "pre_merge_chain_sub_thresh": { + "type": + "number", + "description": "Type: `double`, example: `0.75`. [selective-alignment mode only] \nThe threshold of sub-optimal chains, compared to the best chain on a given target, that will be retained and passed to the next phase of mapping", + "help_text": "Type: `double`, example: `0.75`. [selective-alignment mode only] \nThe threshold of sub-optimal chains, compared to the best chain on a given target, that will be retained and passed to the next phase of mapping. Specifically, if the best chain for a read (or read-end in paired-end mode) to target t has score X_t, then all chains for this read with score \u003e= X_t * preMergeChainSubThresh will be retained and passed to subsequent mapping phases. This value must be in the range [0, 1].\n" + + } + + + , + "post_merge_chain_sub_thresh": { + "type": + "number", + "description": "Type: `double`, example: `0.9`. [selective-alignment mode only] \nThe threshold of sub-optimal chains, compared to the best chain on a given target, that will be retained and passed to the next phase of mapping", + "help_text": "Type: `double`, example: `0.9`. [selective-alignment mode only] \nThe threshold of sub-optimal chains, compared to the best chain on a given target, that will be retained and passed to the next phase of mapping. This is different than post_merge_chain_sub_thresh, because this is applied to pairs of chains (from the ends of paired-end reads) after merging (i.e. after checking concordancy constraints etc.). Specifically, if the best chain pair to target t has score X_t, then all chain pairs for this read pair with score \u003e= X_t * post_merge_chain_sub_thresh will be retained and passed to subsequent mapping phases. This value must be in the range [0, 1]. Note: This option is only meaningful for paired-end libraries, and is ignored for single-end libraries.\n" + + } + + + , + "orphan_chain_sub_thresh": { + "type": + "number", + "description": "Type: `double`, example: `0.95`. [selective-alignment mode only]\nThis threshold sets a global sub-optimality threshold for chains corresponding to orphan mappings", + "help_text": "Type: `double`, example: `0.95`. [selective-alignment mode only]\nThis threshold sets a global sub-optimality threshold for chains corresponding to orphan mappings. That is, if the merging procedure results in no concordant mappings then only orphan mappings with a chain score \u003e= orphan_chain_sub_thresh * bestChainScore will be retained and passed to subsequent mapping phases. This value must be in the range [0, 1]. Note: This option is only meaningful for paired-end libraries, and is ignored for single-end libraries.\n" + + } + + + , + "min_score_fraction": { + "type": + "number", + "description": "Type: `double`, example: `0.65`. [selective-alignment mode only]\nThe fraction of the optimal possible alignment score that a mapping must achieve in order to be considered \"valid\" --- should be in (0,1]", + "help_text": "Type: `double`, example: `0.65`. [selective-alignment mode only]\nThe fraction of the optimal possible alignment score that a mapping must achieve in order to be considered \"valid\" --- should be in (0,1]. Default 0.65\n" + + } + + + , + "mismatch_seed_skip": { + "type": + "integer", + "description": "Type: `integer`, example: `3`. [selective-alignment mode only]\nAfter a k-mer hit is extended to a uni-MEM, the uni-MEM extension can terminate for one of 3 reasons; the end of the read, the end of the unitig, or a mismatch", + "help_text": "Type: `integer`, example: `3`. [selective-alignment mode only]\nAfter a k-mer hit is extended to a uni-MEM, the uni-MEM extension can terminate for one of 3 reasons; the end of the read, the end of the unitig, or a mismatch. If the extension ends because of a mismatch, this is likely the result of a sequencing error. To avoid looking up many k-mers that will likely fail to be located in the index, the search procedure skips by a factor of mismatch_seed_skip until it either (1) finds another match or (2) is k-bases past the mismatch position. This value controls that skip length. A smaller value can increase sensitivity, while a larger value can speed up seeding.\n" + + } + + + , + "disable_chaining_heuristic": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nBy default, the heuristic of (Li 2018) is implemented, which terminates the chaining DP once a given number of valid backpointers are found", + "help_text": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nBy default, the heuristic of (Li 2018) is implemented, which terminates the chaining DP once a given number of valid backpointers are found. This speeds up the seed (MEM) chaining step, but may result in sub-optimal chains in complex situations (e.g. sequences with many repeats and overlapping repeats). Passing this flag will disable the chaining heuristic, and perform the full chaining dynamic program, guaranteeing the optimal chain is found in this step.\n" + , + "default": "False" + } + + + , + "decoy_threshold": { + "type": + "number", + "description": "Type: `double`, example: `1`. [selective-alignment mode only]\nFor an alignemnt to an annotated transcript to be considered invalid, it must have an alignment score \u003c (decoy_threshold * bestDecoyScore)", + "help_text": "Type: `double`, example: `1`. [selective-alignment mode only]\nFor an alignemnt to an annotated transcript to be considered invalid, it must have an alignment score \u003c (decoy_threshold * bestDecoyScore). A value of 1.0 means that any alignment strictly worse than the best decoy alignment will be discarded. A smaller value will allow reads to be allocated to transcripts even if they strictly align better to the decoy sequence.\n" + + } + + + , + "ma": { + "type": + "integer", + "description": "Type: `integer`, example: `2`. [selective-alignment mode only]\nThe value given to a match between read and reference nucleotides in an alignment", + "help_text": "Type: `integer`, example: `2`. [selective-alignment mode only]\nThe value given to a match between read and reference nucleotides in an alignment.\n" + + } + + + , + "mp": { + "type": + "integer", + "description": "Type: `integer`, example: `-4`. [selective-alignment mode only]\nThe value given to a mis-match between read and reference nucleotides in an alignment", + "help_text": "Type: `integer`, example: `-4`. [selective-alignment mode only]\nThe value given to a mis-match between read and reference nucleotides in an alignment.\n" + + } + + + , + "go": { + "type": + "integer", + "description": "Type: `integer`, example: `6`. [selective-alignment mode only]\nThe value given to a gap opening in an alignment", + "help_text": "Type: `integer`, example: `6`. [selective-alignment mode only]\nThe value given to a gap opening in an alignment.\n" + + } + + + , + "ge": { + "type": + "integer", + "description": "Type: `integer`, example: `2`. [selective-alignment mode only]\nThe value given to a gap extension in an alignment", + "help_text": "Type: `integer`, example: `2`. [selective-alignment mode only]\nThe value given to a gap extension in an alignment.\n" + + } + + + , + "bandwidth": { + "type": + "integer", + "description": "Type: `integer`, example: `15`. [selective-alignment mode only]\nThe value used for the bandwidth passed to ksw2", + "help_text": "Type: `integer`, example: `15`. [selective-alignment mode only]\nThe value used for the bandwidth passed to ksw2. A smaller bandwidth can make the alignment verification run more quickly, but could possibly miss valid alignments.\n" + + } + + + , + "allow_dovetail": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nAllow dovetailing mappings", + "help_text": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nAllow dovetailing mappings.\n" + , + "default": "False" + } + + + , + "recover_orphans": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nAttempt to recover the mates of orphaned reads", + "help_text": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nAttempt to recover the mates of orphaned reads. This uses edlib for orphan recovery, and so introduces some computational overhead, but it can improve sensitivity.\n" + , + "default": "False" + } + + + , + "mimicBT2": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nSet flags to mimic parameters similar to Bowtie2 with --no-discordant and --no-mixed flags", + "help_text": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nSet flags to mimic parameters similar to Bowtie2 with --no-discordant and --no-mixed flags. This increases disallows dovetailing reads, and discards orphans. Note, this does not impose the very strict parameters assumed by RSEM+Bowtie2, like gapless alignments. For that behavior, use the --mimic_strictBT2 flag below.\n" + , + "default": "False" + } + + + , + "mimic_strictBT2": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nSet flags to mimic the very strict parameters used by RSEM+Bowtie2", + "help_text": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nSet flags to mimic the very strict parameters used by RSEM+Bowtie2. This increases --min_score_fraction to 0.8, disallows dovetailing reads, discards orphans, and disallows gaps in alignments.\n" + , + "default": "False" + } + + + , + "softclip": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nAllos soft-clipping of reads during selective-alignment", + "help_text": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nAllos soft-clipping of reads during selective-alignment. If this option is provided, then regions at the beginning or end of the read can be withheld from alignment without any effect on the resulting score (i.e. neither adding nor removing from the score). This will drastically reduce the penalty if there are mismatches at the beginning or end of the read due to e.g. low-quality bases or adapters. NOTE: Even with soft-clipping enabled, the read must still achieve a score of at least min_score_fraction * maximum achievable score, where the maximum achievable score is computed based on the full (un-clipped) read length.\n" + , + "default": "False" + } + + + , + "softclip_overhangs": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nAllow soft-clipping of reads that overhang the beginning or ends of the transcript", + "help_text": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nAllow soft-clipping of reads that overhang the beginning or ends of the transcript. In this case, the overhaning section of the read will simply be unaligned, and will not contribute or detract from the alignment score. The default policy is to force an end-to-end alignment of the entire read, so that overhanings will result in some deletion of nucleotides from the read.\n" + , + "default": "False" + } + + + , + "full_length_alignment": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nPerform selective alignment over the full length of the read, beginning from the (approximate) initial mapping location and using extension alignment", + "help_text": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nPerform selective alignment over the full length of the read, beginning from the (approximate) initial mapping location and using extension alignment. This is in contrast with the default behavior which is to only perform alignment between the MEMs in the optimal chain (and before the first and after the last MEM if applicable). The default strategy forces the MEMs to belong to the alignment, but has the benefit that it can discover indels prior to the first hit shared between the read and reference. Except in very rare circumstances, the default mode should be more accurate.\n" + , + "default": "False" + } + + + , + "hard_filter": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nInstead of weighting mappings by their alignment score, this flag will discard any mappings with sub-optimal alignment score", + "help_text": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nInstead of weighting mappings by their alignment score, this flag will discard any mappings with sub-optimal alignment score. The default option of soft-filtering (i.e. weighting mappings by their alignment score) usually yields slightly more accurate abundance estimates but this flag may be desirable if you want more accurate \u0027naive\u0027 equivalence classes, rather than range factorized equivalence classes.\n" + , + "default": "False" + } + + + , + "min_aln_prob": { + "type": + "number", + "description": "Type: `double`, example: `1.0E-5`. The minimum number of fragments that must be assigned to the transcriptome for quantification to proceed", + "help_text": "Type: `double`, example: `1.0E-5`. The minimum number of fragments that must be assigned to the transcriptome for quantification to proceed.\n" + + } + + + , + "write_mappings": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. If this option is provided, then the selective-alignment results will be written out in SAM-compatible format", + "help_text": "Type: `boolean_true`, default: `false`. If this option is provided, then the selective-alignment results will be written out in SAM-compatible format. By default, output will be directed to stdout, but an alternative file name can be provided instead.\n" + , + "default": "False" + } + + + , + "mapping_sam": { + "type": + "string", + "description": "Type: `file`, default: `$id.$key.mapping_sam.sam`, example: `mappings.sam`. Path to file that should output the selective-alignment results in SAM-compatible format", + "help_text": "Type: `file`, default: `$id.$key.mapping_sam.sam`, example: `mappings.sam`. Path to file that should output the selective-alignment results in SAM-compatible format. THis option must be provided while using --write_mappings" + , + "default": "$id.$key.mapping_sam.sam" + } + + + , + "write_qualities": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. This flag only has meaning if mappings are being written (with --write_mappings/-z)", + "help_text": "Type: `boolean_true`, default: `false`. This flag only has meaning if mappings are being written (with --write_mappings/-z). If this flag is provided, then the output SAM file will contain quality strings as well as read sequences. Note that this can greatly increase the size of the output file.\n" + , + "default": "False" + } + + + , + "hit_filter_policy": { + "type": + "string", + "description": "Type: `string`, example: `AFTER`, choices: ``BEFORE`, `AFTER`, `BOTH`, `NONE``. [selective-alignment mode only]\nDetermines the policy by which hits are filtered in selective alignment", + "help_text": "Type: `string`, example: `AFTER`, choices: ``BEFORE`, `AFTER`, `BOTH`, `NONE``. [selective-alignment mode only]\nDetermines the policy by which hits are filtered in selective alignment. Filtering hits after chaining (the default) is more sensitive, but more computationally intensive, because it performs the chaining dynamic program for all hits. Filtering before chaining is faster, but some true hits may be missed. The options are BEFORE, AFTER, BOTH and NONE.\n", + "enum": ["BEFORE", "AFTER", "BOTH", "NONE"] + + + } + + +} +}, + + + "advance options" : { + "title": "Advance options", + "type": "object", + "description": "No description", + "properties": { + + + "alternative_init_mode": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Use an alternative strategy (rather than simple interpolation between) the online and uniform abundance estimates to initialize the EM / VBEM algorithm", + "help_text": "Type: `boolean_true`, default: `false`. Use an alternative strategy (rather than simple interpolation between) the online and uniform abundance estimates to initialize the EM / VBEM algorithm.\n" + , + "default": "False" + } + + + , + "aux_dir": { + "type": + "string", + "description": "Type: `file`, default: `$id.$key.aux_dir.aux_dir`, example: `aux_info`. The sub-directory of the quantification directory where auxiliary information e", + "help_text": "Type: `file`, default: `$id.$key.aux_dir.aux_dir`, example: `aux_info`. The sub-directory of the quantification directory where auxiliary information e.g. bootstraps, bias parameters, etc. will be written.\n" + , + "default": "$id.$key.aux_dir.aux_dir" + } + + + , + "skip_quant": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Skip performing the actual transcript quantification (including any Gibbs sampling or bootstrapping)", + "help_text": "Type: `boolean_true`, default: `false`. Skip performing the actual transcript quantification (including any Gibbs sampling or bootstrapping).\n" + , + "default": "False" + } + + + , + "dump_eq": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Dump the simple equivalence class counts that were computed during mapping or alignment", + "help_text": "Type: `boolean_true`, default: `false`. Dump the simple equivalence class counts that were computed during mapping or alignment.\n" + , + "default": "False" + } + + + , + "dump_eq_weights": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Dump conditional probabilities associated with transcripts when equivalence class information is being dumped to file", + "help_text": "Type: `boolean_true`, default: `false`. Dump conditional probabilities associated with transcripts when equivalence class information is being dumped to file. Note, this will dump the factorization that is actually used by salmon\u0027s offline phase for inference. If you are using range-factorized equivalence classes (the default) then the same transcript set may appear multiple times with different associated conditional probabilities.\n" + , + "default": "False" + } + + + , + "min_assigned_frags": { + "type": + "integer", + "description": "Type: `integer`, example: `10`. The minimum number of fragments that must be assigned to the transcriptome for quantification to proceed", + "help_text": "Type: `integer`, example: `10`. The minimum number of fragments that must be assigned to the transcriptome for quantification to proceed.\n" + + } + + + , + "reduce_GC_memory": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. If this option is selected, a more memory efficient (but slightly slower) representation is used to compute fragment GC content", + "help_text": "Type: `boolean_true`, default: `false`. If this option is selected, a more memory efficient (but slightly slower) representation is used to compute fragment GC content. Enabling this will reduce memory usage, but can also reduce speed. However, the results themselves will remain the same.\n" + , + "default": "False" + } + + + , + "bias_speed_samp": { + "type": + "integer", + "description": "Type: `integer`, example: `5`. The value at which the fragment length PMF is down-sampled when evaluating sequence-specific \u0026 GC fragment bias", + "help_text": "Type: `integer`, example: `5`. The value at which the fragment length PMF is down-sampled when evaluating sequence-specific \u0026 GC fragment bias. Larger values speed up effective length correction, but may decrease the fidelity of bias modeling results.\n" + + } + + + , + "fld_max": { + "type": + "integer", + "description": "Type: `integer`, example: `1000`. The maximum fragment length to consider when building the empirical distribution\n", + "help_text": "Type: `integer`, example: `1000`. The maximum fragment length to consider when building the empirical distribution\n" + + } + + + , + "fld_mean": { + "type": + "integer", + "description": "Type: `integer`, example: `250`. The mean used in the fragment length distribution prior\n", + "help_text": "Type: `integer`, example: `250`. The mean used in the fragment length distribution prior\n" + + } + + + , + "fld_SD": { + "type": + "integer", + "description": "Type: `integer`, example: `25`. The standard deviation used in the fragment length distribution prior\n", + "help_text": "Type: `integer`, example: `25`. The standard deviation used in the fragment length distribution prior\n" + + } + + + , + "forgetting_factor": { + "type": + "number", + "description": "Type: `double`, example: `0.65`. The forgetting factor used in the online learning schedule", + "help_text": "Type: `double`, example: `0.65`. The forgetting factor used in the online learning schedule. A smallervalue results in quicker learning, but higher variance and may be unstable. A larger value results in slower learning but may be more stable. Value should be in the interval (0.5, 1.0].\n" + + } + + + , + "init_uniform": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Initialize the offline inference with uniform parameters, rather than seeding with online parameters", + "help_text": "Type: `boolean_true`, default: `false`. Initialize the offline inference with uniform parameters, rather than seeding with online parameters.\n" + , + "default": "False" + } + + + , + "max_occs_per_hit": { + "type": + "integer", + "description": "Type: `integer`, example: `1000`. When collecting \"hits\" (MEMs), hits having more than max_occs_per_hit occurrences won\u0027t be considered", + "help_text": "Type: `integer`, example: `1000`. When collecting \"hits\" (MEMs), hits having more than max_occs_per_hit occurrences won\u0027t be considered.\n" + + } + + + , + "max_read_occ": { + "type": + "integer", + "description": "Type: `integer`, example: `200`. Reads \"mapping\" to more than this many places won\u0027t be considered", + "help_text": "Type: `integer`, example: `200`. Reads \"mapping\" to more than this many places won\u0027t be considered.\n" + + } + + + , + "no_length_correction": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Entirely disables length correction when estimating the abundance of transcripts", + "help_text": "Type: `boolean_true`, default: `false`. Entirely disables length correction when estimating the abundance of transcripts. This option can be used with protocols where one expects that fragments derive from their underlying targets without regard to that target\u0027s length (e.g. QuantSeq)\n" + , + "default": "False" + } + + + , + "no_effective_length_correction": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Disables effective length correction when computing the probability that a fragment was generated from a transcript", + "help_text": "Type: `boolean_true`, default: `false`. Disables effective length correction when computing the probability that a fragment was generated from a transcript. If this flag is passed in,the fragment length distribution is not taken into account when computing this probability.\n" + , + "default": "False" + } + + + , + "no_single_frag_prob": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Disables the estimation of an associated fragment length probability for single-end reads or for orphaned mappings in paired-end libraries", + "help_text": "Type: `boolean_true`, default: `false`. Disables the estimation of an associated fragment length probability for single-end reads or for orphaned mappings in paired-end libraries. The default behavior is to consider the probability of all possible fragment lengths associated with the retained mapping. Enabling this flag (i.e. turning this default behavior off) will simply not attempt to estimate a fragment length probability in such cases.\n" + , + "default": "False" + } + + + , + "no_frag_length_dist": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Don\u0027t consider concordance with the learned fragment length distribution when trying to determine the probability that a fragment has originated from a specified location", + "help_text": "Type: `boolean_true`, default: `false`. Don\u0027t consider concordance with the learned fragment length distribution when trying to determine the probability that a fragment has originated from a specified location. Normally, Fragments with unlikely lengths will be assigned a smaller relative probability than those with more likely lengths. When this flag is passed in, the observed fragment length has no effect on that fragment\u0027s a priori probability.\n" + , + "default": "False" + } + + + , + "no_bias_length_threshold": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. If this option is enabled, then no (lower) threshold will be set on how short bias correction can make effective lengths", + "help_text": "Type: `boolean_true`, default: `false`. If this option is enabled, then no (lower) threshold will be set on how short bias correction can make effective lengths. This can increase the precision of bias correction, but harm robustness. The default correction applies a threshold.\n" + , + "default": "False" + } + + + , + "num_bias_samples": { + "type": + "integer", + "description": "Type: `integer`, example: `2000000`. Number of fragment mappings to use when learning the sequence-specific bias model", + "help_text": "Type: `integer`, example: `2000000`. Number of fragment mappings to use when learning the sequence-specific bias model.\n" + + } + + + , + "num_aux_model_samples": { + "type": + "integer", + "description": "Type: `integer`, example: `5000000`. The first \u003cnum_aux_model_samples\u003e are used to train the auxiliary model parameters (e", + "help_text": "Type: `integer`, example: `5000000`. The first \u003cnum_aux_model_samples\u003e are used to train the auxiliary model parameters (e.g. fragment length distribution, bias, etc.). After ther first \u003cnum_aux_model_samples\u003e observations the auxiliary model parameters will be assumed to have converged and will be fixed.\n" + + } + + + , + "num_pre_aux_model_samples": { + "type": + "integer", + "description": "Type: `integer`, example: `5000`. The first \u003cnumPreAuxModelSamples\u003e will have their assignment likelihoods and contributions to the transcript abundances computed without applying any auxiliary models", + "help_text": "Type: `integer`, example: `5000`. The first \u003cnumPreAuxModelSamples\u003e will have their assignment likelihoods and contributions to the transcript abundances computed without applying any auxiliary models. The purpose of ignoring the auxiliary models for the first \u003cnum_pre_aux_model_samples\u003e observations is to avoid applying these models before their parameters have been learned sufficiently well.\n" + + } + + + , + "useEM": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Use the traditional EM algorithm for optimization in the batch passes", + "help_text": "Type: `boolean_true`, default: `false`. Use the traditional EM algorithm for optimization in the batch passes.\n" + , + "default": "False" + } + + + , + "useVBOpt": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Use the Variational Bayesian EM [default]\n", + "help_text": "Type: `boolean_true`, default: `false`. Use the Variational Bayesian EM [default]\n" + , + "default": "False" + } + + + , + "range_factorization_bins": { + "type": + "integer", + "description": "Type: `integer`, example: `4`. Factorizes the likelihood used in quantification by adopting a new notion of equivalence classes based on the conditional probabilities with which fragments are generated from different transcripts", + "help_text": "Type: `integer`, example: `4`. Factorizes the likelihood used in quantification by adopting a new notion of equivalence classes based on the conditional probabilities with which fragments are generated from different transcripts. This is a more fine-grained factorization than the normal rich equivalence classes. The default value (4) corresponds to the default used in Zakeri et al. 2017 (doi: 10.1093/bioinformatics/btx262), and larger values imply a more fine-grained factorization. If range factorization is enabled, a common value to select for this parameter is 4. A value of 0 signifies the use of basic rich equivalence classes.\n" + + } + + + , + "num_Gibbs_samples": { + "type": + "integer", + "description": "Type: `integer`, example: `0`. Number of Gibbs sampling rounds to perform", + "help_text": "Type: `integer`, example: `0`. Number of Gibbs sampling rounds to perform.\n" + + } + + + , + "no_Gamma_draw": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. This switch will disable drawing transcript fractions from a Gamma distribution during Gibbs sampling", + "help_text": "Type: `boolean_true`, default: `false`. This switch will disable drawing transcript fractions from a Gamma distribution during Gibbs sampling. In this case the sampler does not account for shot-noise, but only assignment ambiguity\n" + , + "default": "False" + } + + + , + "num_bootstraps": { + "type": + "integer", + "description": "Type: `integer`, example: `0`. Number of bootstrap samples to generate", + "help_text": "Type: `integer`, example: `0`. Number of bootstrap samples to generate. Note: This is mutually exclusive with Gibbs sampling.\n" + + } + + + , + "bootstrap_reproject": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. This switch will learn the parameter distribution from the bootstrapped counts for each sample, but will reproject those parameters onto the original equivalence class counts", + "help_text": "Type: `boolean_true`, default: `false`. This switch will learn the parameter distribution from the bootstrapped counts for each sample, but will reproject those parameters onto the original equivalence class counts.\n" + , + "default": "False" + } + + + , + "thinning_factor": { + "type": + "integer", + "description": "Type: `integer`, example: `16`. Number of steps to discard for every sample kept from the Gibbs chain", + "help_text": "Type: `integer`, example: `16`. Number of steps to discard for every sample kept from the Gibbs chain. The larger this number, the less chance that subsequent samples are auto-correlated, but the slower sampling becomes.\n" + + } + + + , + "quiet": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Be quiet while doing quantification (don\u0027t write informative output to the console unless something goes wrong)", + "help_text": "Type: `boolean_true`, default: `false`. Be quiet while doing quantification (don\u0027t write informative output to the console unless something goes wrong).\n" + , + "default": "False" + } + + + , + "per_transcript_prior": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. The prior (either the default or the argument provided via --vb_prior) will be interpreted as a transcript-level prior (i", + "help_text": "Type: `boolean_true`, default: `false`. The prior (either the default or the argument provided via --vb_prior) will be interpreted as a transcript-level prior (i.e. each transcript will be given a prior read count of this value)\n" + , + "default": "False" + } + + + , + "per_nucleotide_prior": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. The prior (either the default or the argument provided via --vb_prior) will be interpreted as a nucleotide-level prior (i", + "help_text": "Type: `boolean_true`, default: `false`. The prior (either the default or the argument provided via --vb_prior) will be interpreted as a nucleotide-level prior (i.e. each nucleotide will be given a prior read count of this value)\n" + , + "default": "False" + } + + + , + "sig_digits": { + "type": + "integer", + "description": "Type: `integer`, example: `3`. The number of significant digits to write when outputting the EffectiveLength and NumReads columns\n", + "help_text": "Type: `integer`, example: `3`. The number of significant digits to write when outputting the EffectiveLength and NumReads columns\n" + + } + + + , + "vb_prior": { + "type": + "number", + "description": "Type: `double`, example: `0.01`. The prior that will be used in the VBEM algorithm", + "help_text": "Type: `double`, example: `0.01`. The prior that will be used in the VBEM algorithm. This is interpreted as a per-transcript prior, unless the --per_nucleotide_prior flag is also given. If the --per_nucleotide_prior flag is given, this is used as a nucleotide-level prior. If the default is used, it will be divided by 1000 before being used as a nucleotide-level prior, i.e. the default per-nucleotide prior will be 1e-5.\n" + + } + + + , + "write_orphan_links": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Write the transcripts that are linked by orphaned reads", + "help_text": "Type: `boolean_true`, default: `false`. Write the transcripts that are linked by orphaned reads.\n" + , + "default": "False" + } + + + , + "write_unmapped_names": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Write the names of un-mapped reads to the file unmapped_names", + "help_text": "Type: `boolean_true`, default: `false`. Write the names of un-mapped reads to the file unmapped_names.txt in the auxiliary directory.\n" + , + "default": "False" + } + + +} +}, + + + "alignment-specific options" : { + "title": "Alignment-specific options", + "type": "object", + "description": "No description", + "properties": { + + + "no_error_model": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Turn off the alignment error model, which takes into account the the observed frequency of different types of mismatches / indels when computing the likelihood of a given alignment", + "help_text": "Type: `boolean_true`, default: `false`. Turn off the alignment error model, which takes into account the the observed frequency of different types of mismatches / indels when computing the likelihood of a given alignment. Turning this off can speed up alignment-based salmon, but can harm quantification accuracy.\n" + , + "default": "False" + } + + + , + "num_error_bins": { + "type": + "integer", + "description": "Type: `integer`, example: `6`. The number of bins into which to divide each read when learning and applying the error model", + "help_text": "Type: `integer`, example: `6`. The number of bins into which to divide each read when learning and applying the error model. For example, a value of 10 would mean that effectively, a separate error model is leared and applied to each 10th of the read, while a value of 3 would mean that a separate error model is applied to the read beginning (first third), middle (second third) and end (final third).\n" + + } + + + , + "sample_out": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Write a \"postSample", + "help_text": "Type: `boolean_true`, default: `false`. Write a \"postSample.bam\" file in the output directory that will sample the input alignments according to the estimated transcript abundances. If you\u0027re going to perform downstream analysis of the alignments with tools which don\u0027t, themselves, take fragment assignment ambiguity into account, you should use this output.\n" + , + "default": "False" + } + + + , + "sample_unaligned": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. In addition to sampling the aligned reads, also write the un-aligned reads to \"postSample", + "help_text": "Type: `boolean_true`, default: `false`. In addition to sampling the aligned reads, also write the un-aligned reads to \"postSample.bam\".\n" + , + "default": "False" + } + + + , + "gencode": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. This flag will expect the input transcript fasta to be in GENCODE format, and will split the transcript name at the first \u0027|\u0027 character", + "help_text": "Type: `boolean_true`, default: `false`. This flag will expect the input transcript fasta to be in GENCODE format, and will split the transcript name at the first \u0027|\u0027 character. These reduced names will be used in the output and when looking for these transcripts in a gene to transcript GTF.\n" + , + "default": "False" + } + + + , + "mapping_cache_memory_limit": { + "type": + "integer", + "description": "Type: `integer`, example: `2000000`. If the file contained fewer than this many mapped reads, then just keep the data in memory for subsequent rounds of inference", + "help_text": "Type: `integer`, example: `2000000`. If the file contained fewer than this many mapped reads, then just keep the data in memory for subsequent rounds of inference. Obviously, this value should not be too large if you wish to keep a low memory usage, but setting it large enough to accommodate all of the mapped read can substantially speed up inference on \"small\" files that contain only a few million reads.\n" + + } + + +} +}, + + + "nextflow input-output arguments" : { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + + + "publish_dir": { + "type": + "string", + "description": "Type: `string`, required, example: `output/`. Path to an output directory", + "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." + + } + + + , + "param_list": { + "type": + "string", + "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", + "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", + "hidden": true + + } + + +} +} +}, +"allOf": [ + + { + "$ref": "#/definitions/common input options" + }, + + { + "$ref": "#/definitions/mapping input options" + }, + + { + "$ref": "#/definitions/alignment input options" + }, + + { + "$ref": "#/definitions/output" + }, + + { + "$ref": "#/definitions/basic options" + }, + + { + "$ref": "#/definitions/options specific to mapping mode" + }, + + { + "$ref": "#/definitions/advance options" + }, + + { + "$ref": "#/definitions/alignment-specific options" + }, + + { + "$ref": "#/definitions/nextflow input-output arguments" + } +] +} diff --git a/target/nextflow/samtools/samtools_collate/.config.vsh.yaml b/target/nextflow/samtools/samtools_collate/.config.vsh.yaml index 5e3b9e36..574aa712 100644 --- a/target/nextflow/samtools/samtools_collate/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_collate/.config.vsh.yaml @@ -250,7 +250,7 @@ build_info: output: "target/nextflow/samtools/samtools_collate" executable: "target/nextflow/samtools/samtools_collate/main.nf" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/samtools/samtools_collate/main.nf b/target/nextflow/samtools/samtools_collate/main.nf index 09a40367..4ee74cd5 100644 --- a/target/nextflow/samtools/samtools_collate/main.nf +++ b/target/nextflow/samtools/samtools_collate/main.nf @@ -3088,7 +3088,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_collate", "viash_version" : "0.9.0-RC6", - "git_commit" : "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a", + "git_commit" : "ec69d9af7a59c2618a49bef7d0bf9afc743ca065", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml b/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml index 1af9ddf7..9d17cba0 100644 --- a/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml @@ -229,7 +229,7 @@ build_info: output: "target/nextflow/samtools/samtools_faidx" executable: "target/nextflow/samtools/samtools_faidx/main.nf" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/samtools/samtools_faidx/main.nf b/target/nextflow/samtools/samtools_faidx/main.nf index 9a2c3406..54751158 100644 --- a/target/nextflow/samtools/samtools_faidx/main.nf +++ b/target/nextflow/samtools/samtools_faidx/main.nf @@ -3060,7 +3060,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_faidx", "viash_version" : "0.9.0-RC6", - "git_commit" : "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a", + "git_commit" : "ec69d9af7a59c2618a49bef7d0bf9afc743ca065", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml b/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml index 1812b0cb..3f97b5e8 100644 --- a/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml @@ -417,7 +417,7 @@ build_info: output: "target/nextflow/samtools/samtools_fastq" executable: "target/nextflow/samtools/samtools_fastq/main.nf" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/samtools/samtools_fastq/main.nf b/target/nextflow/samtools/samtools_fastq/main.nf index 9ec7c42b..996d2713 100644 --- a/target/nextflow/samtools/samtools_fastq/main.nf +++ b/target/nextflow/samtools/samtools_fastq/main.nf @@ -3252,7 +3252,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_fastq", "viash_version" : "0.9.0-RC6", - "git_commit" : "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a", + "git_commit" : "ec69d9af7a59c2618a49bef7d0bf9afc743ca065", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml b/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml index f04e70a8..7fa3b3b3 100644 --- a/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml @@ -159,7 +159,7 @@ build_info: output: "target/nextflow/samtools/samtools_flagstat" executable: "target/nextflow/samtools/samtools_flagstat/main.nf" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/samtools/samtools_flagstat/main.nf b/target/nextflow/samtools/samtools_flagstat/main.nf index d89f0bc4..90fb0618 100644 --- a/target/nextflow/samtools/samtools_flagstat/main.nf +++ b/target/nextflow/samtools/samtools_flagstat/main.nf @@ -2976,7 +2976,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_flagstat", "viash_version" : "0.9.0-RC6", - "git_commit" : "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a", + "git_commit" : "ec69d9af7a59c2618a49bef7d0bf9afc743ca065", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml b/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml index 60800311..50e92aef 100644 --- a/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml @@ -169,7 +169,7 @@ build_info: output: "target/nextflow/samtools/samtools_idxstats" executable: "target/nextflow/samtools/samtools_idxstats/main.nf" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/samtools/samtools_idxstats/main.nf b/target/nextflow/samtools/samtools_idxstats/main.nf index 70f8957c..d61be097 100644 --- a/target/nextflow/samtools/samtools_idxstats/main.nf +++ b/target/nextflow/samtools/samtools_idxstats/main.nf @@ -2988,7 +2988,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_idxstats", "viash_version" : "0.9.0-RC6", - "git_commit" : "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a", + "git_commit" : "ec69d9af7a59c2618a49bef7d0bf9afc743ca065", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/samtools/samtools_index/.config.vsh.yaml b/target/nextflow/samtools/samtools_index/.config.vsh.yaml index 4ace8702..5f995da1 100644 --- a/target/nextflow/samtools/samtools_index/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_index/.config.vsh.yaml @@ -175,7 +175,7 @@ build_info: output: "target/nextflow/samtools/samtools_index" executable: "target/nextflow/samtools/samtools_index/main.nf" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/samtools/samtools_index/main.nf b/target/nextflow/samtools/samtools_index/main.nf index 9a93b1be..33790909 100644 --- a/target/nextflow/samtools/samtools_index/main.nf +++ b/target/nextflow/samtools/samtools_index/main.nf @@ -3001,7 +3001,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_index", "viash_version" : "0.9.0-RC6", - "git_commit" : "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a", + "git_commit" : "ec69d9af7a59c2618a49bef7d0bf9afc743ca065", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/samtools/samtools_sort/.config.vsh.yaml b/target/nextflow/samtools/samtools_sort/.config.vsh.yaml index 787d571e..38069589 100644 --- a/target/nextflow/samtools/samtools_sort/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_sort/.config.vsh.yaml @@ -318,7 +318,7 @@ build_info: output: "target/nextflow/samtools/samtools_sort" executable: "target/nextflow/samtools/samtools_sort/main.nf" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/samtools/samtools_sort/main.nf b/target/nextflow/samtools/samtools_sort/main.nf index b8a7582c..38488cd7 100644 --- a/target/nextflow/samtools/samtools_sort/main.nf +++ b/target/nextflow/samtools/samtools_sort/main.nf @@ -3173,7 +3173,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_sort", "viash_version" : "0.9.0-RC6", - "git_commit" : "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a", + "git_commit" : "ec69d9af7a59c2618a49bef7d0bf9afc743ca065", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/samtools/samtools_stats/.config.vsh.yaml b/target/nextflow/samtools/samtools_stats/.config.vsh.yaml index b762244a..1d7e93da 100644 --- a/target/nextflow/samtools/samtools_stats/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_stats/.config.vsh.yaml @@ -380,7 +380,7 @@ build_info: output: "target/nextflow/samtools/samtools_stats" executable: "target/nextflow/samtools/samtools_stats/main.nf" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/samtools/samtools_stats/main.nf b/target/nextflow/samtools/samtools_stats/main.nf index 4f67d855..cac2a1cc 100644 --- a/target/nextflow/samtools/samtools_stats/main.nf +++ b/target/nextflow/samtools/samtools_stats/main.nf @@ -3238,7 +3238,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_stats", "viash_version" : "0.9.0-RC6", - "git_commit" : "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a", + "git_commit" : "ec69d9af7a59c2618a49bef7d0bf9afc743ca065", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/samtools/samtools_view/.config.vsh.yaml b/target/nextflow/samtools/samtools_view/.config.vsh.yaml index baff2760..7b0e1305 100644 --- a/target/nextflow/samtools/samtools_view/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_view/.config.vsh.yaml @@ -651,7 +651,7 @@ build_info: output: "target/nextflow/samtools/samtools_view" executable: "target/nextflow/samtools/samtools_view/main.nf" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/samtools/samtools_view/main.nf b/target/nextflow/samtools/samtools_view/main.nf index bc87b338..e1e3db76 100644 --- a/target/nextflow/samtools/samtools_view/main.nf +++ b/target/nextflow/samtools/samtools_view/main.nf @@ -3424,7 +3424,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_view", "viash_version" : "0.9.0-RC6", - "git_commit" : "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a", + "git_commit" : "ec69d9af7a59c2618a49bef7d0bf9afc743ca065", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/star/star_align_reads/.config.vsh.yaml b/target/nextflow/star/star_align_reads/.config.vsh.yaml index 55243b77..023e7815 100644 --- a/target/nextflow/star/star_align_reads/.config.vsh.yaml +++ b/target/nextflow/star/star_align_reads/.config.vsh.yaml @@ -2108,7 +2108,7 @@ build_info: output: "target/nextflow/star/star_align_reads" executable: "target/nextflow/star/star_align_reads/main.nf" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/star/star_align_reads/main.nf b/target/nextflow/star/star_align_reads/main.nf index f8a7a1c1..8647b000 100644 --- a/target/nextflow/star/star_align_reads/main.nf +++ b/target/nextflow/star/star_align_reads/main.nf @@ -5023,7 +5023,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/star/star_align_reads", "viash_version" : "0.9.0-RC6", - "git_commit" : "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a", + "git_commit" : "ec69d9af7a59c2618a49bef7d0bf9afc743ca065", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/star/star_genome_generate/.config.vsh.yaml b/target/nextflow/star/star_genome_generate/.config.vsh.yaml index a433014f..6576e85b 100644 --- a/target/nextflow/star/star_genome_generate/.config.vsh.yaml +++ b/target/nextflow/star/star_genome_generate/.config.vsh.yaml @@ -319,7 +319,7 @@ build_info: output: "target/nextflow/star/star_genome_generate" executable: "target/nextflow/star/star_genome_generate/main.nf" viash_version: "0.9.0-RC6" - git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a" + git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/star/star_genome_generate/main.nf b/target/nextflow/star/star_genome_generate/main.nf index de0058d7..52c68cd4 100644 --- a/target/nextflow/star/star_genome_generate/main.nf +++ b/target/nextflow/star/star_genome_generate/main.nf @@ -3143,7 +3143,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/star/star_genome_generate", "viash_version" : "0.9.0-RC6", - "git_commit" : "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a", + "git_commit" : "ec69d9af7a59c2618a49bef7d0bf9afc743ca065", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : {