From cdb68529f28bf9ca82570211b6cfc7d84fb1b57a Mon Sep 17 00:00:00 2001 From: CI Date: Thu, 12 Sep 2024 13:38:40 +0000 Subject: [PATCH] Build branch v0.2 with version 0.2.0 (5526b3e) Build pipeline: viash-hub.biobox.v0.2-zzqh5 Source commit: https://github.com/viash-hub/biobox/commit/5526b3e939030daea80595fa98387b469329bbfa Source message: Release v0.2.0 --- CHANGELOG.md | 2 +- _viash.yaml | 3 +- nextflow.config | 2 +- .../agat_convert_bed2gff/.config.vsh.yaml | 14 +++--- .../agat_convert_bed2gff/agat_convert_bed2gff | 20 ++++---- .../agat_convert_embl2gff/.config.vsh.yaml | 14 +++--- .../agat_convert_embl2gff | 20 ++++---- .../agat_convert_sp_gff2gtf/.config.vsh.yaml | 14 +++--- .../agat_convert_sp_gff2gtf | 20 ++++---- .../agat_convert_sp_gff2tsv/.config.vsh.yaml | 14 +++--- .../agat_convert_sp_gff2tsv | 20 ++++---- .../agat_convert_sp_gxf2gxf/.config.vsh.yaml | 14 +++--- .../agat_convert_sp_gxf2gxf | 20 ++++---- target/executable/arriba/.config.vsh.yaml | 14 +++--- target/executable/arriba/arriba | 20 ++++---- .../bcftools/bcftools_sort/.config.vsh.yaml | 14 +++--- .../bcftools/bcftools_sort/bcftools_sort | 20 ++++---- .../executable/bcl_convert/.config.vsh.yaml | 14 +++--- target/executable/bcl_convert/bcl_convert | 20 ++++---- .../.config.vsh.yaml | 14 +++--- .../bd_rhapsody_make_reference | 20 ++++---- .../bedtools_bamtofastq/.config.vsh.yaml | 14 +++--- .../bedtools_bamtofastq/bedtools_bamtofastq | 20 ++++---- .../bedtools_bed12tobed6/.config.vsh.yaml | 14 +++--- .../bedtools_bed12tobed6/bedtools_bed12tobed6 | 20 ++++---- .../bedtools_bedtobam/.config.vsh.yaml | 14 +++--- .../bedtools_bedtobam/bedtools_bedtobam | 20 ++++---- .../bedtools_getfasta/.config.vsh.yaml | 14 +++--- .../bedtools_getfasta/bedtools_getfasta | 20 ++++---- .../bedtools_groupby/.config.vsh.yaml | 14 +++--- .../bedtools_groupby/bedtools_groupby | 20 ++++---- .../bedtools_intersect/.config.vsh.yaml | 14 +++--- .../bedtools_intersect/bedtools_intersect | 20 ++++---- .../bedtools/bedtools_links/.config.vsh.yaml | 14 +++--- .../bedtools/bedtools_links/bedtools_links | 20 ++++---- .../bedtools/bedtools_merge/.config.vsh.yaml | 14 +++--- .../bedtools/bedtools_merge/bedtools_merge | 20 ++++---- .../bedtools/bedtools_sort/.config.vsh.yaml | 14 +++--- .../bedtools/bedtools_sort/bedtools_sort | 20 ++++---- .../busco_download_datasets/.config.vsh.yaml | 14 +++--- .../busco_download_datasets | 20 ++++---- .../busco_list_datasets/.config.vsh.yaml | 14 +++--- .../busco_list_datasets/busco_list_datasets | 20 ++++---- .../busco/busco_run/.config.vsh.yaml | 14 +++--- target/executable/busco/busco_run/busco_run | 20 ++++---- target/executable/cutadapt/.config.vsh.yaml | 14 +++--- target/executable/cutadapt/cutadapt | 20 ++++---- target/executable/falco/.config.vsh.yaml | 14 +++--- target/executable/falco/falco | 20 ++++---- target/executable/fastp/.config.vsh.yaml | 14 +++--- target/executable/fastp/fastp | 20 ++++---- target/executable/fastqc/.config.vsh.yaml | 14 +++--- target/executable/fastqc/fastqc | 20 ++++---- .../executable/featurecounts/.config.vsh.yaml | 14 +++--- target/executable/featurecounts/featurecounts | 20 ++++---- target/executable/gffread/.config.vsh.yaml | 14 +++--- target/executable/gffread/gffread | 20 ++++---- .../lofreq/lofreq_call/.config.vsh.yaml | 14 +++--- .../executable/lofreq/lofreq_call/lofreq_call | 20 ++++---- .../lofreq/lofreq_indelqual/.config.vsh.yaml | 14 +++--- .../lofreq/lofreq_indelqual/lofreq_indelqual | 20 ++++---- target/executable/multiqc/.config.vsh.yaml | 14 +++--- target/executable/multiqc/multiqc | 20 ++++---- target/executable/pear/.config.vsh.yaml | 14 +++--- target/executable/pear/pear | 20 ++++---- .../qualimap/qualimap_rnaseq/.config.vsh.yaml | 14 +++--- .../qualimap/qualimap_rnaseq/qualimap_rnaseq | 20 ++++---- .../rsem_prepare_reference/.config.vsh.yaml | 14 +++--- .../rsem_prepare_reference | 20 ++++---- .../salmon/salmon_index/.config.vsh.yaml | 14 +++--- .../salmon/salmon_index/salmon_index | 20 ++++---- .../salmon/salmon_quant/.config.vsh.yaml | 14 +++--- .../salmon/salmon_quant/salmon_quant | 20 ++++---- .../samtools_collate/.config.vsh.yaml | 14 +++--- .../samtools_collate/samtools_collate | 20 ++++---- .../samtools/samtools_faidx/.config.vsh.yaml | 14 +++--- .../samtools/samtools_faidx/samtools_faidx | 20 ++++---- .../samtools/samtools_fasta/.config.vsh.yaml | 14 +++--- .../samtools/samtools_fasta/samtools_fasta | 20 ++++---- .../samtools/samtools_fastq/.config.vsh.yaml | 14 +++--- .../samtools/samtools_fastq/samtools_fastq | 20 ++++---- .../samtools_flagstat/.config.vsh.yaml | 14 +++--- .../samtools_flagstat/samtools_flagstat | 20 ++++---- .../samtools_idxstats/.config.vsh.yaml | 14 +++--- .../samtools_idxstats/samtools_idxstats | 20 ++++---- .../samtools/samtools_index/.config.vsh.yaml | 14 +++--- .../samtools/samtools_index/samtools_index | 20 ++++---- .../samtools/samtools_sort/.config.vsh.yaml | 14 +++--- .../samtools/samtools_sort/samtools_sort | 20 ++++---- .../samtools/samtools_stats/.config.vsh.yaml | 14 +++--- .../samtools/samtools_stats/samtools_stats | 20 ++++---- .../samtools/samtools_view/.config.vsh.yaml | 14 +++--- .../samtools/samtools_view/samtools_view | 20 ++++---- .../seqtk/seqtk_sample/.config.vsh.yaml | 14 +++--- .../seqtk/seqtk_sample/seqtk_sample | 20 ++++---- .../seqtk/seqtk_subseq/.config.vsh.yaml | 14 +++--- .../seqtk/seqtk_subseq/seqtk_subseq | 20 ++++---- .../star/star_align_reads/.config.vsh.yaml | 14 +++--- .../star/star_align_reads/star_align_reads | 20 ++++---- .../star_genome_generate/.config.vsh.yaml | 14 +++--- .../star_genome_generate/star_genome_generate | 20 ++++---- .../umi_tools_dedup/.config.vsh.yaml | 14 +++--- .../umi_tools/umi_tools_dedup/umi_tools_dedup | 20 ++++---- .../umi_tools_extract/.config.vsh.yaml | 14 +++--- .../umi_tools_extract/umi_tools_extract | 20 ++++---- .../agat_convert_bed2gff/.config.vsh.yaml | 14 +++--- .../agat/agat_convert_bed2gff/main.nf | 47 +++++++++++------- .../agat/agat_convert_bed2gff/nextflow.config | 2 +- .../agat_convert_embl2gff/.config.vsh.yaml | 14 +++--- .../agat/agat_convert_embl2gff/main.nf | 47 +++++++++++------- .../agat_convert_embl2gff/nextflow.config | 2 +- .../agat_convert_sp_gff2gtf/.config.vsh.yaml | 14 +++--- .../agat/agat_convert_sp_gff2gtf/main.nf | 47 +++++++++++------- .../agat_convert_sp_gff2gtf/nextflow.config | 2 +- .../agat_convert_sp_gff2tsv/.config.vsh.yaml | 14 +++--- .../agat/agat_convert_sp_gff2tsv/main.nf | 47 +++++++++++------- .../agat_convert_sp_gff2tsv/nextflow.config | 2 +- .../agat_convert_sp_gxf2gxf/.config.vsh.yaml | 14 +++--- .../agat/agat_convert_sp_gxf2gxf/main.nf | 47 +++++++++++------- .../agat_convert_sp_gxf2gxf/nextflow.config | 2 +- target/nextflow/arriba/.config.vsh.yaml | 14 +++--- target/nextflow/arriba/main.nf | 47 +++++++++++------- target/nextflow/arriba/nextflow.config | 2 +- .../bcftools/bcftools_sort/.config.vsh.yaml | 14 +++--- .../nextflow/bcftools/bcftools_sort/main.nf | 47 +++++++++++------- .../bcftools/bcftools_sort/nextflow.config | 2 +- target/nextflow/bcl_convert/.config.vsh.yaml | 14 +++--- target/nextflow/bcl_convert/main.nf | 47 +++++++++++------- target/nextflow/bcl_convert/nextflow.config | 2 +- .../.config.vsh.yaml | 14 +++--- .../bd_rhapsody_make_reference/main.nf | 47 +++++++++++------- .../nextflow.config | 2 +- .../bedtools_bamtofastq/.config.vsh.yaml | 14 +++--- .../bedtools/bedtools_bamtofastq/main.nf | 47 +++++++++++------- .../bedtools_bamtofastq/nextflow.config | 2 +- .../bedtools_bed12tobed6/.config.vsh.yaml | 14 +++--- .../bedtools/bedtools_bed12tobed6/main.nf | 47 +++++++++++------- .../bedtools_bed12tobed6/nextflow.config | 2 +- .../bedtools_bedtobam/.config.vsh.yaml | 14 +++--- .../bedtools/bedtools_bedtobam/main.nf | 47 +++++++++++------- .../bedtools_bedtobam/nextflow.config | 2 +- .../bedtools_getfasta/.config.vsh.yaml | 14 +++--- .../bedtools/bedtools_getfasta/main.nf | 47 +++++++++++------- .../bedtools_getfasta/nextflow.config | 2 +- .../bedtools_groupby/.config.vsh.yaml | 14 +++--- .../bedtools/bedtools_groupby/main.nf | 47 +++++++++++------- .../bedtools/bedtools_groupby/nextflow.config | 2 +- .../bedtools_intersect/.config.vsh.yaml | 14 +++--- .../bedtools/bedtools_intersect/main.nf | 47 +++++++++++------- .../bedtools_intersect/nextflow.config | 2 +- .../bedtools/bedtools_links/.config.vsh.yaml | 14 +++--- .../nextflow/bedtools/bedtools_links/main.nf | 47 +++++++++++------- .../bedtools/bedtools_links/nextflow.config | 2 +- .../bedtools/bedtools_merge/.config.vsh.yaml | 14 +++--- .../nextflow/bedtools/bedtools_merge/main.nf | 47 +++++++++++------- .../bedtools/bedtools_merge/nextflow.config | 2 +- .../bedtools/bedtools_sort/.config.vsh.yaml | 14 +++--- .../nextflow/bedtools/bedtools_sort/main.nf | 47 +++++++++++------- .../bedtools/bedtools_sort/nextflow.config | 2 +- .../busco_download_datasets/.config.vsh.yaml | 14 +++--- .../busco/busco_download_datasets/main.nf | 47 +++++++++++------- .../busco_download_datasets/nextflow.config | 2 +- .../busco_list_datasets/.config.vsh.yaml | 14 +++--- .../busco/busco_list_datasets/main.nf | 47 +++++++++++------- .../busco/busco_list_datasets/nextflow.config | 2 +- .../nextflow/busco/busco_run/.config.vsh.yaml | 14 +++--- target/nextflow/busco/busco_run/main.nf | 47 +++++++++++------- .../nextflow/busco/busco_run/nextflow.config | 2 +- target/nextflow/cutadapt/.config.vsh.yaml | 14 +++--- target/nextflow/cutadapt/main.nf | 47 +++++++++++------- target/nextflow/cutadapt/nextflow.config | 2 +- target/nextflow/falco/.config.vsh.yaml | 14 +++--- target/nextflow/falco/main.nf | 47 +++++++++++------- target/nextflow/falco/nextflow.config | 2 +- target/nextflow/fastp/.config.vsh.yaml | 14 +++--- target/nextflow/fastp/main.nf | 47 +++++++++++------- target/nextflow/fastp/nextflow.config | 2 +- target/nextflow/fastqc/.config.vsh.yaml | 14 +++--- target/nextflow/fastqc/main.nf | 47 +++++++++++------- target/nextflow/fastqc/nextflow.config | 2 +- .../nextflow/featurecounts/.config.vsh.yaml | 14 +++--- target/nextflow/featurecounts/main.nf | 47 +++++++++++------- target/nextflow/featurecounts/nextflow.config | 2 +- target/nextflow/gffread/.config.vsh.yaml | 14 +++--- target/nextflow/gffread/main.nf | 47 +++++++++++------- target/nextflow/gffread/nextflow.config | 2 +- .../lofreq/lofreq_call/.config.vsh.yaml | 14 +++--- target/nextflow/lofreq/lofreq_call/main.nf | 47 +++++++++++------- .../lofreq/lofreq_call/nextflow.config | 2 +- .../lofreq/lofreq_indelqual/.config.vsh.yaml | 14 +++--- .../nextflow/lofreq/lofreq_indelqual/main.nf | 47 +++++++++++------- .../lofreq/lofreq_indelqual/nextflow.config | 2 +- target/nextflow/multiqc/.config.vsh.yaml | 14 +++--- target/nextflow/multiqc/main.nf | 47 +++++++++++------- target/nextflow/multiqc/nextflow.config | 2 +- target/nextflow/pear/.config.vsh.yaml | 14 +++--- target/nextflow/pear/main.nf | 47 +++++++++++------- target/nextflow/pear/nextflow.config | 2 +- .../qualimap/qualimap_rnaseq/.config.vsh.yaml | 14 +++--- .../nextflow/qualimap/qualimap_rnaseq/main.nf | 47 +++++++++++------- .../qualimap/qualimap_rnaseq/nextflow.config | 2 +- .../rsem_prepare_reference/.config.vsh.yaml | 14 +++--- .../rsem/rsem_prepare_reference/main.nf | 47 +++++++++++------- .../rsem_prepare_reference/nextflow.config | 2 +- .../salmon/salmon_index/.config.vsh.yaml | 14 +++--- target/nextflow/salmon/salmon_index/main.nf | 47 +++++++++++------- .../salmon/salmon_index/nextflow.config | 2 +- .../salmon/salmon_quant/.config.vsh.yaml | 14 +++--- target/nextflow/salmon/salmon_quant/main.nf | 47 +++++++++++------- .../salmon/salmon_quant/nextflow.config | 2 +- .../samtools_collate/.config.vsh.yaml | 14 +++--- .../samtools/samtools_collate/main.nf | 47 +++++++++++------- .../samtools/samtools_collate/nextflow.config | 2 +- .../samtools/samtools_faidx/.config.vsh.yaml | 14 +++--- .../nextflow/samtools/samtools_faidx/main.nf | 47 +++++++++++------- .../samtools/samtools_faidx/nextflow.config | 2 +- .../samtools/samtools_fasta/.config.vsh.yaml | 14 +++--- .../nextflow/samtools/samtools_fasta/main.nf | 47 +++++++++++------- .../samtools/samtools_fasta/nextflow.config | 2 +- .../samtools/samtools_fastq/.config.vsh.yaml | 14 +++--- .../nextflow/samtools/samtools_fastq/main.nf | 47 +++++++++++------- .../samtools/samtools_fastq/nextflow.config | 2 +- .../samtools_flagstat/.config.vsh.yaml | 14 +++--- .../samtools/samtools_flagstat/main.nf | 47 +++++++++++------- .../samtools_flagstat/nextflow.config | 2 +- .../samtools_idxstats/.config.vsh.yaml | 14 +++--- .../samtools/samtools_idxstats/main.nf | 47 +++++++++++------- .../samtools_idxstats/nextflow.config | 2 +- .../samtools/samtools_index/.config.vsh.yaml | 14 +++--- .../nextflow/samtools/samtools_index/main.nf | 47 +++++++++++------- .../samtools/samtools_index/nextflow.config | 2 +- .../samtools/samtools_sort/.config.vsh.yaml | 14 +++--- .../nextflow/samtools/samtools_sort/main.nf | 47 +++++++++++------- .../samtools/samtools_sort/nextflow.config | 2 +- .../samtools/samtools_stats/.config.vsh.yaml | 14 +++--- .../nextflow/samtools/samtools_stats/main.nf | 47 +++++++++++------- .../samtools/samtools_stats/nextflow.config | 2 +- .../samtools/samtools_view/.config.vsh.yaml | 14 +++--- .../nextflow/samtools/samtools_view/main.nf | 47 +++++++++++------- .../samtools/samtools_view/nextflow.config | 2 +- .../seqtk/seqtk_sample/.config.vsh.yaml | 14 +++--- target/nextflow/seqtk/seqtk_sample/main.nf | 47 +++++++++++------- .../seqtk/seqtk_sample/nextflow.config | 2 +- .../seqtk/seqtk_subseq/.config.vsh.yaml | 14 +++--- target/nextflow/seqtk/seqtk_subseq/main.nf | 47 +++++++++++------- .../seqtk/seqtk_subseq/nextflow.config | 2 +- .../star/star_align_reads/.config.vsh.yaml | 14 +++--- target/nextflow/star/star_align_reads/main.nf | 49 ++++++++++++------- .../star/star_align_reads/nextflow.config | 2 +- .../star_genome_generate/.config.vsh.yaml | 14 +++--- .../star/star_genome_generate/main.nf | 47 +++++++++++------- .../star/star_genome_generate/nextflow.config | 2 +- .../umi_tools_dedup/.config.vsh.yaml | 14 +++--- .../umi_tools/umi_tools_dedup/main.nf | 47 +++++++++++------- .../umi_tools/umi_tools_dedup/nextflow.config | 2 +- .../umi_tools_extract/.config.vsh.yaml | 14 +++--- .../umi_tools/umi_tools_extract/main.nf | 47 +++++++++++------- .../umi_tools_extract/nextflow.config | 2 +- 258 files changed, 2759 insertions(+), 2197 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 98e78c17..f3dca8fd 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,4 +1,4 @@ -# biobox x.x.x +# biobox 0.2.0 ## BREAKING CHANGES diff --git a/_viash.yaml b/_viash.yaml index ab4f3828..a898ff17 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -1,4 +1,5 @@ name: biobox +version: 0.2.0 description: | A collection of bioinformatics tools for working with sequence data. license: MIT @@ -7,7 +8,7 @@ links: issue_tracker: https://github.com/viash-hub/biobox/issues repository: https://github.com/viash-hub/biobox -viash_version: 0.9.0-RC7 +viash_version: 0.9.0 config_mods: | .requirements.commands := ['ps'] diff --git a/nextflow.config b/nextflow.config index 22ae7819..bdd66d18 100644 --- a/nextflow.config +++ b/nextflow.config @@ -1,6 +1,6 @@ manifest { name = "biobox" - version = "v0.2" + version = "0.2.0" defaultBranch = "main" nextflowVersion = "!>=20.12.1-edge" } diff --git a/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml b/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml index cd082f87..b0c219e6 100644 --- a/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml +++ b/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "agat_convert_bed2gff" namespace: "agat" -version: "v0.2" +version: "0.2.0" authors: - name: "Leïla Paquay" roles: @@ -218,7 +218,7 @@ engines: id: "docker" image: "quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -234,22 +234,22 @@ build_info: engine: "docker|native" output: "target/executable/agat/agat_convert_bed2gff" executable: "target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff b/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff index c8864885..c97d038f 100755 --- a/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff +++ b/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff @@ -1,10 +1,10 @@ #!/usr/bin/env bash -# agat_convert_bed2gff v0.2 +# agat_convert_bed2gff 0.2.0 # -# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. +# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. # # The component may contain files which fall under a different license. The # authors of this component should specify the license in the header of such @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "agat_convert_bed2gff v0.2" + echo "agat_convert_bed2gff 0.2.0" echo "" echo "The script takes a bed file as input, and will translate it in gff format. The" echo "BED format is described here The script converts 0-based, half-open [start-1," @@ -515,10 +515,10 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t LABEL org.opencontainers.image.authors="Leïla Paquay" LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_bed2gff" -LABEL org.opencontainers.image.created="2024-09-12T12:36:22Z" +LABEL org.opencontainers.image.created="2024-09-12T13:23:23Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="f22ab0eab58dcd6bff89d8d73fe951953ff1260f" -LABEL org.opencontainers.image.version="v0.2" +LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" +LABEL org.opencontainers.image.version="0.2.0" VIASHDOCKER fi @@ -654,7 +654,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "agat_convert_bed2gff v0.2" + echo "agat_convert_bed2gff 0.2.0" exit ;; --bed) @@ -851,7 +851,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/agat/agat_convert_bed2gff:v0.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/agat/agat_convert_bed2gff:0.2.0' fi # print dockerfile diff --git a/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml b/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml index 0602500f..90be12ee 100644 --- a/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml +++ b/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "agat_convert_embl2gff" namespace: "agat" -version: "v0.2" +version: "0.2.0" authors: - name: "Leïla Paquay" roles: @@ -208,7 +208,7 @@ engines: id: "docker" image: "quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -224,22 +224,22 @@ build_info: engine: "docker|native" output: "target/executable/agat/agat_convert_embl2gff" executable: "target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff b/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff index 99e897c9..ddaa98df 100755 --- a/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff +++ b/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff @@ -1,10 +1,10 @@ #!/usr/bin/env bash -# agat_convert_embl2gff v0.2 +# agat_convert_embl2gff 0.2.0 # -# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. +# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. # # The component may contain files which fall under a different license. The # authors of this component should specify the license in the header of such @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "agat_convert_embl2gff v0.2" + echo "agat_convert_embl2gff 0.2.0" echo "" echo "The script takes an EMBL file as input, and will translate it in gff format." echo "" @@ -505,10 +505,10 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t LABEL org.opencontainers.image.authors="Leïla Paquay" LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_embl2gff" -LABEL org.opencontainers.image.created="2024-09-12T12:36:22Z" +LABEL org.opencontainers.image.created="2024-09-12T13:23:23Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="f22ab0eab58dcd6bff89d8d73fe951953ff1260f" -LABEL org.opencontainers.image.version="v0.2" +LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" +LABEL org.opencontainers.image.version="0.2.0" VIASHDOCKER fi @@ -644,7 +644,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "agat_convert_embl2gff v0.2" + echo "agat_convert_embl2gff 0.2.0" exit ;; --embl) @@ -858,7 +858,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/agat/agat_convert_embl2gff:v0.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/agat/agat_convert_embl2gff:0.2.0' fi # print dockerfile diff --git a/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml b/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml index ee6e4575..65fdedef 100644 --- a/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml +++ b/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "agat_convert_sp_gff2gtf" namespace: "agat" -version: "v0.2" +version: "0.2.0" authors: - name: "Leïla Paquay" roles: @@ -211,7 +211,7 @@ engines: id: "docker" image: "quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -227,22 +227,22 @@ build_info: engine: "docker|native" output: "target/executable/agat/agat_convert_sp_gff2gtf" executable: "target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf b/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf index 838d9fb3..e863af61 100755 --- a/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf +++ b/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf @@ -1,10 +1,10 @@ #!/usr/bin/env bash -# agat_convert_sp_gff2gtf v0.2 +# agat_convert_sp_gff2gtf 0.2.0 # -# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. +# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. # # The component may contain files which fall under a different license. The # authors of this component should specify the license in the header of such @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "agat_convert_sp_gff2gtf v0.2" + echo "agat_convert_sp_gff2gtf 0.2.0" echo "" echo "The script aims to convert any GTF/GFF file into a proper GTF file. Full" echo "information about the format can be found here:" @@ -519,10 +519,10 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t LABEL org.opencontainers.image.authors="Leïla Paquay" LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_sp_gff2gtf" -LABEL org.opencontainers.image.created="2024-09-12T12:36:23Z" +LABEL org.opencontainers.image.created="2024-09-12T13:23:23Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="f22ab0eab58dcd6bff89d8d73fe951953ff1260f" -LABEL org.opencontainers.image.version="v0.2" +LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" +LABEL org.opencontainers.image.version="0.2.0" VIASHDOCKER fi @@ -658,7 +658,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "agat_convert_sp_gff2gtf v0.2" + echo "agat_convert_sp_gff2gtf 0.2.0" exit ;; --gff) @@ -829,7 +829,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/agat/agat_convert_sp_gff2gtf:v0.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/agat/agat_convert_sp_gff2gtf:0.2.0' fi # print dockerfile diff --git a/target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml b/target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml index d0e163a1..97f88a49 100644 --- a/target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml +++ b/target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "agat_convert_sp_gff2tsv" namespace: "agat" -version: "v0.2" +version: "0.2.0" authors: - name: "Leïla Paquay" roles: @@ -171,7 +171,7 @@ engines: id: "docker" image: "quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -187,22 +187,22 @@ build_info: engine: "docker|native" output: "target/executable/agat/agat_convert_sp_gff2tsv" executable: "target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv b/target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv index 9c0e8f85..75c82b06 100755 --- a/target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv +++ b/target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv @@ -1,10 +1,10 @@ #!/usr/bin/env bash -# agat_convert_sp_gff2tsv v0.2 +# agat_convert_sp_gff2tsv 0.2.0 # -# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. +# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. # # The component may contain files which fall under a different license. The # authors of this component should specify the license in the header of such @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "agat_convert_sp_gff2tsv v0.2" + echo "agat_convert_sp_gff2tsv 0.2.0" echo "" echo "The script aims to convert gtf/gff file into tabulated file. Attribute's" echo "tags from the 9th column become column titles." @@ -484,10 +484,10 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t LABEL org.opencontainers.image.authors="Leïla Paquay" LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_sp_gff2tsv" -LABEL org.opencontainers.image.created="2024-09-12T12:36:22Z" +LABEL org.opencontainers.image.created="2024-09-12T13:23:23Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="f22ab0eab58dcd6bff89d8d73fe951953ff1260f" -LABEL org.opencontainers.image.version="v0.2" +LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" +LABEL org.opencontainers.image.version="0.2.0" VIASHDOCKER fi @@ -623,7 +623,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "agat_convert_sp_gff2tsv v0.2" + echo "agat_convert_sp_gff2tsv 0.2.0" exit ;; --gff) @@ -777,7 +777,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/agat/agat_convert_sp_gff2tsv:v0.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/agat/agat_convert_sp_gff2tsv:0.2.0' fi # print dockerfile diff --git a/target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml b/target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml index 8c7219e8..d1d3866a 100644 --- a/target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml +++ b/target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "agat_convert_sp_gxf2gxf" namespace: "agat" -version: "v0.2" +version: "0.2.0" authors: - name: "Leïla Paquay" roles: @@ -178,7 +178,7 @@ engines: id: "docker" image: "quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -194,22 +194,22 @@ build_info: engine: "docker|native" output: "target/executable/agat/agat_convert_sp_gxf2gxf" executable: "target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf b/target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf index 200b32bc..96c68859 100755 --- a/target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf +++ b/target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf @@ -1,10 +1,10 @@ #!/usr/bin/env bash -# agat_convert_sp_gxf2gxf v0.2 +# agat_convert_sp_gxf2gxf 0.2.0 # -# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. +# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. # # The component may contain files which fall under a different license. The # authors of this component should specify the license in the header of such @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "agat_convert_sp_gxf2gxf v0.2" + echo "agat_convert_sp_gxf2gxf 0.2.0" echo "" echo "This script fixes and/or standardizes any GTF/GFF file into full sorted" echo "GTF/GFF file. It AGAT parser removes duplicate features, fixes" @@ -493,10 +493,10 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t LABEL org.opencontainers.image.authors="Leïla Paquay" LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_sp_gxf2gxf" -LABEL org.opencontainers.image.created="2024-09-12T12:36:21Z" +LABEL org.opencontainers.image.created="2024-09-12T13:23:22Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="f22ab0eab58dcd6bff89d8d73fe951953ff1260f" -LABEL org.opencontainers.image.version="v0.2" +LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" +LABEL org.opencontainers.image.version="0.2.0" VIASHDOCKER fi @@ -632,7 +632,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "agat_convert_sp_gxf2gxf v0.2" + echo "agat_convert_sp_gxf2gxf 0.2.0" exit ;; --gxf) @@ -786,7 +786,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/agat/agat_convert_sp_gxf2gxf:v0.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/agat/agat_convert_sp_gxf2gxf:0.2.0' fi # print dockerfile diff --git a/target/executable/arriba/.config.vsh.yaml b/target/executable/arriba/.config.vsh.yaml index 33bf6e85..2296f8d4 100644 --- a/target/executable/arriba/.config.vsh.yaml +++ b/target/executable/arriba/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "arriba" -version: "v0.2" +version: "0.2.0" authors: - name: "Robrecht Cannoodt" roles: @@ -688,7 +688,7 @@ engines: id: "docker" image: "quay.io/biocontainers/arriba:2.4.0--h0033a41_2" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -705,22 +705,22 @@ build_info: engine: "docker|native" output: "target/executable/arriba" executable: "target/executable/arriba/arriba" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/arriba/arriba b/target/executable/arriba/arriba index 78cc3c02..880c6c8a 100755 --- a/target/executable/arriba/arriba +++ b/target/executable/arriba/arriba @@ -1,10 +1,10 @@ #!/usr/bin/env bash -# arriba v0.2 +# arriba 0.2.0 # -# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. +# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. # # The component may contain files which fall under a different license. The # authors of this component should specify the license in the header of such @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "arriba v0.2" + echo "arriba 0.2.0" echo "" echo "Detect gene fusions from RNA-Seq data" echo "" @@ -754,10 +754,10 @@ RUN arriba -h | grep 'Version:' 2>&1 | sed 's/Version:\s\(.*\)/arriba: "\1"/' > LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component arriba" -LABEL org.opencontainers.image.created="2024-09-12T12:36:24Z" +LABEL org.opencontainers.image.created="2024-09-12T13:23:25Z" LABEL org.opencontainers.image.source="https://github.com/suhrig/arriba" -LABEL org.opencontainers.image.revision="f22ab0eab58dcd6bff89d8d73fe951953ff1260f" -LABEL org.opencontainers.image.version="v0.2" +LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" +LABEL org.opencontainers.image.version="0.2.0" VIASHDOCKER fi @@ -893,7 +893,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "arriba v0.2" + echo "arriba 0.2.0" exit ;; --bam) @@ -1619,7 +1619,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/arriba:v0.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/arriba:0.2.0' fi # print dockerfile diff --git a/target/executable/bcftools/bcftools_sort/.config.vsh.yaml b/target/executable/bcftools/bcftools_sort/.config.vsh.yaml index 57e1c249..a50f7a27 100644 --- a/target/executable/bcftools/bcftools_sort/.config.vsh.yaml +++ b/target/executable/bcftools/bcftools_sort/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bcftools_sort" namespace: "bcftools" -version: "v0.2" +version: "0.2.0" authors: - name: "Theodoro Gasperin Terra Camargo" roles: @@ -162,7 +162,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -184,22 +184,22 @@ build_info: engine: "docker|native" output: "target/executable/bcftools/bcftools_sort" executable: "target/executable/bcftools/bcftools_sort/bcftools_sort" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bcftools/bcftools_sort/bcftools_sort b/target/executable/bcftools/bcftools_sort/bcftools_sort index 070b0a99..92451663 100755 --- a/target/executable/bcftools/bcftools_sort/bcftools_sort +++ b/target/executable/bcftools/bcftools_sort/bcftools_sort @@ -1,10 +1,10 @@ #!/usr/bin/env bash -# bcftools_sort v0.2 +# bcftools_sort 0.2.0 # -# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. +# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. # # The component may contain files which fall under a different license. The # authors of this component should specify the license in the header of such @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "bcftools_sort v0.2" + echo "bcftools_sort 0.2.0" echo "" echo "Sorts VCF/BCF files." echo "" @@ -483,10 +483,10 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_sort" -LABEL org.opencontainers.image.created="2024-09-12T12:36:17Z" +LABEL org.opencontainers.image.created="2024-09-12T13:23:18Z" LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools" -LABEL org.opencontainers.image.revision="f22ab0eab58dcd6bff89d8d73fe951953ff1260f" -LABEL org.opencontainers.image.version="v0.2" +LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" +LABEL org.opencontainers.image.version="0.2.0" VIASHDOCKER fi @@ -622,7 +622,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "bcftools_sort v0.2" + echo "bcftools_sort 0.2.0" exit ;; --input) @@ -764,7 +764,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/bcftools/bcftools_sort:v0.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/bcftools/bcftools_sort:0.2.0' fi # print dockerfile diff --git a/target/executable/bcl_convert/.config.vsh.yaml b/target/executable/bcl_convert/.config.vsh.yaml index 5e4a471a..62449adf 100644 --- a/target/executable/bcl_convert/.config.vsh.yaml +++ b/target/executable/bcl_convert/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "bcl_convert" -version: "v0.2" +version: "0.2.0" authors: - name: "Toni Verbeiren" roles: @@ -386,7 +386,7 @@ engines: id: "docker" image: "debian:trixie-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -417,22 +417,22 @@ build_info: engine: "docker|native" output: "target/executable/bcl_convert" executable: "target/executable/bcl_convert/bcl_convert" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bcl_convert/bcl_convert b/target/executable/bcl_convert/bcl_convert index 5f558ec5..f59040f8 100755 --- a/target/executable/bcl_convert/bcl_convert +++ b/target/executable/bcl_convert/bcl_convert @@ -1,10 +1,10 @@ #!/usr/bin/env bash -# bcl_convert v0.2 +# bcl_convert 0.2.0 # -# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. +# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. # # The component may contain files which fall under a different license. The # authors of this component should specify the license in the header of such @@ -175,7 +175,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "bcl_convert v0.2" + echo "bcl_convert 0.2.0" echo "" echo "Convert bcl files to fastq files using bcl-convert." echo "Information about upgrading from bcl2fastq via" @@ -599,10 +599,10 @@ RUN echo "bcl-convert: \"$(bcl-convert -V 2>&1 >/dev/null | sed -n '/Version/ s/ LABEL org.opencontainers.image.authors="Toni Verbeiren, Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component bcl_convert" -LABEL org.opencontainers.image.created="2024-09-12T12:36:23Z" +LABEL org.opencontainers.image.created="2024-09-12T13:23:24Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox" -LABEL org.opencontainers.image.revision="f22ab0eab58dcd6bff89d8d73fe951953ff1260f" -LABEL org.opencontainers.image.version="v0.2" +LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" +LABEL org.opencontainers.image.version="0.2.0" VIASHDOCKER fi @@ -738,7 +738,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "bcl_convert v0.2" + echo "bcl_convert 0.2.0" exit ;; --bcl_input_directory) @@ -1100,7 +1100,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/bcl_convert:v0.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/bcl_convert:0.2.0' fi # print dockerfile diff --git a/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml b/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml index a325255a..ce6f84b8 100644 --- a/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml +++ b/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bd_rhapsody_make_reference" namespace: "bd_rhapsody" -version: "v0.2" +version: "0.2.0" authors: - name: "Robrecht Cannoodt" roles: @@ -243,7 +243,7 @@ engines: id: "docker" image: "bdgenomics/rhapsody:2.2.1" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -269,22 +269,22 @@ build_info: engine: "docker|native" output: "target/executable/bd_rhapsody/bd_rhapsody_make_reference" executable: "target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference b/target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference index 01d4481a..68699da2 100755 --- a/target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference +++ b/target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference @@ -1,10 +1,10 @@ #!/usr/bin/env bash -# bd_rhapsody_make_reference v0.2 +# bd_rhapsody_make_reference 0.2.0 # -# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. +# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. # # The component may contain files which fall under a different license. The # authors of this component should specify the license in the header of such @@ -175,7 +175,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "bd_rhapsody_make_reference v0.2" + echo "bd_rhapsody_make_reference 0.2.0" echo "" echo "The Reference Files Generator creates an archive containing Genome Index" echo "and Transcriptome annotation files needed for the BD Rhapsody Sequencing" @@ -549,10 +549,10 @@ RUN echo "bdgenomics/rhapsody: 2.2.1" > /var/software_versions.txt LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Weiwei Schultz" LABEL org.opencontainers.image.description="Companion container for running component bd_rhapsody bd_rhapsody_make_reference" -LABEL org.opencontainers.image.created="2024-09-12T12:36:26Z" +LABEL org.opencontainers.image.created="2024-09-12T13:23:27Z" LABEL org.opencontainers.image.source="https://bitbucket.org/CRSwDev/cwl/src/master/v2.2.1/Extra_Utilities/" -LABEL org.opencontainers.image.revision="f22ab0eab58dcd6bff89d8d73fe951953ff1260f" -LABEL org.opencontainers.image.version="v0.2" +LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" +LABEL org.opencontainers.image.version="0.2.0" VIASHDOCKER fi @@ -688,7 +688,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "bd_rhapsody_make_reference v0.2" + echo "bd_rhapsody_make_reference 0.2.0" exit ;; --genome_fasta) @@ -879,7 +879,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/bd_rhapsody/bd_rhapsody_make_reference:v0.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/bd_rhapsody/bd_rhapsody_make_reference:0.2.0' fi # print dockerfile diff --git a/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml b/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml index 3cd88597..81cb8fd8 100644 --- a/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bedtools_bamtofastq" namespace: "bedtools" -version: "v0.2" +version: "0.2.0" authors: - name: "Theodoro Gasperin Terra Camargo" roles: @@ -164,7 +164,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -186,22 +186,22 @@ build_info: engine: "docker|native" output: "target/executable/bedtools/bedtools_bamtofastq" executable: "target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq b/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq index bf23ccf1..81e65254 100755 --- a/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq +++ b/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq @@ -1,10 +1,10 @@ #!/usr/bin/env bash -# bedtools_bamtofastq v0.2 +# bedtools_bamtofastq 0.2.0 # -# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. +# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. # # The component may contain files which fall under a different license. The # authors of this component should specify the license in the header of such @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "bedtools_bamtofastq v0.2" + echo "bedtools_bamtofastq 0.2.0" echo "" echo "Conversion tool for extracting FASTQ records from sequence alignments in BAM" echo "format." @@ -483,10 +483,10 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bamtofastq" -LABEL org.opencontainers.image.created="2024-09-12T12:36:11Z" +LABEL org.opencontainers.image.created="2024-09-12T13:23:12Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="f22ab0eab58dcd6bff89d8d73fe951953ff1260f" -LABEL org.opencontainers.image.version="v0.2" +LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" +LABEL org.opencontainers.image.version="0.2.0" VIASHDOCKER fi @@ -622,7 +622,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "bedtools_bamtofastq v0.2" + echo "bedtools_bamtofastq 0.2.0" exit ;; --input) @@ -769,7 +769,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/bedtools/bedtools_bamtofastq:v0.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/bedtools/bedtools_bamtofastq:0.2.0' fi # print dockerfile diff --git a/target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml b/target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml index d43f96e8..3e240fab 100644 --- a/target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bedtools_bed12tobed6" namespace: "bedtools" -version: "v0.2" +version: "0.2.0" authors: - name: "Theodoro Gasperin Terra Camargo" roles: @@ -153,7 +153,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -175,22 +175,22 @@ build_info: engine: "docker|native" output: "target/executable/bedtools/bedtools_bed12tobed6" executable: "target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6 b/target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6 index e2b7bbe1..75b5e8a1 100755 --- a/target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6 +++ b/target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6 @@ -1,10 +1,10 @@ #!/usr/bin/env bash -# bedtools_bed12tobed6 v0.2 +# bedtools_bed12tobed6 0.2.0 # -# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. +# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. # # The component may contain files which fall under a different license. The # authors of this component should specify the license in the header of such @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "bedtools_bed12tobed6 v0.2" + echo "bedtools_bed12tobed6 0.2.0" echo "" echo "Converts BED features in BED12 (a.k.a. “blocked” BED features such as genes) to" echo "discrete BED6 features." @@ -480,10 +480,10 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bed12tobed6" -LABEL org.opencontainers.image.created="2024-09-12T12:36:10Z" +LABEL org.opencontainers.image.created="2024-09-12T13:23:10Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="f22ab0eab58dcd6bff89d8d73fe951953ff1260f" -LABEL org.opencontainers.image.version="v0.2" +LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" +LABEL org.opencontainers.image.version="0.2.0" VIASHDOCKER fi @@ -619,7 +619,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "bedtools_bed12tobed6 v0.2" + echo "bedtools_bed12tobed6 0.2.0" exit ;; --input) @@ -754,7 +754,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/bedtools/bedtools_bed12tobed6:v0.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/bedtools/bedtools_bed12tobed6:0.2.0' fi # print dockerfile diff --git a/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml b/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml index bc2ceac5..8a99759a 100644 --- a/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bedtools_bedtobam" namespace: "bedtools" -version: "v0.2" +version: "0.2.0" authors: - name: "Theodoro Gasperin Terra Camargo" roles: @@ -186,7 +186,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -213,22 +213,22 @@ build_info: engine: "docker|native" output: "target/executable/bedtools/bedtools_bedtobam" executable: "target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam b/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam index beebdc63..ea07841b 100755 --- a/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam +++ b/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam @@ -1,10 +1,10 @@ #!/usr/bin/env bash -# bedtools_bedtobam v0.2 +# bedtools_bedtobam 0.2.0 # -# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. +# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. # # The component may contain files which fall under a different license. The # authors of this component should specify the license in the header of such @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "bedtools_bedtobam v0.2" + echo "bedtools_bedtobam 0.2.0" echo "" echo "Converts feature records (bed/gff/vcf) to BAM format." echo "" @@ -496,10 +496,10 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bedtobam" -LABEL org.opencontainers.image.created="2024-09-12T12:36:12Z" +LABEL org.opencontainers.image.created="2024-09-12T13:23:13Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="f22ab0eab58dcd6bff89d8d73fe951953ff1260f" -LABEL org.opencontainers.image.version="v0.2" +LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" +LABEL org.opencontainers.image.version="0.2.0" VIASHDOCKER fi @@ -635,7 +635,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "bedtools_bedtobam v0.2" + echo "bedtools_bedtobam 0.2.0" exit ;; --input) @@ -809,7 +809,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/bedtools/bedtools_bedtobam:v0.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/bedtools/bedtools_bedtobam:0.2.0' fi # print dockerfile diff --git a/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml b/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml index 590b76aa..7f674a27 100644 --- a/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bedtools_getfasta" namespace: "bedtools" -version: "v0.2" +version: "0.2.0" authors: - name: "Dries Schaumont" roles: @@ -209,7 +209,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -231,22 +231,22 @@ build_info: engine: "docker|native" output: "target/executable/bedtools/bedtools_getfasta" executable: "target/executable/bedtools/bedtools_getfasta/bedtools_getfasta" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta b/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta index ca445891..b63954c0 100755 --- a/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta +++ b/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta @@ -1,10 +1,10 @@ #!/usr/bin/env bash -# bedtools_getfasta v0.2 +# bedtools_getfasta 0.2.0 # -# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. +# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. # # The component may contain files which fall under a different license. The # authors of this component should specify the license in the header of such @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "bedtools_getfasta v0.2" + echo "bedtools_getfasta 0.2.0" echo "" echo "Extract sequences from a FASTA file for each of the intervals defined in a" echo "BED/GFF/VCF file." @@ -526,10 +526,10 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_getfasta" -LABEL org.opencontainers.image.created="2024-09-12T12:36:10Z" +LABEL org.opencontainers.image.created="2024-09-12T13:23:11Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="f22ab0eab58dcd6bff89d8d73fe951953ff1260f" -LABEL org.opencontainers.image.version="v0.2" +LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" +LABEL org.opencontainers.image.version="0.2.0" VIASHDOCKER fi @@ -665,7 +665,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "bedtools_getfasta v0.2" + echo "bedtools_getfasta 0.2.0" exit ;; --input_fasta) @@ -840,7 +840,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/bedtools/bedtools_getfasta:v0.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/bedtools/bedtools_getfasta:0.2.0' fi # print dockerfile diff --git a/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml b/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml index 2fc17b4b..8a813def 100644 --- a/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bedtools_groupby" namespace: "bedtools" -version: "v0.2" +version: "0.2.0" authors: - name: "Theodoro Gasperin Terra Camargo" roles: @@ -250,7 +250,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -272,22 +272,22 @@ build_info: engine: "docker|native" output: "target/executable/bedtools/bedtools_groupby" executable: "target/executable/bedtools/bedtools_groupby/bedtools_groupby" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_groupby/bedtools_groupby b/target/executable/bedtools/bedtools_groupby/bedtools_groupby index 7270e1ca..9df637a2 100755 --- a/target/executable/bedtools/bedtools_groupby/bedtools_groupby +++ b/target/executable/bedtools/bedtools_groupby/bedtools_groupby @@ -1,10 +1,10 @@ #!/usr/bin/env bash -# bedtools_groupby v0.2 +# bedtools_groupby 0.2.0 # -# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. +# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. # # The component may contain files which fall under a different license. The # authors of this component should specify the license in the header of such @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "bedtools_groupby v0.2" + echo "bedtools_groupby 0.2.0" echo "" echo "Summarizes a dataset column based upon common column groupings." echo "Akin to the SQL \"group by\" command." @@ -552,10 +552,10 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_groupby" -LABEL org.opencontainers.image.created="2024-09-12T12:36:11Z" +LABEL org.opencontainers.image.created="2024-09-12T13:23:12Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="f22ab0eab58dcd6bff89d8d73fe951953ff1260f" -LABEL org.opencontainers.image.version="v0.2" +LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" +LABEL org.opencontainers.image.version="0.2.0" VIASHDOCKER fi @@ -691,7 +691,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "bedtools_groupby v0.2" + echo "bedtools_groupby 0.2.0" exit ;; --input) @@ -938,7 +938,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/bedtools/bedtools_groupby:v0.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/bedtools/bedtools_groupby:0.2.0' fi # print dockerfile diff --git a/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml b/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml index ed2574d5..23529582 100644 --- a/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bedtools_intersect" namespace: "bedtools" -version: "v0.2" +version: "0.2.0" authors: - name: "Theodoro Gasperin Terra Camargo" roles: @@ -387,7 +387,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -409,22 +409,22 @@ build_info: engine: "docker|native" output: "target/executable/bedtools/bedtools_intersect" executable: "target/executable/bedtools/bedtools_intersect/bedtools_intersect" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_intersect/bedtools_intersect b/target/executable/bedtools/bedtools_intersect/bedtools_intersect index ce559775..47f7ab5f 100755 --- a/target/executable/bedtools/bedtools_intersect/bedtools_intersect +++ b/target/executable/bedtools/bedtools_intersect/bedtools_intersect @@ -1,10 +1,10 @@ #!/usr/bin/env bash -# bedtools_intersect v0.2 +# bedtools_intersect 0.2.0 # -# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. +# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. # # The component may contain files which fall under a different license. The # authors of this component should specify the license in the header of such @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "bedtools_intersect v0.2" + echo "bedtools_intersect 0.2.0" echo "" echo "bedtools intersect allows one to screen for overlaps between two sets of genomic" echo "features." @@ -633,10 +633,10 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_intersect" -LABEL org.opencontainers.image.created="2024-09-12T12:36:10Z" +LABEL org.opencontainers.image.created="2024-09-12T13:23:11Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="f22ab0eab58dcd6bff89d8d73fe951953ff1260f" -LABEL org.opencontainers.image.version="v0.2" +LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" +LABEL org.opencontainers.image.version="0.2.0" VIASHDOCKER fi @@ -772,7 +772,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "bedtools_intersect v0.2" + echo "bedtools_intersect 0.2.0" exit ;; --input_a) @@ -1171,7 +1171,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/bedtools/bedtools_intersect:v0.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/bedtools/bedtools_intersect:0.2.0' fi # print dockerfile diff --git a/target/executable/bedtools/bedtools_links/.config.vsh.yaml b/target/executable/bedtools/bedtools_links/.config.vsh.yaml index eec0cb1c..6dd22666 100644 --- a/target/executable/bedtools/bedtools_links/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_links/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bedtools_links" namespace: "bedtools" -version: "v0.2" +version: "0.2.0" authors: - name: "Theodoro Gasperin Terra Camargo" roles: @@ -187,7 +187,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -209,22 +209,22 @@ build_info: engine: "docker|native" output: "target/executable/bedtools/bedtools_links" executable: "target/executable/bedtools/bedtools_links/bedtools_links" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_links/bedtools_links b/target/executable/bedtools/bedtools_links/bedtools_links index 9a0acef3..3d95793f 100755 --- a/target/executable/bedtools/bedtools_links/bedtools_links +++ b/target/executable/bedtools/bedtools_links/bedtools_links @@ -1,10 +1,10 @@ #!/usr/bin/env bash -# bedtools_links v0.2 +# bedtools_links 0.2.0 # -# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. +# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. # # The component may contain files which fall under a different license. The # authors of this component should specify the license in the header of such @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "bedtools_links v0.2" + echo "bedtools_links 0.2.0" echo "" echo "Creates an HTML file with links to an instance of the UCSC Genome Browser for" echo "all features / intervals in a file." @@ -500,10 +500,10 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_links" -LABEL org.opencontainers.image.created="2024-09-12T12:36:11Z" +LABEL org.opencontainers.image.created="2024-09-12T13:23:11Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="f22ab0eab58dcd6bff89d8d73fe951953ff1260f" -LABEL org.opencontainers.image.version="v0.2" +LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" +LABEL org.opencontainers.image.version="0.2.0" VIASHDOCKER fi @@ -639,7 +639,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "bedtools_links v0.2" + echo "bedtools_links 0.2.0" exit ;; --input) @@ -815,7 +815,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/bedtools/bedtools_links:v0.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/bedtools/bedtools_links:0.2.0' fi # print dockerfile diff --git a/target/executable/bedtools/bedtools_merge/.config.vsh.yaml b/target/executable/bedtools/bedtools_merge/.config.vsh.yaml index 62d60920..5e2a176c 100644 --- a/target/executable/bedtools/bedtools_merge/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_merge/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bedtools_merge" namespace: "bedtools" -version: "v0.2" +version: "0.2.0" authors: - name: "Theodoro Gasperin Terra Camargo" roles: @@ -256,7 +256,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -278,22 +278,22 @@ build_info: engine: "docker|native" output: "target/executable/bedtools/bedtools_merge" executable: "target/executable/bedtools/bedtools_merge/bedtools_merge" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_merge/bedtools_merge b/target/executable/bedtools/bedtools_merge/bedtools_merge index c297beba..ca603176 100755 --- a/target/executable/bedtools/bedtools_merge/bedtools_merge +++ b/target/executable/bedtools/bedtools_merge/bedtools_merge @@ -1,10 +1,10 @@ #!/usr/bin/env bash -# bedtools_merge v0.2 +# bedtools_merge 0.2.0 # -# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. +# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. # # The component may contain files which fall under a different license. The # authors of this component should specify the license in the header of such @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "bedtools_merge v0.2" + echo "bedtools_merge 0.2.0" echo "" echo "Merges overlapping BED/GFF/VCF entries into a single interval." echo "" @@ -558,10 +558,10 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_merge" -LABEL org.opencontainers.image.created="2024-09-12T12:36:09Z" +LABEL org.opencontainers.image.created="2024-09-12T13:23:10Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="f22ab0eab58dcd6bff89d8d73fe951953ff1260f" -LABEL org.opencontainers.image.version="v0.2" +LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" +LABEL org.opencontainers.image.version="0.2.0" VIASHDOCKER fi @@ -697,7 +697,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "bedtools_merge v0.2" + echo "bedtools_merge 0.2.0" exit ;; --input) @@ -948,7 +948,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/bedtools/bedtools_merge:v0.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/bedtools/bedtools_merge:0.2.0' fi # print dockerfile diff --git a/target/executable/bedtools/bedtools_sort/.config.vsh.yaml b/target/executable/bedtools/bedtools_sort/.config.vsh.yaml index 82edaa01..4e2522ca 100644 --- a/target/executable/bedtools/bedtools_sort/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_sort/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bedtools_sort" namespace: "bedtools" -version: "v0.2" +version: "0.2.0" authors: - name: "Theodoro Gasperin Terra Camargo" roles: @@ -199,7 +199,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -221,22 +221,22 @@ build_info: engine: "docker|native" output: "target/executable/bedtools/bedtools_sort" executable: "target/executable/bedtools/bedtools_sort/bedtools_sort" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_sort/bedtools_sort b/target/executable/bedtools/bedtools_sort/bedtools_sort index ef4eef79..0a849ac7 100755 --- a/target/executable/bedtools/bedtools_sort/bedtools_sort +++ b/target/executable/bedtools/bedtools_sort/bedtools_sort @@ -1,10 +1,10 @@ #!/usr/bin/env bash -# bedtools_sort v0.2 +# bedtools_sort 0.2.0 # -# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. +# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. # # The component may contain files which fall under a different license. The # authors of this component should specify the license in the header of such @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "bedtools_sort v0.2" + echo "bedtools_sort 0.2.0" echo "" echo "Sorts a feature file (bed/gff/vcf) by chromosome and other criteria." echo "" @@ -509,10 +509,10 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_sort" -LABEL org.opencontainers.image.created="2024-09-12T12:36:11Z" +LABEL org.opencontainers.image.created="2024-09-12T13:23:12Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="f22ab0eab58dcd6bff89d8d73fe951953ff1260f" -LABEL org.opencontainers.image.version="v0.2" +LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" +LABEL org.opencontainers.image.version="0.2.0" VIASHDOCKER fi @@ -648,7 +648,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "bedtools_sort v0.2" + echo "bedtools_sort 0.2.0" exit ;; --input) @@ -836,7 +836,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/bedtools/bedtools_sort:v0.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/bedtools/bedtools_sort:0.2.0' fi # print dockerfile diff --git a/target/executable/busco/busco_download_datasets/.config.vsh.yaml b/target/executable/busco/busco_download_datasets/.config.vsh.yaml index 0c396ede..3ab46e38 100644 --- a/target/executable/busco/busco_download_datasets/.config.vsh.yaml +++ b/target/executable/busco/busco_download_datasets/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "busco_download_datasets" namespace: "busco" -version: "v0.2" +version: "0.2.0" authors: - name: "Dorien Roosen" roles: @@ -141,7 +141,7 @@ engines: id: "docker" image: "quay.io/biocontainers/busco:5.7.1--pyhdfd78af_0" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -157,22 +157,22 @@ build_info: engine: "docker|native" output: "target/executable/busco/busco_download_datasets" executable: "target/executable/busco/busco_download_datasets/busco_download_datasets" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/busco/busco_download_datasets/busco_download_datasets b/target/executable/busco/busco_download_datasets/busco_download_datasets index 8dcde5d1..f8f8faa4 100755 --- a/target/executable/busco/busco_download_datasets/busco_download_datasets +++ b/target/executable/busco/busco_download_datasets/busco_download_datasets @@ -1,10 +1,10 @@ #!/usr/bin/env bash -# busco_download_datasets v0.2 +# busco_download_datasets 0.2.0 # -# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. +# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. # # The component may contain files which fall under a different license. The # authors of this component should specify the license in the header of such @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "busco_download_datasets v0.2" + echo "busco_download_datasets 0.2.0" echo "" echo "Downloads available busco datasets" echo "" @@ -475,10 +475,10 @@ RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_version LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component busco busco_download_datasets" -LABEL org.opencontainers.image.created="2024-09-12T12:36:20Z" +LABEL org.opencontainers.image.created="2024-09-12T13:23:21Z" LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco" -LABEL org.opencontainers.image.revision="f22ab0eab58dcd6bff89d8d73fe951953ff1260f" -LABEL org.opencontainers.image.version="v0.2" +LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" +LABEL org.opencontainers.image.version="0.2.0" VIASHDOCKER fi @@ -614,7 +614,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "busco_download_datasets v0.2" + echo "busco_download_datasets 0.2.0" exit ;; --download) @@ -727,7 +727,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/busco/busco_download_datasets:v0.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/busco/busco_download_datasets:0.2.0' fi # print dockerfile diff --git a/target/executable/busco/busco_list_datasets/.config.vsh.yaml b/target/executable/busco/busco_list_datasets/.config.vsh.yaml index ce80e0de..fde9e6a2 100644 --- a/target/executable/busco/busco_list_datasets/.config.vsh.yaml +++ b/target/executable/busco/busco_list_datasets/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "busco_list_datasets" namespace: "busco" -version: "v0.2" +version: "0.2.0" authors: - name: "Dorien Roosen" roles: @@ -128,7 +128,7 @@ engines: id: "docker" image: "quay.io/biocontainers/busco:5.7.1--pyhdfd78af_0" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -144,22 +144,22 @@ build_info: engine: "docker|native" output: "target/executable/busco/busco_list_datasets" executable: "target/executable/busco/busco_list_datasets/busco_list_datasets" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/busco/busco_list_datasets/busco_list_datasets b/target/executable/busco/busco_list_datasets/busco_list_datasets index 32171074..5e3d21f1 100755 --- a/target/executable/busco/busco_list_datasets/busco_list_datasets +++ b/target/executable/busco/busco_list_datasets/busco_list_datasets @@ -1,10 +1,10 @@ #!/usr/bin/env bash -# busco_list_datasets v0.2 +# busco_list_datasets 0.2.0 # -# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. +# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. # # The component may contain files which fall under a different license. The # authors of this component should specify the license in the header of such @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "busco_list_datasets v0.2" + echo "busco_list_datasets 0.2.0" echo "" echo "Lists the available busco datasets" echo "" @@ -465,10 +465,10 @@ RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_version LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component busco busco_list_datasets" -LABEL org.opencontainers.image.created="2024-09-12T12:36:20Z" +LABEL org.opencontainers.image.created="2024-09-12T13:23:21Z" LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco" -LABEL org.opencontainers.image.revision="f22ab0eab58dcd6bff89d8d73fe951953ff1260f" -LABEL org.opencontainers.image.version="v0.2" +LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" +LABEL org.opencontainers.image.version="0.2.0" VIASHDOCKER fi @@ -604,7 +604,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "busco_list_datasets v0.2" + echo "busco_list_datasets 0.2.0" exit ;; --output) @@ -712,7 +712,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/busco/busco_list_datasets:v0.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/busco/busco_list_datasets:0.2.0' fi # print dockerfile diff --git a/target/executable/busco/busco_run/.config.vsh.yaml b/target/executable/busco/busco_run/.config.vsh.yaml index 2997d990..90209d89 100644 --- a/target/executable/busco/busco_run/.config.vsh.yaml +++ b/target/executable/busco/busco_run/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "busco_run" namespace: "busco" -version: "v0.2" +version: "0.2.0" authors: - name: "Dorien Roosen" roles: @@ -406,7 +406,7 @@ engines: id: "docker" image: "quay.io/biocontainers/busco:5.7.1--pyhdfd78af_0" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -422,22 +422,22 @@ build_info: engine: "docker|native" output: "target/executable/busco/busco_run" executable: "target/executable/busco/busco_run/busco_run" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/busco/busco_run/busco_run b/target/executable/busco/busco_run/busco_run index fb2b511f..708498d6 100755 --- a/target/executable/busco/busco_run/busco_run +++ b/target/executable/busco/busco_run/busco_run @@ -1,10 +1,10 @@ #!/usr/bin/env bash -# busco_run v0.2 +# busco_run 0.2.0 # -# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. +# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. # # The component may contain files which fall under a different license. The # authors of this component should specify the license in the header of such @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "busco_run v0.2" + echo "busco_run 0.2.0" echo "" echo "Assessment of genome assembly and annotation completeness with single copy" echo "orthologs" @@ -632,10 +632,10 @@ RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_version LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component busco busco_run" -LABEL org.opencontainers.image.created="2024-09-12T12:36:21Z" +LABEL org.opencontainers.image.created="2024-09-12T13:23:21Z" LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco" -LABEL org.opencontainers.image.revision="f22ab0eab58dcd6bff89d8d73fe951953ff1260f" -LABEL org.opencontainers.image.version="v0.2" +LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" +LABEL org.opencontainers.image.version="0.2.0" VIASHDOCKER fi @@ -771,7 +771,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "busco_run v0.2" + echo "busco_run 0.2.0" exit ;; --input) @@ -1126,7 +1126,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/busco/busco_run:v0.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/busco/busco_run:0.2.0' fi # print dockerfile diff --git a/target/executable/cutadapt/.config.vsh.yaml b/target/executable/cutadapt/.config.vsh.yaml index 63e36d40..864464d5 100644 --- a/target/executable/cutadapt/.config.vsh.yaml +++ b/target/executable/cutadapt/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "cutadapt" -version: "v0.2" +version: "0.2.0" authors: - name: "Toni Verbeiren" roles: @@ -718,7 +718,7 @@ engines: id: "docker" image: "python:3.12" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "python" @@ -739,22 +739,22 @@ build_info: engine: "docker|native" output: "target/executable/cutadapt" executable: "target/executable/cutadapt/cutadapt" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/cutadapt/cutadapt b/target/executable/cutadapt/cutadapt index cc148a79..d7dd8908 100755 --- a/target/executable/cutadapt/cutadapt +++ b/target/executable/cutadapt/cutadapt @@ -1,10 +1,10 @@ #!/usr/bin/env bash -# cutadapt v0.2 +# cutadapt 0.2.0 # -# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. +# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. # # The component may contain files which fall under a different license. The # authors of this component should specify the license in the header of such @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "cutadapt v0.2" + echo "cutadapt 0.2.0" echo "" echo "Cutadapt removes adapter sequences from high-throughput sequencing reads." echo "" @@ -831,10 +831,10 @@ RUN cutadapt --version | sed 's/\(.*\)/cutadapt: "\1"/' > /var/software_versions LABEL org.opencontainers.image.authors="Toni Verbeiren" LABEL org.opencontainers.image.description="Companion container for running component cutadapt" -LABEL org.opencontainers.image.created="2024-09-12T12:36:25Z" +LABEL org.opencontainers.image.created="2024-09-12T13:23:26Z" LABEL org.opencontainers.image.source="https://github.com/marcelm/cutadapt" -LABEL org.opencontainers.image.revision="f22ab0eab58dcd6bff89d8d73fe951953ff1260f" -LABEL org.opencontainers.image.version="v0.2" +LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" +LABEL org.opencontainers.image.version="0.2.0" VIASHDOCKER fi @@ -970,7 +970,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "cutadapt v0.2" + echo "cutadapt 0.2.0" exit ;; --adapter) @@ -1785,7 +1785,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/cutadapt:v0.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/cutadapt:0.2.0' fi # print dockerfile diff --git a/target/executable/falco/.config.vsh.yaml b/target/executable/falco/.config.vsh.yaml index 1fba3573..b6aceb89 100644 --- a/target/executable/falco/.config.vsh.yaml +++ b/target/executable/falco/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "falco" -version: "v0.2" +version: "0.2.0" authors: - name: "Toni Verbeiren" roles: @@ -287,7 +287,7 @@ engines: id: "docker" image: "debian:trixie-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -316,22 +316,22 @@ build_info: engine: "docker|native" output: "target/executable/falco" executable: "target/executable/falco/falco" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/falco/falco b/target/executable/falco/falco index b86a375c..8c4e44dd 100755 --- a/target/executable/falco/falco +++ b/target/executable/falco/falco @@ -1,10 +1,10 @@ #!/usr/bin/env bash -# falco v0.2 +# falco 0.2.0 # -# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. +# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. # # The component may contain files which fall under a different license. The # authors of this component should specify the license in the header of such @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "falco v0.2" + echo "falco 0.2.0" echo "" echo "A C++ drop-in replacement of FastQC to assess the quality of sequence read data" echo "" @@ -589,10 +589,10 @@ RUN echo "falco: \"$(falco -v | sed -n 's/^falco //p')\"" > /var/software_versio LABEL org.opencontainers.image.authors="Toni Verbeiren" LABEL org.opencontainers.image.description="Companion container for running component falco" -LABEL org.opencontainers.image.created="2024-09-12T12:36:26Z" +LABEL org.opencontainers.image.created="2024-09-12T13:23:27Z" LABEL org.opencontainers.image.source="https://github.com/smithlabcode/falco" -LABEL org.opencontainers.image.revision="f22ab0eab58dcd6bff89d8d73fe951953ff1260f" -LABEL org.opencontainers.image.version="v0.2" +LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" +LABEL org.opencontainers.image.version="0.2.0" VIASHDOCKER fi @@ -728,7 +728,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "falco v0.2" + echo "falco 0.2.0" exit ;; --input) @@ -996,7 +996,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/falco:v0.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/falco:0.2.0' fi # print dockerfile diff --git a/target/executable/fastp/.config.vsh.yaml b/target/executable/fastp/.config.vsh.yaml index da352935..0300f8a8 100644 --- a/target/executable/fastp/.config.vsh.yaml +++ b/target/executable/fastp/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "fastp" -version: "v0.2" +version: "0.2.0" authors: - name: "Robrecht Cannoodt" roles: @@ -1066,7 +1066,7 @@ engines: id: "docker" image: "quay.io/biocontainers/fastp:0.23.4--hadf994f_2" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -1082,22 +1082,22 @@ build_info: engine: "docker|native" output: "target/executable/fastp" executable: "target/executable/fastp/fastp" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/fastp/fastp b/target/executable/fastp/fastp index 5ddee71a..d5ec27e3 100755 --- a/target/executable/fastp/fastp +++ b/target/executable/fastp/fastp @@ -1,10 +1,10 @@ #!/usr/bin/env bash -# fastp v0.2 +# fastp 0.2.0 # -# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. +# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. # # The component may contain files which fall under a different license. The # authors of this component should specify the license in the header of such @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "fastp v0.2" + echo "fastp 0.2.0" echo "" echo "An ultra-fast all-in-one FASTQ preprocessor" echo "(QC/adapters/trimming/filtering/splitting/merging...)." @@ -1028,10 +1028,10 @@ RUN fastp --version 2>&1 | sed 's# #: "#;s#$#"#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component fastp" -LABEL org.opencontainers.image.created="2024-09-12T12:36:23Z" +LABEL org.opencontainers.image.created="2024-09-12T13:23:24Z" LABEL org.opencontainers.image.source="https://github.com/OpenGene/fastp" -LABEL org.opencontainers.image.revision="f22ab0eab58dcd6bff89d8d73fe951953ff1260f" -LABEL org.opencontainers.image.version="v0.2" +LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" +LABEL org.opencontainers.image.version="0.2.0" VIASHDOCKER fi @@ -1167,7 +1167,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "fastp v0.2" + echo "fastp 0.2.0" exit ;; --in1) @@ -2183,7 +2183,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/fastp:v0.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/fastp:0.2.0' fi # print dockerfile diff --git a/target/executable/fastqc/.config.vsh.yaml b/target/executable/fastqc/.config.vsh.yaml index 6bbdf9b0..757c0da0 100644 --- a/target/executable/fastqc/.config.vsh.yaml +++ b/target/executable/fastqc/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "fastqc" -version: "v0.2" +version: "0.2.0" authors: - name: "Theodoro Gasperin Terra Camargo" roles: @@ -323,7 +323,7 @@ engines: id: "docker" image: "biocontainers/fastqc:v0.11.9_cv8" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -339,22 +339,22 @@ build_info: engine: "docker|native" output: "target/executable/fastqc" executable: "target/executable/fastqc/fastqc" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/fastqc/fastqc b/target/executable/fastqc/fastqc index 01ede962..23ba5bc0 100755 --- a/target/executable/fastqc/fastqc +++ b/target/executable/fastqc/fastqc @@ -1,10 +1,10 @@ #!/usr/bin/env bash -# fastqc v0.2 +# fastqc 0.2.0 # -# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. +# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. # # The component may contain files which fall under a different license. The # authors of this component should specify the license in the header of such @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "fastqc v0.2" + echo "fastqc 0.2.0" echo "" echo "FastQC - A high throughput sequence QC analysis tool." echo "" @@ -601,10 +601,10 @@ RUN echo "fastqc: $(fastqc --version | sed -n 's/^FastQC //p')" > /var/software_ LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component fastqc" -LABEL org.opencontainers.image.created="2024-09-12T12:36:16Z" +LABEL org.opencontainers.image.created="2024-09-12T13:23:17Z" LABEL org.opencontainers.image.source="https://github.com/s-andrews/FastQC" -LABEL org.opencontainers.image.revision="f22ab0eab58dcd6bff89d8d73fe951953ff1260f" -LABEL org.opencontainers.image.version="v0.2" +LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" +LABEL org.opencontainers.image.version="0.2.0" VIASHDOCKER fi @@ -740,7 +740,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "fastqc v0.2" + echo "fastqc 0.2.0" exit ;; --input) @@ -1018,7 +1018,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/fastqc:v0.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/fastqc:0.2.0' fi # print dockerfile diff --git a/target/executable/featurecounts/.config.vsh.yaml b/target/executable/featurecounts/.config.vsh.yaml index 39658666..54657c64 100644 --- a/target/executable/featurecounts/.config.vsh.yaml +++ b/target/executable/featurecounts/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "featurecounts" -version: "v0.2" +version: "0.2.0" authors: - name: "Sai Nirmayi Yasa" roles: @@ -627,7 +627,7 @@ engines: id: "docker" image: "quay.io/biocontainers/subread:2.0.6--he4a0461_0" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -644,22 +644,22 @@ build_info: engine: "docker|native" output: "target/executable/featurecounts" executable: "target/executable/featurecounts/featurecounts" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/featurecounts/featurecounts b/target/executable/featurecounts/featurecounts index 998eb9d8..2cb2cef2 100755 --- a/target/executable/featurecounts/featurecounts +++ b/target/executable/featurecounts/featurecounts @@ -1,10 +1,10 @@ #!/usr/bin/env bash -# featurecounts v0.2 +# featurecounts 0.2.0 # -# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. +# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. # # The component may contain files which fall under a different license. The # authors of this component should specify the license in the header of such @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "featurecounts v0.2" + echo "featurecounts 0.2.0" echo "" echo "featureCounts is a read summarization program for counting reads generated from" echo "either RNA or genomic DNA sequencing experiments by implementing highly" @@ -754,10 +754,10 @@ RUN featureCounts -v 2>&1 | sed 's/featureCounts v\([0-9.]*\)/featureCounts: \1/ LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa" LABEL org.opencontainers.image.description="Companion container for running component featurecounts" -LABEL org.opencontainers.image.created="2024-09-12T12:36:18Z" +LABEL org.opencontainers.image.created="2024-09-12T13:23:19Z" LABEL org.opencontainers.image.source="https://github.com/ShiLab-Bioinformatics/subread" -LABEL org.opencontainers.image.revision="f22ab0eab58dcd6bff89d8d73fe951953ff1260f" -LABEL org.opencontainers.image.version="v0.2" +LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" +LABEL org.opencontainers.image.version="0.2.0" VIASHDOCKER fi @@ -893,7 +893,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "featurecounts v0.2" + echo "featurecounts 0.2.0" exit ;; --annotation) @@ -1497,7 +1497,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/featurecounts:v0.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/featurecounts:0.2.0' fi # print dockerfile diff --git a/target/executable/gffread/.config.vsh.yaml b/target/executable/gffread/.config.vsh.yaml index 2aa871f2..07de39eb 100644 --- a/target/executable/gffread/.config.vsh.yaml +++ b/target/executable/gffread/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "gffread" -version: "v0.2" +version: "0.2.0" authors: - name: "Emma Rousseau" roles: @@ -668,7 +668,7 @@ engines: id: "docker" image: "quay.io/biocontainers/gffread:0.12.7--hdcf5f25_3" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -684,22 +684,22 @@ build_info: engine: "docker|native" output: "target/executable/gffread" executable: "target/executable/gffread/gffread" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/gffread/gffread b/target/executable/gffread/gffread index e63c9a7a..e5219ed3 100755 --- a/target/executable/gffread/gffread +++ b/target/executable/gffread/gffread @@ -1,10 +1,10 @@ #!/usr/bin/env bash -# gffread v0.2 +# gffread 0.2.0 # -# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. +# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. # # The component may contain files which fall under a different license. The # authors of this component should specify the license in the header of such @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "gffread v0.2" + echo "gffread 0.2.0" echo "" echo "Validate, filter, convert and perform various other operations on GFF files." echo "" @@ -807,10 +807,10 @@ RUN echo "gffread: \"$(gffread --version 2>&1)\"" > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component gffread" -LABEL org.opencontainers.image.created="2024-09-12T12:36:09Z" +LABEL org.opencontainers.image.created="2024-09-12T13:23:10Z" LABEL org.opencontainers.image.source="https://github.com/gpertea/gffread" -LABEL org.opencontainers.image.revision="f22ab0eab58dcd6bff89d8d73fe951953ff1260f" -LABEL org.opencontainers.image.version="v0.2" +LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" +LABEL org.opencontainers.image.version="0.2.0" VIASHDOCKER fi @@ -946,7 +946,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "gffread v0.2" + echo "gffread 0.2.0" exit ;; --input) @@ -1685,7 +1685,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/gffread:v0.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/gffread:0.2.0' fi # print dockerfile diff --git a/target/executable/lofreq/lofreq_call/.config.vsh.yaml b/target/executable/lofreq/lofreq_call/.config.vsh.yaml index 7f33bde5..5be6efd7 100644 --- a/target/executable/lofreq/lofreq_call/.config.vsh.yaml +++ b/target/executable/lofreq/lofreq_call/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "lofreq_call" namespace: "lofreq" -version: "v0.2" +version: "0.2.0" authors: - name: "Kai Waldrant" roles: @@ -489,7 +489,7 @@ engines: id: "docker" image: "quay.io/biocontainers/lofreq:2.1.5--py38h794fc9e_10" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -506,22 +506,22 @@ build_info: engine: "docker|native" output: "target/executable/lofreq/lofreq_call" executable: "target/executable/lofreq/lofreq_call/lofreq_call" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/lofreq/lofreq_call/lofreq_call b/target/executable/lofreq/lofreq_call/lofreq_call index 788033fc..3eb8b53f 100755 --- a/target/executable/lofreq/lofreq_call/lofreq_call +++ b/target/executable/lofreq/lofreq_call/lofreq_call @@ -1,10 +1,10 @@ #!/usr/bin/env bash -# lofreq_call v0.2 +# lofreq_call 0.2.0 # -# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. +# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. # # The component may contain files which fall under a different license. The # authors of this component should specify the license in the header of such @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "lofreq_call v0.2" + echo "lofreq_call 0.2.0" echo "" echo "Call variants from a BAM file." echo "" @@ -656,10 +656,10 @@ echo "lofreq: $version" > /var/software_versions.txt LABEL org.opencontainers.image.authors="Kai Waldrant" LABEL org.opencontainers.image.description="Companion container for running component lofreq lofreq_call" -LABEL org.opencontainers.image.created="2024-09-12T12:36:18Z" +LABEL org.opencontainers.image.created="2024-09-12T13:23:19Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox" -LABEL org.opencontainers.image.revision="f22ab0eab58dcd6bff89d8d73fe951953ff1260f" -LABEL org.opencontainers.image.version="v0.2" +LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" +LABEL org.opencontainers.image.version="0.2.0" VIASHDOCKER fi @@ -795,7 +795,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "lofreq_call v0.2" + echo "lofreq_call 0.2.0" exit ;; --input) @@ -1319,7 +1319,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/lofreq/lofreq_call:v0.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/lofreq/lofreq_call:0.2.0' fi # print dockerfile diff --git a/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml b/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml index f9912888..c74fd637 100644 --- a/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml +++ b/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "lofreq_indelqual" namespace: "lofreq" -version: "v0.2" +version: "0.2.0" authors: - name: "Kai Waldrant" roles: @@ -197,7 +197,7 @@ engines: id: "docker" image: "quay.io/biocontainers/lofreq:2.1.5--py38h794fc9e_10" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -214,22 +214,22 @@ build_info: engine: "docker|native" output: "target/executable/lofreq/lofreq_indelqual" executable: "target/executable/lofreq/lofreq_indelqual/lofreq_indelqual" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual b/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual index cc713b7d..18f8d759 100755 --- a/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual +++ b/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual @@ -1,10 +1,10 @@ #!/usr/bin/env bash -# lofreq_indelqual v0.2 +# lofreq_indelqual 0.2.0 # -# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. +# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. # # The component may contain files which fall under a different license. The # authors of this component should specify the license in the header of such @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "lofreq_indelqual v0.2" + echo "lofreq_indelqual 0.2.0" echo "" echo "Insert indel qualities into BAM file (required for indel predictions)." echo "" @@ -501,10 +501,10 @@ echo "lofreq: $version" > /var/software_versions.txt LABEL org.opencontainers.image.authors="Kai Waldrant" LABEL org.opencontainers.image.description="Companion container for running component lofreq lofreq_indelqual" -LABEL org.opencontainers.image.created="2024-09-12T12:36:18Z" +LABEL org.opencontainers.image.created="2024-09-12T13:23:19Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox" -LABEL org.opencontainers.image.revision="f22ab0eab58dcd6bff89d8d73fe951953ff1260f" -LABEL org.opencontainers.image.version="v0.2" +LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" +LABEL org.opencontainers.image.version="0.2.0" VIASHDOCKER fi @@ -640,7 +640,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "lofreq_indelqual v0.2" + echo "lofreq_indelqual 0.2.0" exit ;; --input) @@ -803,7 +803,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/lofreq/lofreq_indelqual:v0.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/lofreq/lofreq_indelqual:0.2.0' fi # print dockerfile diff --git a/target/executable/multiqc/.config.vsh.yaml b/target/executable/multiqc/.config.vsh.yaml index 0b911317..aaadc5e6 100644 --- a/target/executable/multiqc/.config.vsh.yaml +++ b/target/executable/multiqc/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "multiqc" -version: "v0.2" +version: "0.2.0" authors: - name: "Dorien Roosen" roles: @@ -433,7 +433,7 @@ engines: id: "docker" image: "quay.io/biocontainers/multiqc:1.21--pyhdfd78af_0" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -455,22 +455,22 @@ build_info: engine: "docker|native" output: "target/executable/multiqc" executable: "target/executable/multiqc/multiqc" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/multiqc/multiqc b/target/executable/multiqc/multiqc index 29b4716e..bcec38c6 100755 --- a/target/executable/multiqc/multiqc +++ b/target/executable/multiqc/multiqc @@ -1,10 +1,10 @@ #!/usr/bin/env bash -# multiqc v0.2 +# multiqc 0.2.0 # -# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. +# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. # # The component may contain files which fall under a different license. The # authors of this component should specify the license in the header of such @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "multiqc v0.2" + echo "multiqc 0.2.0" echo "" echo "MultiQC aggregates results from bioinformatics analyses across many samples into" echo "a single report." @@ -637,10 +637,10 @@ RUN multiqc --version | sed 's/multiqc, version\s\(.*\)/multiqc: "\1"/' > /var/s LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component multiqc" -LABEL org.opencontainers.image.created="2024-09-12T12:36:26Z" +LABEL org.opencontainers.image.created="2024-09-12T13:23:26Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox" -LABEL org.opencontainers.image.revision="f22ab0eab58dcd6bff89d8d73fe951953ff1260f" -LABEL org.opencontainers.image.version="v0.2" +LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" +LABEL org.opencontainers.image.version="0.2.0" VIASHDOCKER fi @@ -776,7 +776,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "multiqc v0.2" + echo "multiqc 0.2.0" exit ;; --input) @@ -1185,7 +1185,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/multiqc:v0.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/multiqc:0.2.0' fi # print dockerfile diff --git a/target/executable/pear/.config.vsh.yaml b/target/executable/pear/.config.vsh.yaml index 1e6e7b35..5e9f7c81 100644 --- a/target/executable/pear/.config.vsh.yaml +++ b/target/executable/pear/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "pear" -version: "v0.2" +version: "0.2.0" authors: - name: "Kai Waldrant" roles: @@ -380,7 +380,7 @@ engines: id: "docker" image: "quay.io/biocontainers/pear:0.9.6--h9d449c0_10" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -397,22 +397,22 @@ build_info: engine: "docker|native" output: "target/executable/pear" executable: "target/executable/pear/pear" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/pear/pear b/target/executable/pear/pear index a5358d6f..c530b2ec 100755 --- a/target/executable/pear/pear +++ b/target/executable/pear/pear @@ -1,10 +1,10 @@ #!/usr/bin/env bash -# pear v0.2 +# pear 0.2.0 # -# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. +# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. # # The component may contain files which fall under a different license. The # authors of this component should specify the license in the header of such @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "pear v0.2" + echo "pear 0.2.0" echo "" echo "PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger." echo "It is fully parallelized and can run with as low as just a few kilobytes of" @@ -597,10 +597,10 @@ echo "pear: $version" > /var/software_versions.txt LABEL org.opencontainers.image.authors="Kai Waldrant" LABEL org.opencontainers.image.description="Companion container for running component pear" -LABEL org.opencontainers.image.created="2024-09-12T12:36:12Z" +LABEL org.opencontainers.image.created="2024-09-12T13:23:13Z" LABEL org.opencontainers.image.source="https://github.com/tseemann/PEAR" -LABEL org.opencontainers.image.revision="f22ab0eab58dcd6bff89d8d73fe951953ff1260f" -LABEL org.opencontainers.image.version="v0.2" +LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" +LABEL org.opencontainers.image.version="0.2.0" VIASHDOCKER fi @@ -736,7 +736,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "pear v0.2" + echo "pear 0.2.0" exit ;; --forward_fastq) @@ -1112,7 +1112,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/pear:v0.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/pear:0.2.0' fi # print dockerfile diff --git a/target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml b/target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml index 1164d859..87d84267 100644 --- a/target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml +++ b/target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "qualimap_rnaseq" namespace: "qualimap" -version: "v0.2" +version: "0.2.0" authors: - name: "Dorien Roosen" roles: @@ -247,7 +247,7 @@ engines: id: "docker" image: "quay.io/biocontainers/qualimap:2.3--hdfd78af_0" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -263,22 +263,22 @@ build_info: engine: "docker|native" output: "target/executable/qualimap/qualimap_rnaseq" executable: "target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq b/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq index df504229..ef0e8824 100755 --- a/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq +++ b/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq @@ -1,10 +1,10 @@ #!/usr/bin/env bash -# qualimap_rnaseq v0.2 +# qualimap_rnaseq 0.2.0 # -# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. +# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. # # The component may contain files which fall under a different license. The # authors of this component should specify the license in the header of such @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "qualimap_rnaseq v0.2" + echo "qualimap_rnaseq 0.2.0" echo "" echo "Qualimap RNA-seq QC reports quality control metrics and bias estimations" echo "which are specific for whole transcriptome sequencing, including reads genomic" @@ -527,10 +527,10 @@ RUN echo QualiMap: $(qualimap 2>&1 | grep QualiMap | sed 's/^.*QualiMap//') > /v LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component qualimap qualimap_rnaseq" -LABEL org.opencontainers.image.created="2024-09-12T12:36:16Z" +LABEL org.opencontainers.image.created="2024-09-12T13:23:17Z" LABEL org.opencontainers.image.source="https://bitbucket.org/kokonech/qualimap/commits/branch/master" -LABEL org.opencontainers.image.revision="f22ab0eab58dcd6bff89d8d73fe951953ff1260f" -LABEL org.opencontainers.image.version="v0.2" +LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" +LABEL org.opencontainers.image.version="0.2.0" VIASHDOCKER fi @@ -666,7 +666,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "qualimap_rnaseq v0.2" + echo "qualimap_rnaseq 0.2.0" exit ;; --bam) @@ -877,7 +877,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/qualimap/qualimap_rnaseq:v0.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/qualimap/qualimap_rnaseq:0.2.0' fi # print dockerfile diff --git a/target/executable/rsem/rsem_prepare_reference/.config.vsh.yaml b/target/executable/rsem/rsem_prepare_reference/.config.vsh.yaml index 9a4e012a..d6a4216e 100644 --- a/target/executable/rsem/rsem_prepare_reference/.config.vsh.yaml +++ b/target/executable/rsem/rsem_prepare_reference/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "rsem_prepare_reference" namespace: "rsem" -version: "v0.2" +version: "0.2.0" authors: - name: "Sai Nirmayi Yasa" roles: @@ -352,7 +352,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -415,22 +415,22 @@ build_info: engine: "docker|native" output: "target/executable/rsem/rsem_prepare_reference" executable: "target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference b/target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference index 75d2e300..4d767518 100755 --- a/target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference +++ b/target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference @@ -1,10 +1,10 @@ #!/usr/bin/env bash -# rsem_prepare_reference v0.2 +# rsem_prepare_reference 0.2.0 # -# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. +# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. # # The component may contain files which fall under a different license. The # authors of this component should specify the license in the header of such @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "rsem_prepare_reference v0.2" + echo "rsem_prepare_reference 0.2.0" echo "" echo "RSEM is a software package for estimating gene and isoform expression levels" echo "from RNA-Seq data. This component prepares transcript references for RSEM." @@ -656,10 +656,10 @@ echo "HISAT2: `hisat2 --version | grep -oP 'hisat2-align-s version \K\d+\.\d+\.\ LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa" LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_prepare_reference" -LABEL org.opencontainers.image.created="2024-09-12T12:36:21Z" +LABEL org.opencontainers.image.created="2024-09-12T13:23:22Z" LABEL org.opencontainers.image.source="https://github.com/deweylab/RSEM" -LABEL org.opencontainers.image.revision="f22ab0eab58dcd6bff89d8d73fe951953ff1260f" -LABEL org.opencontainers.image.version="v0.2" +LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" +LABEL org.opencontainers.image.version="0.2.0" VIASHDOCKER fi @@ -795,7 +795,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "rsem_prepare_reference v0.2" + echo "rsem_prepare_reference 0.2.0" exit ;; --reference_fasta_files) @@ -1092,7 +1092,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/rsem/rsem_prepare_reference:v0.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/rsem/rsem_prepare_reference:0.2.0' fi # print dockerfile diff --git a/target/executable/salmon/salmon_index/.config.vsh.yaml b/target/executable/salmon/salmon_index/.config.vsh.yaml index 146119a5..dbe29cd1 100644 --- a/target/executable/salmon/salmon_index/.config.vsh.yaml +++ b/target/executable/salmon/salmon_index/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "salmon_index" namespace: "salmon" -version: "v0.2" +version: "0.2.0" authors: - name: "Sai Nirmayi Yasa" roles: @@ -260,7 +260,7 @@ engines: id: "docker" image: "quay.io/biocontainers/salmon:1.10.2--hecfa306_0" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -276,22 +276,22 @@ build_info: engine: "docker|native" output: "target/executable/salmon/salmon_index" executable: "target/executable/salmon/salmon_index/salmon_index" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/salmon/salmon_index/salmon_index b/target/executable/salmon/salmon_index/salmon_index index f2060ce7..eeb42d3f 100755 --- a/target/executable/salmon/salmon_index/salmon_index +++ b/target/executable/salmon/salmon_index/salmon_index @@ -1,10 +1,10 @@ #!/usr/bin/env bash -# salmon_index v0.2 +# salmon_index 0.2.0 # -# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. +# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. # # The component may contain files which fall under a different license. The # authors of this component should specify the license in the header of such @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "salmon_index v0.2" + echo "salmon_index 0.2.0" echo "" echo "Salmon is a tool for wicked-fast transcript quantification from RNA-seq data. It" echo "can either make use of pre-computed alignments (in the form of a SAM/BAM file)" @@ -546,10 +546,10 @@ RUN salmon index -v 2>&1 | sed 's/salmon \([0-9.]*\)/salmon: \1/' > /var/softwar LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa" LABEL org.opencontainers.image.description="Companion container for running component salmon salmon_index" -LABEL org.opencontainers.image.created="2024-09-12T12:36:24Z" +LABEL org.opencontainers.image.created="2024-09-12T13:23:25Z" LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon" -LABEL org.opencontainers.image.revision="f22ab0eab58dcd6bff89d8d73fe951953ff1260f" -LABEL org.opencontainers.image.version="v0.2" +LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" +LABEL org.opencontainers.image.version="0.2.0" VIASHDOCKER fi @@ -685,7 +685,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "salmon_index v0.2" + echo "salmon_index 0.2.0" exit ;; --genome) @@ -919,7 +919,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/salmon/salmon_index:v0.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/salmon/salmon_index:0.2.0' fi # print dockerfile diff --git a/target/executable/salmon/salmon_quant/.config.vsh.yaml b/target/executable/salmon/salmon_quant/.config.vsh.yaml index 936921b3..eecc02c0 100644 --- a/target/executable/salmon/salmon_quant/.config.vsh.yaml +++ b/target/executable/salmon/salmon_quant/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "salmon_quant" namespace: "salmon" -version: "v0.2" +version: "0.2.0" authors: - name: "Sai Nirmayi Yasa" roles: @@ -1156,7 +1156,7 @@ engines: id: "docker" image: "quay.io/biocontainers/salmon:1.10.2--hecfa306_0" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -1172,22 +1172,22 @@ build_info: engine: "docker|native" output: "target/executable/salmon/salmon_quant" executable: "target/executable/salmon/salmon_quant/salmon_quant" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/salmon/salmon_quant/salmon_quant b/target/executable/salmon/salmon_quant/salmon_quant index 96ce2c03..a2cac963 100755 --- a/target/executable/salmon/salmon_quant/salmon_quant +++ b/target/executable/salmon/salmon_quant/salmon_quant @@ -1,10 +1,10 @@ #!/usr/bin/env bash -# salmon_quant v0.2 +# salmon_quant 0.2.0 # -# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. +# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. # # The component may contain files which fall under a different license. The # authors of this component should specify the license in the header of such @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "salmon_quant v0.2" + echo "salmon_quant 0.2.0" echo "" echo "Salmon is a tool for wicked-fast transcript quantification from RNA-seq data. It" echo "can either make use of pre-computed alignments (in the form of a SAM/BAM file)" @@ -1168,10 +1168,10 @@ RUN salmon index -v 2>&1 | sed 's/salmon \([0-9.]*\)/salmon: \1/' > /var/softwar LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa" LABEL org.opencontainers.image.description="Companion container for running component salmon salmon_quant" -LABEL org.opencontainers.image.created="2024-09-12T12:36:25Z" +LABEL org.opencontainers.image.created="2024-09-12T13:23:25Z" LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon" -LABEL org.opencontainers.image.revision="f22ab0eab58dcd6bff89d8d73fe951953ff1260f" -LABEL org.opencontainers.image.version="v0.2" +LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" +LABEL org.opencontainers.image.version="0.2.0" VIASHDOCKER fi @@ -1307,7 +1307,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "salmon_quant v0.2" + echo "salmon_quant 0.2.0" exit ;; --lib_type) @@ -2274,7 +2274,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/salmon/salmon_quant:v0.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/salmon/salmon_quant:0.2.0' fi # print dockerfile diff --git a/target/executable/samtools/samtools_collate/.config.vsh.yaml b/target/executable/samtools/samtools_collate/.config.vsh.yaml index 4db7825d..4d9bf2ff 100644 --- a/target/executable/samtools/samtools_collate/.config.vsh.yaml +++ b/target/executable/samtools/samtools_collate/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "samtools_collate" namespace: "samtools" -version: "v0.2" +version: "0.2.0" authors: - name: "Emma Rousseau" roles: @@ -246,7 +246,7 @@ engines: id: "docker" image: "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -263,22 +263,22 @@ build_info: engine: "docker|native" output: "target/executable/samtools/samtools_collate" executable: "target/executable/samtools/samtools_collate/samtools_collate" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/samtools/samtools_collate/samtools_collate b/target/executable/samtools/samtools_collate/samtools_collate index f3210db0..cee0efba 100755 --- a/target/executable/samtools/samtools_collate/samtools_collate +++ b/target/executable/samtools/samtools_collate/samtools_collate @@ -1,10 +1,10 @@ #!/usr/bin/env bash -# samtools_collate v0.2 +# samtools_collate 0.2.0 # -# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. +# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. # # The component may contain files which fall under a different license. The # authors of this component should specify the license in the header of such @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "samtools_collate v0.2" + echo "samtools_collate 0.2.0" echo "" echo "Shuffles and groups reads in SAM/BAM/CRAM files together by their names." echo "" @@ -519,10 +519,10 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_collate" -LABEL org.opencontainers.image.created="2024-09-12T12:36:14Z" +LABEL org.opencontainers.image.created="2024-09-12T13:23:15Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="f22ab0eab58dcd6bff89d8d73fe951953ff1260f" -LABEL org.opencontainers.image.version="v0.2" +LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" +LABEL org.opencontainers.image.version="0.2.0" VIASHDOCKER fi @@ -658,7 +658,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "samtools_collate v0.2" + echo "samtools_collate 0.2.0" exit ;; --input) @@ -914,7 +914,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/samtools/samtools_collate:v0.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/samtools/samtools_collate:0.2.0' fi # print dockerfile diff --git a/target/executable/samtools/samtools_faidx/.config.vsh.yaml b/target/executable/samtools/samtools_faidx/.config.vsh.yaml index d4ffcb14..8f8e42a9 100644 --- a/target/executable/samtools/samtools_faidx/.config.vsh.yaml +++ b/target/executable/samtools/samtools_faidx/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "samtools_faidx" namespace: "samtools" -version: "v0.2" +version: "0.2.0" authors: - name: "Emma Rousseau" roles: @@ -225,7 +225,7 @@ engines: id: "docker" image: "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -242,22 +242,22 @@ build_info: engine: "docker|native" output: "target/executable/samtools/samtools_faidx" executable: "target/executable/samtools/samtools_faidx/samtools_faidx" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/samtools/samtools_faidx/samtools_faidx b/target/executable/samtools/samtools_faidx/samtools_faidx index 4bb6eb2f..8590b714 100755 --- a/target/executable/samtools/samtools_faidx/samtools_faidx +++ b/target/executable/samtools/samtools_faidx/samtools_faidx @@ -1,10 +1,10 @@ #!/usr/bin/env bash -# samtools_faidx v0.2 +# samtools_faidx 0.2.0 # -# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. +# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. # # The component may contain files which fall under a different license. The # authors of this component should specify the license in the header of such @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "samtools_faidx v0.2" + echo "samtools_faidx 0.2.0" echo "" echo "Indexes FASTA files to enable random access to fasta and fastq files." echo "" @@ -512,10 +512,10 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_faidx" -LABEL org.opencontainers.image.created="2024-09-12T12:36:14Z" +LABEL org.opencontainers.image.created="2024-09-12T13:23:15Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="f22ab0eab58dcd6bff89d8d73fe951953ff1260f" -LABEL org.opencontainers.image.version="v0.2" +LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" +LABEL org.opencontainers.image.version="0.2.0" VIASHDOCKER fi @@ -651,7 +651,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "samtools_faidx v0.2" + echo "samtools_faidx 0.2.0" exit ;; --input) @@ -857,7 +857,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/samtools/samtools_faidx:v0.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/samtools/samtools_faidx:0.2.0' fi # print dockerfile diff --git a/target/executable/samtools/samtools_fasta/.config.vsh.yaml b/target/executable/samtools/samtools_fasta/.config.vsh.yaml index 582b4aa0..cb99b077 100644 --- a/target/executable/samtools/samtools_fasta/.config.vsh.yaml +++ b/target/executable/samtools/samtools_fasta/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "samtools_fasta" namespace: "samtools" -version: "v0.2" +version: "0.2.0" authors: - name: "Emma Rousseau" roles: @@ -415,7 +415,7 @@ engines: id: "docker" image: "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -432,22 +432,22 @@ build_info: engine: "docker|native" output: "target/executable/samtools/samtools_fasta" executable: "target/executable/samtools/samtools_fasta/samtools_fasta" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/samtools/samtools_fasta/samtools_fasta b/target/executable/samtools/samtools_fasta/samtools_fasta index 2b5b67ad..c4181b8c 100755 --- a/target/executable/samtools/samtools_fasta/samtools_fasta +++ b/target/executable/samtools/samtools_fasta/samtools_fasta @@ -1,10 +1,10 @@ #!/usr/bin/env bash -# samtools_fasta v0.2 +# samtools_fasta 0.2.0 # -# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. +# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. # # The component may contain files which fall under a different license. The # authors of this component should specify the license in the header of such @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "samtools_fasta v0.2" + echo "samtools_fasta 0.2.0" echo "" echo "Converts a SAM, BAM or CRAM to FASTA format." echo "" @@ -625,10 +625,10 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_fasta" -LABEL org.opencontainers.image.created="2024-09-12T12:36:15Z" +LABEL org.opencontainers.image.created="2024-09-12T13:23:16Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="f22ab0eab58dcd6bff89d8d73fe951953ff1260f" -LABEL org.opencontainers.image.version="v0.2" +LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" +LABEL org.opencontainers.image.version="0.2.0" VIASHDOCKER fi @@ -764,7 +764,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "samtools_fasta v0.2" + echo "samtools_fasta 0.2.0" exit ;; --input) @@ -1215,7 +1215,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/samtools/samtools_fasta:v0.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/samtools/samtools_fasta:0.2.0' fi # print dockerfile diff --git a/target/executable/samtools/samtools_fastq/.config.vsh.yaml b/target/executable/samtools/samtools_fastq/.config.vsh.yaml index 49d6af7e..4fda082e 100644 --- a/target/executable/samtools/samtools_fastq/.config.vsh.yaml +++ b/target/executable/samtools/samtools_fastq/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "samtools_fastq" namespace: "samtools" -version: "v0.2" +version: "0.2.0" authors: - name: "Emma Rousseau" roles: @@ -415,7 +415,7 @@ engines: id: "docker" image: "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -432,22 +432,22 @@ build_info: engine: "docker|native" output: "target/executable/samtools/samtools_fastq" executable: "target/executable/samtools/samtools_fastq/samtools_fastq" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/samtools/samtools_fastq/samtools_fastq b/target/executable/samtools/samtools_fastq/samtools_fastq index 9d46abce..69322d42 100755 --- a/target/executable/samtools/samtools_fastq/samtools_fastq +++ b/target/executable/samtools/samtools_fastq/samtools_fastq @@ -1,10 +1,10 @@ #!/usr/bin/env bash -# samtools_fastq v0.2 +# samtools_fastq 0.2.0 # -# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. +# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. # # The component may contain files which fall under a different license. The # authors of this component should specify the license in the header of such @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "samtools_fastq v0.2" + echo "samtools_fastq 0.2.0" echo "" echo "Converts a SAM, BAM or CRAM to FASTQ format." echo "" @@ -626,10 +626,10 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_fastq" -LABEL org.opencontainers.image.created="2024-09-12T12:36:14Z" +LABEL org.opencontainers.image.created="2024-09-12T13:23:15Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="f22ab0eab58dcd6bff89d8d73fe951953ff1260f" -LABEL org.opencontainers.image.version="v0.2" +LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" +LABEL org.opencontainers.image.version="0.2.0" VIASHDOCKER fi @@ -765,7 +765,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "samtools_fastq v0.2" + echo "samtools_fastq 0.2.0" exit ;; --input) @@ -1216,7 +1216,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/samtools/samtools_fastq:v0.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/samtools/samtools_fastq:0.2.0' fi # print dockerfile diff --git a/target/executable/samtools/samtools_flagstat/.config.vsh.yaml b/target/executable/samtools/samtools_flagstat/.config.vsh.yaml index 10021528..f8b4a9fa 100644 --- a/target/executable/samtools/samtools_flagstat/.config.vsh.yaml +++ b/target/executable/samtools/samtools_flagstat/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "samtools_flagstat" namespace: "samtools" -version: "v0.2" +version: "0.2.0" authors: - name: "Emma Rousseau" roles: @@ -155,7 +155,7 @@ engines: id: "docker" image: "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -172,22 +172,22 @@ build_info: engine: "docker|native" output: "target/executable/samtools/samtools_flagstat" executable: "target/executable/samtools/samtools_flagstat/samtools_flagstat" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/samtools/samtools_flagstat/samtools_flagstat b/target/executable/samtools/samtools_flagstat/samtools_flagstat index 596e6563..daf04311 100755 --- a/target/executable/samtools/samtools_flagstat/samtools_flagstat +++ b/target/executable/samtools/samtools_flagstat/samtools_flagstat @@ -1,10 +1,10 @@ #!/usr/bin/env bash -# samtools_flagstat v0.2 +# samtools_flagstat 0.2.0 # -# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. +# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. # # The component may contain files which fall under a different license. The # authors of this component should specify the license in the header of such @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "samtools_flagstat v0.2" + echo "samtools_flagstat 0.2.0" echo "" echo "Counts the number of alignments in SAM/BAM/CRAM files for each FLAG type." echo "" @@ -474,10 +474,10 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_flagstat" -LABEL org.opencontainers.image.created="2024-09-12T12:36:13Z" +LABEL org.opencontainers.image.created="2024-09-12T13:23:14Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="f22ab0eab58dcd6bff89d8d73fe951953ff1260f" -LABEL org.opencontainers.image.version="v0.2" +LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" +LABEL org.opencontainers.image.version="0.2.0" VIASHDOCKER fi @@ -613,7 +613,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "samtools_flagstat v0.2" + echo "samtools_flagstat 0.2.0" exit ;; --bam) @@ -737,7 +737,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/samtools/samtools_flagstat:v0.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/samtools/samtools_flagstat:0.2.0' fi # print dockerfile diff --git a/target/executable/samtools/samtools_idxstats/.config.vsh.yaml b/target/executable/samtools/samtools_idxstats/.config.vsh.yaml index d9711a19..ca34c12b 100644 --- a/target/executable/samtools/samtools_idxstats/.config.vsh.yaml +++ b/target/executable/samtools/samtools_idxstats/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "samtools_idxstats" namespace: "samtools" -version: "v0.2" +version: "0.2.0" authors: - name: "Emma Rousseau" roles: @@ -165,7 +165,7 @@ engines: id: "docker" image: "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -182,22 +182,22 @@ build_info: engine: "docker|native" output: "target/executable/samtools/samtools_idxstats" executable: "target/executable/samtools/samtools_idxstats/samtools_idxstats" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/samtools/samtools_idxstats/samtools_idxstats b/target/executable/samtools/samtools_idxstats/samtools_idxstats index 2ab9fc1f..da52e779 100755 --- a/target/executable/samtools/samtools_idxstats/samtools_idxstats +++ b/target/executable/samtools/samtools_idxstats/samtools_idxstats @@ -1,10 +1,10 @@ #!/usr/bin/env bash -# samtools_idxstats v0.2 +# samtools_idxstats 0.2.0 # -# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. +# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. # # The component may contain files which fall under a different license. The # authors of this component should specify the license in the header of such @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "samtools_idxstats v0.2" + echo "samtools_idxstats 0.2.0" echo "" echo "Reports alignment summary statistics for a BAM file." echo "" @@ -478,10 +478,10 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_idxstats" -LABEL org.opencontainers.image.created="2024-09-12T12:36:13Z" +LABEL org.opencontainers.image.created="2024-09-12T13:23:14Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="f22ab0eab58dcd6bff89d8d73fe951953ff1260f" -LABEL org.opencontainers.image.version="v0.2" +LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" +LABEL org.opencontainers.image.version="0.2.0" VIASHDOCKER fi @@ -617,7 +617,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "samtools_idxstats v0.2" + echo "samtools_idxstats 0.2.0" exit ;; --bam) @@ -752,7 +752,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/samtools/samtools_idxstats:v0.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/samtools/samtools_idxstats:0.2.0' fi # print dockerfile diff --git a/target/executable/samtools/samtools_index/.config.vsh.yaml b/target/executable/samtools/samtools_index/.config.vsh.yaml index 7f910368..26be7fd1 100644 --- a/target/executable/samtools/samtools_index/.config.vsh.yaml +++ b/target/executable/samtools/samtools_index/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "samtools_index" namespace: "samtools" -version: "v0.2" +version: "0.2.0" authors: - name: "Emma Rousseau" roles: @@ -171,7 +171,7 @@ engines: id: "docker" image: "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -188,22 +188,22 @@ build_info: engine: "docker|native" output: "target/executable/samtools/samtools_index" executable: "target/executable/samtools/samtools_index/samtools_index" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/samtools/samtools_index/samtools_index b/target/executable/samtools/samtools_index/samtools_index index ac288c3f..dd3ae2ce 100755 --- a/target/executable/samtools/samtools_index/samtools_index +++ b/target/executable/samtools/samtools_index/samtools_index @@ -1,10 +1,10 @@ #!/usr/bin/env bash -# samtools_index v0.2 +# samtools_index 0.2.0 # -# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. +# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. # # The component may contain files which fall under a different license. The # authors of this component should specify the license in the header of such @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "samtools_index v0.2" + echo "samtools_index 0.2.0" echo "" echo "Index SAM/BAM/CRAM files." echo "" @@ -485,10 +485,10 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_index" -LABEL org.opencontainers.image.created="2024-09-12T12:36:12Z" +LABEL org.opencontainers.image.created="2024-09-12T13:23:13Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="f22ab0eab58dcd6bff89d8d73fe951953ff1260f" -LABEL org.opencontainers.image.version="v0.2" +LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" +LABEL org.opencontainers.image.version="0.2.0" VIASHDOCKER fi @@ -624,7 +624,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "samtools_index v0.2" + echo "samtools_index 0.2.0" exit ;; --input) @@ -780,7 +780,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/samtools/samtools_index:v0.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/samtools/samtools_index:0.2.0' fi # print dockerfile diff --git a/target/executable/samtools/samtools_sort/.config.vsh.yaml b/target/executable/samtools/samtools_sort/.config.vsh.yaml index da69d7c6..6ed05fe0 100644 --- a/target/executable/samtools/samtools_sort/.config.vsh.yaml +++ b/target/executable/samtools/samtools_sort/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "samtools_sort" namespace: "samtools" -version: "v0.2" +version: "0.2.0" authors: - name: "Emma Rousseau" roles: @@ -314,7 +314,7 @@ engines: id: "docker" image: "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -331,22 +331,22 @@ build_info: engine: "docker|native" output: "target/executable/samtools/samtools_sort" executable: "target/executable/samtools/samtools_sort/samtools_sort" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/samtools/samtools_sort/samtools_sort b/target/executable/samtools/samtools_sort/samtools_sort index 41470d92..06550e40 100755 --- a/target/executable/samtools/samtools_sort/samtools_sort +++ b/target/executable/samtools/samtools_sort/samtools_sort @@ -1,10 +1,10 @@ #!/usr/bin/env bash -# samtools_sort v0.2 +# samtools_sort 0.2.0 # -# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. +# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. # # The component may contain files which fall under a different license. The # authors of this component should specify the license in the header of such @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "samtools_sort v0.2" + echo "samtools_sort 0.2.0" echo "" echo "Sort SAM/BAM/CRAM file." echo "" @@ -556,10 +556,10 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_sort" -LABEL org.opencontainers.image.created="2024-09-12T12:36:15Z" +LABEL org.opencontainers.image.created="2024-09-12T13:23:16Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="f22ab0eab58dcd6bff89d8d73fe951953ff1260f" -LABEL org.opencontainers.image.version="v0.2" +LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" +LABEL org.opencontainers.image.version="0.2.0" VIASHDOCKER fi @@ -695,7 +695,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "samtools_sort v0.2" + echo "samtools_sort 0.2.0" exit ;; --input) @@ -1035,7 +1035,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/samtools/samtools_sort:v0.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/samtools/samtools_sort:0.2.0' fi # print dockerfile diff --git a/target/executable/samtools/samtools_stats/.config.vsh.yaml b/target/executable/samtools/samtools_stats/.config.vsh.yaml index da8fb583..f85292ea 100644 --- a/target/executable/samtools/samtools_stats/.config.vsh.yaml +++ b/target/executable/samtools/samtools_stats/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "samtools_stats" namespace: "samtools" -version: "v0.2" +version: "0.2.0" authors: - name: "Emma Rousseau" roles: @@ -383,7 +383,7 @@ engines: id: "docker" image: "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -400,22 +400,22 @@ build_info: engine: "docker|native" output: "target/executable/samtools/samtools_stats" executable: "target/executable/samtools/samtools_stats/samtools_stats" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/samtools/samtools_stats/samtools_stats b/target/executable/samtools/samtools_stats/samtools_stats index 124f13c3..5aa676d2 100755 --- a/target/executable/samtools/samtools_stats/samtools_stats +++ b/target/executable/samtools/samtools_stats/samtools_stats @@ -1,10 +1,10 @@ #!/usr/bin/env bash -# samtools_stats v0.2 +# samtools_stats 0.2.0 # -# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. +# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. # # The component may contain files which fall under a different license. The # authors of this component should specify the license in the header of such @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "samtools_stats v0.2" + echo "samtools_stats 0.2.0" echo "" echo "Reports alignment summary statistics for a BAM file." echo "" @@ -575,10 +575,10 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_stats" -LABEL org.opencontainers.image.created="2024-09-12T12:36:16Z" +LABEL org.opencontainers.image.created="2024-09-12T13:23:16Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="f22ab0eab58dcd6bff89d8d73fe951953ff1260f" -LABEL org.opencontainers.image.version="v0.2" +LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" +LABEL org.opencontainers.image.version="0.2.0" VIASHDOCKER fi @@ -714,7 +714,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "samtools_stats v0.2" + echo "samtools_stats 0.2.0" exit ;; --input) @@ -1158,7 +1158,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/samtools/samtools_stats:v0.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/samtools/samtools_stats:0.2.0' fi # print dockerfile diff --git a/target/executable/samtools/samtools_view/.config.vsh.yaml b/target/executable/samtools/samtools_view/.config.vsh.yaml index fd1006d2..836c41b6 100644 --- a/target/executable/samtools/samtools_view/.config.vsh.yaml +++ b/target/executable/samtools/samtools_view/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "samtools_view" namespace: "samtools" -version: "v0.2" +version: "0.2.0" authors: - name: "Emma Rousseau" roles: @@ -647,7 +647,7 @@ engines: id: "docker" image: "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -664,22 +664,22 @@ build_info: engine: "docker|native" output: "target/executable/samtools/samtools_view" executable: "target/executable/samtools/samtools_view/samtools_view" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/samtools/samtools_view/samtools_view b/target/executable/samtools/samtools_view/samtools_view index 9ea65b7c..d0b2ae30 100755 --- a/target/executable/samtools/samtools_view/samtools_view +++ b/target/executable/samtools/samtools_view/samtools_view @@ -1,10 +1,10 @@ #!/usr/bin/env bash -# samtools_view v0.2 +# samtools_view 0.2.0 # -# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. +# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. # # The component may contain files which fall under a different license. The # authors of this component should specify the license in the header of such @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "samtools_view v0.2" + echo "samtools_view 0.2.0" echo "" echo "Views and converts SAM/BAM/CRAM files." echo "" @@ -825,10 +825,10 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_view" -LABEL org.opencontainers.image.created="2024-09-12T12:36:13Z" +LABEL org.opencontainers.image.created="2024-09-12T13:23:14Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="f22ab0eab58dcd6bff89d8d73fe951953ff1260f" -LABEL org.opencontainers.image.version="v0.2" +LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" +LABEL org.opencontainers.image.version="0.2.0" VIASHDOCKER fi @@ -964,7 +964,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "samtools_view v0.2" + echo "samtools_view 0.2.0" exit ;; --input) @@ -1636,7 +1636,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/samtools/samtools_view:v0.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/samtools/samtools_view:0.2.0' fi # print dockerfile diff --git a/target/executable/seqtk/seqtk_sample/.config.vsh.yaml b/target/executable/seqtk/seqtk_sample/.config.vsh.yaml index 26e5e4e9..c7ef2b11 100644 --- a/target/executable/seqtk/seqtk_sample/.config.vsh.yaml +++ b/target/executable/seqtk/seqtk_sample/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "seqtk_sample" namespace: "seqtk" -version: "v0.2" +version: "0.2.0" authors: - name: "Jakub Majercik" roles: @@ -160,7 +160,7 @@ engines: id: "docker" image: "quay.io/biocontainers/seqtk:1.4--he4a0461_2" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" entrypoint: [] cmd: null @@ -172,22 +172,22 @@ build_info: engine: "docker|native" output: "target/executable/seqtk/seqtk_sample" executable: "target/executable/seqtk/seqtk_sample/seqtk_sample" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/seqtk/seqtk_sample/seqtk_sample b/target/executable/seqtk/seqtk_sample/seqtk_sample index cd2cec2d..2d93d9c9 100755 --- a/target/executable/seqtk/seqtk_sample/seqtk_sample +++ b/target/executable/seqtk/seqtk_sample/seqtk_sample @@ -1,10 +1,10 @@ #!/usr/bin/env bash -# seqtk_sample v0.2 +# seqtk_sample 0.2.0 # -# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. +# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. # # The component may contain files which fall under a different license. The # authors of this component should specify the license in the header of such @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "seqtk_sample v0.2" + echo "seqtk_sample 0.2.0" echo "" echo "Subsamples sequences from FASTA/Q files." echo "" @@ -481,10 +481,10 @@ FROM quay.io/biocontainers/seqtk:1.4--he4a0461_2 ENTRYPOINT [] LABEL org.opencontainers.image.authors="Jakub Majercik" LABEL org.opencontainers.image.description="Companion container for running component seqtk seqtk_sample" -LABEL org.opencontainers.image.created="2024-09-12T12:36:27Z" +LABEL org.opencontainers.image.created="2024-09-12T13:23:28Z" LABEL org.opencontainers.image.source="https://github.com/lh3/seqtk/tree/v1.4" -LABEL org.opencontainers.image.revision="f22ab0eab58dcd6bff89d8d73fe951953ff1260f" -LABEL org.opencontainers.image.version="v0.2" +LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" +LABEL org.opencontainers.image.version="0.2.0" VIASHDOCKER fi @@ -620,7 +620,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "seqtk_sample v0.2" + echo "seqtk_sample 0.2.0" exit ;; --input) @@ -760,7 +760,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/seqtk/seqtk_sample:v0.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/seqtk/seqtk_sample:0.2.0' fi # print dockerfile diff --git a/target/executable/seqtk/seqtk_subseq/.config.vsh.yaml b/target/executable/seqtk/seqtk_subseq/.config.vsh.yaml index b43c50cb..f81e9a22 100644 --- a/target/executable/seqtk/seqtk_subseq/.config.vsh.yaml +++ b/target/executable/seqtk/seqtk_subseq/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "seqtk_subseq" namespace: "seqtk" -version: "v0.2" +version: "0.2.0" authors: - name: "Theodoro Gasperin Terra Camargo" roles: @@ -179,7 +179,7 @@ engines: id: "docker" image: "quay.io/biocontainers/seqtk:1.4--he4a0461_2" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -195,22 +195,22 @@ build_info: engine: "docker|native" output: "target/executable/seqtk/seqtk_subseq" executable: "target/executable/seqtk/seqtk_subseq/seqtk_subseq" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/seqtk/seqtk_subseq/seqtk_subseq b/target/executable/seqtk/seqtk_subseq/seqtk_subseq index eb1ec35a..27922475 100755 --- a/target/executable/seqtk/seqtk_subseq/seqtk_subseq +++ b/target/executable/seqtk/seqtk_subseq/seqtk_subseq @@ -1,10 +1,10 @@ #!/usr/bin/env bash -# seqtk_subseq v0.2 +# seqtk_subseq 0.2.0 # -# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. +# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. # # The component may contain files which fall under a different license. The # authors of this component should specify the license in the header of such @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "seqtk_subseq v0.2" + echo "seqtk_subseq 0.2.0" echo "" echo "Extract subsequences from FASTA/Q files. Takes as input a FASTA/Q file and a" echo "name.lst (sequence ids file) or a reg.bed (genomic regions file)." @@ -491,10 +491,10 @@ RUN echo $(echo $(seqtk 2>&1) | sed -n 's/.*\(Version: [^ ]*\).*/\1/p') > /var/s LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component seqtk seqtk_subseq" -LABEL org.opencontainers.image.created="2024-09-12T12:36:27Z" +LABEL org.opencontainers.image.created="2024-09-12T13:23:27Z" LABEL org.opencontainers.image.source="https://github.com/lh3/seqtk/tree/v1.4" -LABEL org.opencontainers.image.revision="f22ab0eab58dcd6bff89d8d73fe951953ff1260f" -LABEL org.opencontainers.image.version="v0.2" +LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" +LABEL org.opencontainers.image.version="0.2.0" VIASHDOCKER fi @@ -630,7 +630,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "seqtk_subseq v0.2" + echo "seqtk_subseq 0.2.0" exit ;; --input) @@ -797,7 +797,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/seqtk/seqtk_subseq:v0.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/seqtk/seqtk_subseq:0.2.0' fi # print dockerfile diff --git a/target/executable/star/star_align_reads/.config.vsh.yaml b/target/executable/star/star_align_reads/.config.vsh.yaml index 551e8226..a00e3a29 100644 --- a/target/executable/star/star_align_reads/.config.vsh.yaml +++ b/target/executable/star/star_align_reads/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "star_align_reads" namespace: "star" -version: "v0.2" +version: "0.2.0" authors: - name: "Angela Oliveira Pisco" roles: @@ -2624,7 +2624,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -2662,22 +2662,22 @@ build_info: engine: "docker|native" output: "target/executable/star/star_align_reads" executable: "target/executable/star/star_align_reads/star_align_reads" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/star/star_align_reads/star_align_reads b/target/executable/star/star_align_reads/star_align_reads index 825c8234..cbe464ff 100755 --- a/target/executable/star/star_align_reads/star_align_reads +++ b/target/executable/star/star_align_reads/star_align_reads @@ -1,10 +1,10 @@ #!/usr/bin/env bash -# star_align_reads v0.2 +# star_align_reads 0.2.0 # -# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. +# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. # # The component may contain files which fall under a different license. The # authors of this component should specify the license in the header of such @@ -175,7 +175,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "star_align_reads v0.2" + echo "star_align_reads 0.2.0" echo "" echo "Aligns reads to a reference genome using STAR." echo "" @@ -1920,10 +1920,10 @@ RUN STAR --version | sed 's#\(.*\)#star: "\1"#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component star star_align_reads" -LABEL org.opencontainers.image.created="2024-09-12T12:36:19Z" +LABEL org.opencontainers.image.created="2024-09-12T13:23:20Z" LABEL org.opencontainers.image.source="https://github.com/alexdobin/STAR" -LABEL org.opencontainers.image.revision="f22ab0eab58dcd6bff89d8d73fe951953ff1260f" -LABEL org.opencontainers.image.version="v0.2" +LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" +LABEL org.opencontainers.image.version="0.2.0" VIASHDOCKER fi @@ -2059,7 +2059,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "star_align_reads v0.2" + echo "star_align_reads 0.2.0" exit ;; --run_rng_seed) @@ -4542,7 +4542,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/star/star_align_reads:v0.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/star/star_align_reads:0.2.0' fi # print dockerfile diff --git a/target/executable/star/star_genome_generate/.config.vsh.yaml b/target/executable/star/star_genome_generate/.config.vsh.yaml index be4b638b..b04babe7 100644 --- a/target/executable/star/star_genome_generate/.config.vsh.yaml +++ b/target/executable/star/star_genome_generate/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "star_genome_generate" namespace: "star" -version: "v0.2" +version: "0.2.0" authors: - name: "Sai Nirmayi Yasa" roles: @@ -305,7 +305,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -332,22 +332,22 @@ build_info: engine: "docker|native" output: "target/executable/star/star_genome_generate" executable: "target/executable/star/star_genome_generate/star_genome_generate" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/star/star_genome_generate/star_genome_generate b/target/executable/star/star_genome_generate/star_genome_generate index c32b320f..56e99286 100755 --- a/target/executable/star/star_genome_generate/star_genome_generate +++ b/target/executable/star/star_genome_generate/star_genome_generate @@ -1,10 +1,10 @@ #!/usr/bin/env bash -# star_genome_generate v0.2 +# star_genome_generate 0.2.0 # -# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. +# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. # # The component may contain files which fall under a different license. The # authors of this component should specify the license in the header of such @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "star_genome_generate v0.2" + echo "star_genome_generate 0.2.0" echo "" echo "Create index for STAR" echo "" @@ -577,10 +577,10 @@ RUN STAR --version | sed 's#\(.*\)#star: "\1"#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa" LABEL org.opencontainers.image.description="Companion container for running component star star_genome_generate" -LABEL org.opencontainers.image.created="2024-09-12T12:36:19Z" +LABEL org.opencontainers.image.created="2024-09-12T13:23:20Z" LABEL org.opencontainers.image.source="https://github.com/alexdobin/STAR" -LABEL org.opencontainers.image.revision="f22ab0eab58dcd6bff89d8d73fe951953ff1260f" -LABEL org.opencontainers.image.version="v0.2" +LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" +LABEL org.opencontainers.image.version="0.2.0" VIASHDOCKER fi @@ -716,7 +716,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "star_genome_generate v0.2" + echo "star_genome_generate 0.2.0" exit ;; --genome_fasta_files) @@ -1012,7 +1012,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/star/star_genome_generate:v0.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/star/star_genome_generate:0.2.0' fi # print dockerfile diff --git a/target/executable/umi_tools/umi_tools_dedup/.config.vsh.yaml b/target/executable/umi_tools/umi_tools_dedup/.config.vsh.yaml index ff280345..bad69ea0 100644 --- a/target/executable/umi_tools/umi_tools_dedup/.config.vsh.yaml +++ b/target/executable/umi_tools/umi_tools_dedup/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "umi_tools_dedup" namespace: "umi_tools" -version: "v0.2" +version: "0.2.0" authors: - name: "Emma Rousseau" roles: @@ -594,7 +594,7 @@ engines: id: "docker" image: "quay.io/biocontainers/umi_tools:1.1.5--py39hf95cd2a_1" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -610,22 +610,22 @@ build_info: engine: "docker|native" output: "target/executable/umi_tools/umi_tools_dedup" executable: "target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup b/target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup index 0f3eaf66..546d71e9 100755 --- a/target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup +++ b/target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup @@ -1,10 +1,10 @@ #!/usr/bin/env bash -# umi_tools_dedup v0.2 +# umi_tools_dedup 0.2.0 # -# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. +# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. # # The component may contain files which fall under a different license. The # authors of this component should specify the license in the header of such @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "umi_tools_dedup v0.2" + echo "umi_tools_dedup 0.2.0" echo "" echo "Deduplicate reads based on the mapping co-ordinate and the UMI attached to the" echo "read." @@ -770,10 +770,10 @@ RUN umi_tools -v | sed 's/ version//g' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component umi_tools umi_tools_dedup" -LABEL org.opencontainers.image.created="2024-09-12T12:36:17Z" +LABEL org.opencontainers.image.created="2024-09-12T13:23:18Z" LABEL org.opencontainers.image.source="https://github.com/CGATOxford/UMI-tools" -LABEL org.opencontainers.image.revision="f22ab0eab58dcd6bff89d8d73fe951953ff1260f" -LABEL org.opencontainers.image.version="v0.2" +LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" +LABEL org.opencontainers.image.version="0.2.0" VIASHDOCKER fi @@ -909,7 +909,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "umi_tools_dedup v0.2" + echo "umi_tools_dedup 0.2.0" exit ;; --input) @@ -1475,7 +1475,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/umi_tools/umi_tools_dedup:v0.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/umi_tools/umi_tools_dedup:0.2.0' fi # print dockerfile diff --git a/target/executable/umi_tools/umi_tools_extract/.config.vsh.yaml b/target/executable/umi_tools/umi_tools_extract/.config.vsh.yaml index 12f1fd42..54ab9ed6 100644 --- a/target/executable/umi_tools/umi_tools_extract/.config.vsh.yaml +++ b/target/executable/umi_tools/umi_tools_extract/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "umi_tools_extract" namespace: "umi_tools" -version: "v0.2" +version: "0.2.0" argument_groups: - name: "Input" arguments: @@ -432,7 +432,7 @@ engines: id: "docker" image: "quay.io/biocontainers/umi_tools:1.1.4--py310h4b81fae_2" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -448,22 +448,22 @@ build_info: engine: "docker|native" output: "target/executable/umi_tools/umi_tools_extract" executable: "target/executable/umi_tools/umi_tools_extract/umi_tools_extract" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/umi_tools/umi_tools_extract/umi_tools_extract b/target/executable/umi_tools/umi_tools_extract/umi_tools_extract index 6c7a365a..ad067d9f 100755 --- a/target/executable/umi_tools/umi_tools_extract/umi_tools_extract +++ b/target/executable/umi_tools/umi_tools_extract/umi_tools_extract @@ -1,10 +1,10 @@ #!/usr/bin/env bash -# umi_tools_extract v0.2 +# umi_tools_extract 0.2.0 # -# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. +# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. # # The component may contain files which fall under a different license. The # authors of this component should specify the license in the header of such @@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "umi_tools_extract v0.2" + echo "umi_tools_extract 0.2.0" echo "" echo "Flexible removal of UMI sequences from fastq reads." echo "UMIs are removed and appended to the read name. Any other barcode, for example a" @@ -637,10 +637,10 @@ ENTRYPOINT [] RUN umi_tools -v | sed 's/ version//g' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component umi_tools umi_tools_extract" -LABEL org.opencontainers.image.created="2024-09-12T12:36:17Z" +LABEL org.opencontainers.image.created="2024-09-12T13:23:17Z" LABEL org.opencontainers.image.source="https://github.com/CGATOxford/UMI-tools" -LABEL org.opencontainers.image.revision="f22ab0eab58dcd6bff89d8d73fe951953ff1260f" -LABEL org.opencontainers.image.version="v0.2" +LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" +LABEL org.opencontainers.image.version="0.2.0" VIASHDOCKER fi @@ -776,7 +776,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "umi_tools_extract v0.2" + echo "umi_tools_extract 0.2.0" exit ;; --input) @@ -1189,7 +1189,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/umi_tools/umi_tools_extract:v0.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/umi_tools/umi_tools_extract:0.2.0' fi # print dockerfile diff --git a/target/nextflow/agat/agat_convert_bed2gff/.config.vsh.yaml b/target/nextflow/agat/agat_convert_bed2gff/.config.vsh.yaml index ea262c1d..14a5457d 100644 --- a/target/nextflow/agat/agat_convert_bed2gff/.config.vsh.yaml +++ b/target/nextflow/agat/agat_convert_bed2gff/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "agat_convert_bed2gff" namespace: "agat" -version: "v0.2" +version: "0.2.0" authors: - name: "Leïla Paquay" roles: @@ -218,7 +218,7 @@ engines: id: "docker" image: "quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -234,22 +234,22 @@ build_info: engine: "docker|native" output: "target/nextflow/agat/agat_convert_bed2gff" executable: "target/nextflow/agat/agat_convert_bed2gff/main.nf" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/agat/agat_convert_bed2gff/main.nf b/target/nextflow/agat/agat_convert_bed2gff/main.nf index 19b7eaae..40ed988a 100644 --- a/target/nextflow/agat/agat_convert_bed2gff/main.nf +++ b/target/nextflow/agat/agat_convert_bed2gff/main.nf @@ -1,8 +1,8 @@ -// agat_convert_bed2gff v0.2 +// agat_convert_bed2gff 0.2.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such @@ -1731,7 +1731,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1802,7 +1804,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1844,7 +1848,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2803,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "agat_convert_bed2gff", "namespace" : "agat", - "version" : "v0.2", + "version" : "0.2.0", "authors" : [ { "name" : "Leïla Paquay", @@ -3064,7 +3070,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.2", + "target_tag" : "0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3085,22 +3091,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/agat/agat_convert_bed2gff", - "viash_version" : "0.9.0-RC7", - "git_commit" : "f22ab0eab58dcd6bff89d8d73fe951953ff1260f", + "viash_version" : "0.9.0", + "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.2", + "version" : "0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.0-RC7", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.2'" + ".engines[.type == 'docker'].target_tag := '0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3253,7 +3259,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -3384,7 +3394,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -3392,8 +3403,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -3430,6 +3441,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -3441,10 +3453,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -3529,7 +3540,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/agat/agat_convert_bed2gff", - "tag" : "v0.2" + "tag" : "0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/agat/agat_convert_bed2gff/nextflow.config b/target/nextflow/agat/agat_convert_bed2gff/nextflow.config index 6bc4750d..d0abfb6b 100644 --- a/target/nextflow/agat/agat_convert_bed2gff/nextflow.config +++ b/target/nextflow/agat/agat_convert_bed2gff/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'agat/agat_convert_bed2gff' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.2' + version = '0.2.0' description = 'The script takes a bed file as input, and will translate it in gff format. The BED format is described here The script converts 0-based, half-open [start-1, end) bed file to 1-based, closed [start, end] General Feature Format v3 (GFF3).\n' author = 'Leïla Paquay' } diff --git a/target/nextflow/agat/agat_convert_embl2gff/.config.vsh.yaml b/target/nextflow/agat/agat_convert_embl2gff/.config.vsh.yaml index 74440e6d..b534591d 100644 --- a/target/nextflow/agat/agat_convert_embl2gff/.config.vsh.yaml +++ b/target/nextflow/agat/agat_convert_embl2gff/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "agat_convert_embl2gff" namespace: "agat" -version: "v0.2" +version: "0.2.0" authors: - name: "Leïla Paquay" roles: @@ -208,7 +208,7 @@ engines: id: "docker" image: "quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -224,22 +224,22 @@ build_info: engine: "docker|native" output: "target/nextflow/agat/agat_convert_embl2gff" executable: "target/nextflow/agat/agat_convert_embl2gff/main.nf" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/agat/agat_convert_embl2gff/main.nf b/target/nextflow/agat/agat_convert_embl2gff/main.nf index c931adca..ac0c9682 100644 --- a/target/nextflow/agat/agat_convert_embl2gff/main.nf +++ b/target/nextflow/agat/agat_convert_embl2gff/main.nf @@ -1,8 +1,8 @@ -// agat_convert_embl2gff v0.2 +// agat_convert_embl2gff 0.2.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such @@ -1731,7 +1731,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1802,7 +1804,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1844,7 +1848,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2803,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "agat_convert_embl2gff", "namespace" : "agat", - "version" : "v0.2", + "version" : "0.2.0", "authors" : [ { "name" : "Leïla Paquay", @@ -3057,7 +3063,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.2", + "target_tag" : "0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3078,22 +3084,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/agat/agat_convert_embl2gff", - "viash_version" : "0.9.0-RC7", - "git_commit" : "f22ab0eab58dcd6bff89d8d73fe951953ff1260f", + "viash_version" : "0.9.0", + "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.2", + "version" : "0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.0-RC7", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.2'" + ".engines[.type == 'docker'].target_tag := '0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3249,7 +3255,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -3380,7 +3390,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -3388,8 +3399,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -3426,6 +3437,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -3437,10 +3449,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -3525,7 +3536,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/agat/agat_convert_embl2gff", - "tag" : "v0.2" + "tag" : "0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/agat/agat_convert_embl2gff/nextflow.config b/target/nextflow/agat/agat_convert_embl2gff/nextflow.config index 74fa9052..5660e990 100644 --- a/target/nextflow/agat/agat_convert_embl2gff/nextflow.config +++ b/target/nextflow/agat/agat_convert_embl2gff/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'agat/agat_convert_embl2gff' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.2' + version = '0.2.0' description = 'The script takes an EMBL file as input, and will translate it in gff format.\n' author = 'Leïla Paquay' } diff --git a/target/nextflow/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml b/target/nextflow/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml index 880bcef6..28cb1e30 100644 --- a/target/nextflow/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml +++ b/target/nextflow/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "agat_convert_sp_gff2gtf" namespace: "agat" -version: "v0.2" +version: "0.2.0" authors: - name: "Leïla Paquay" roles: @@ -211,7 +211,7 @@ engines: id: "docker" image: "quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -227,22 +227,22 @@ build_info: engine: "docker|native" output: "target/nextflow/agat/agat_convert_sp_gff2gtf" executable: "target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf b/target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf index 7d7a2d2c..a76022a2 100644 --- a/target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf +++ b/target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf @@ -1,8 +1,8 @@ -// agat_convert_sp_gff2gtf v0.2 +// agat_convert_sp_gff2gtf 0.2.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such @@ -1731,7 +1731,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1802,7 +1804,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1844,7 +1848,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2803,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "agat_convert_sp_gff2gtf", "namespace" : "agat", - "version" : "v0.2", + "version" : "0.2.0", "authors" : [ { "name" : "Leïla Paquay", @@ -3040,7 +3046,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.2", + "target_tag" : "0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3061,22 +3067,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/agat/agat_convert_sp_gff2gtf", - "viash_version" : "0.9.0-RC7", - "git_commit" : "f22ab0eab58dcd6bff89d8d73fe951953ff1260f", + "viash_version" : "0.9.0", + "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.2", + "version" : "0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.0-RC7", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.2'" + ".engines[.type == 'docker'].target_tag := '0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3216,7 +3222,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -3347,7 +3357,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -3355,8 +3366,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -3393,6 +3404,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -3404,10 +3416,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -3492,7 +3503,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/agat/agat_convert_sp_gff2gtf", - "tag" : "v0.2" + "tag" : "0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/agat/agat_convert_sp_gff2gtf/nextflow.config b/target/nextflow/agat/agat_convert_sp_gff2gtf/nextflow.config index 0c91bfb9..72b08431 100644 --- a/target/nextflow/agat/agat_convert_sp_gff2gtf/nextflow.config +++ b/target/nextflow/agat/agat_convert_sp_gff2gtf/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'agat/agat_convert_sp_gff2gtf' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.2' + version = '0.2.0' description = 'The script aims to convert any GTF/GFF file into a proper GTF file. Full\ninformation about the format can be found here:\nhttps://agat.readthedocs.io/en/latest/gxf.html You can choose among 7\ndifferent GTF types (1, 2, 2.1, 2.2, 2.5, 3 or relax). Depending the\nversion selected the script will filter out the features that are not\naccepted. For GTF2.5 and 3, every level1 feature (e.g nc_gene\npseudogene) will be converted into gene feature and every level2 feature\n(e.g mRNA ncRNA) will be converted into transcript feature. Using the\n"relax" option you will produce a GTF-like output keeping all original\nfeature types (3rd column). No modification will occur e.g. mRNA to\ntranscript.\n\nTo be fully GTF compliant all feature have a gene_id and a transcript_id\nattribute. The gene_id is unique identifier for the genomic source of\nthe transcript, which is used to group transcripts into genes. The\ntranscript_id is a unique identifier for the predicted transcript, which\nis used to group features into transcripts.\n' author = 'Leïla Paquay' } diff --git a/target/nextflow/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml b/target/nextflow/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml index 46c78e18..f01745fc 100644 --- a/target/nextflow/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml +++ b/target/nextflow/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "agat_convert_sp_gff2tsv" namespace: "agat" -version: "v0.2" +version: "0.2.0" authors: - name: "Leïla Paquay" roles: @@ -171,7 +171,7 @@ engines: id: "docker" image: "quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -187,22 +187,22 @@ build_info: engine: "docker|native" output: "target/nextflow/agat/agat_convert_sp_gff2tsv" executable: "target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf b/target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf index 7f174d02..4e9e9e6f 100644 --- a/target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf +++ b/target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf @@ -1,8 +1,8 @@ -// agat_convert_sp_gff2tsv v0.2 +// agat_convert_sp_gff2tsv 0.2.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such @@ -1731,7 +1731,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1802,7 +1804,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1844,7 +1848,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2803,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "agat_convert_sp_gff2tsv", "namespace" : "agat", - "version" : "v0.2", + "version" : "0.2.0", "authors" : [ { "name" : "Leïla Paquay", @@ -3018,7 +3024,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.2", + "target_tag" : "0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3039,22 +3045,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/agat/agat_convert_sp_gff2tsv", - "viash_version" : "0.9.0-RC7", - "git_commit" : "f22ab0eab58dcd6bff89d8d73fe951953ff1260f", + "viash_version" : "0.9.0", + "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.2", + "version" : "0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.0-RC7", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.2'" + ".engines[.type == 'docker'].target_tag := '0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3192,7 +3198,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -3323,7 +3333,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -3331,8 +3342,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -3369,6 +3380,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -3380,10 +3392,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -3468,7 +3479,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/agat/agat_convert_sp_gff2tsv", - "tag" : "v0.2" + "tag" : "0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/agat/agat_convert_sp_gff2tsv/nextflow.config b/target/nextflow/agat/agat_convert_sp_gff2tsv/nextflow.config index cd9e786e..897aedaa 100644 --- a/target/nextflow/agat/agat_convert_sp_gff2tsv/nextflow.config +++ b/target/nextflow/agat/agat_convert_sp_gff2tsv/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'agat/agat_convert_sp_gff2tsv' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.2' + version = '0.2.0' description = 'The script aims to convert gtf/gff file into tabulated file. Attribute\'s\ntags from the 9th column become column titles.\n' author = 'Leïla Paquay' } diff --git a/target/nextflow/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml b/target/nextflow/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml index 4b33d138..a7631567 100644 --- a/target/nextflow/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml +++ b/target/nextflow/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "agat_convert_sp_gxf2gxf" namespace: "agat" -version: "v0.2" +version: "0.2.0" authors: - name: "Leïla Paquay" roles: @@ -178,7 +178,7 @@ engines: id: "docker" image: "quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -194,22 +194,22 @@ build_info: engine: "docker|native" output: "target/nextflow/agat/agat_convert_sp_gxf2gxf" executable: "target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf b/target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf index c3d5fd3c..ba693e23 100644 --- a/target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf +++ b/target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf @@ -1,8 +1,8 @@ -// agat_convert_sp_gxf2gxf v0.2 +// agat_convert_sp_gxf2gxf 0.2.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such @@ -1731,7 +1731,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1802,7 +1804,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1844,7 +1848,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2803,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "agat_convert_sp_gxf2gxf", "namespace" : "agat", - "version" : "v0.2", + "version" : "0.2.0", "authors" : [ { "name" : "Leïla Paquay", @@ -3018,7 +3024,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.2", + "target_tag" : "0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3039,22 +3045,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/agat/agat_convert_sp_gxf2gxf", - "viash_version" : "0.9.0-RC7", - "git_commit" : "f22ab0eab58dcd6bff89d8d73fe951953ff1260f", + "viash_version" : "0.9.0", + "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.2", + "version" : "0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.0-RC7", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.2'" + ".engines[.type == 'docker'].target_tag := '0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3192,7 +3198,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -3323,7 +3333,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -3331,8 +3342,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -3369,6 +3380,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -3380,10 +3392,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -3468,7 +3479,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/agat/agat_convert_sp_gxf2gxf", - "tag" : "v0.2" + "tag" : "0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/agat/agat_convert_sp_gxf2gxf/nextflow.config b/target/nextflow/agat/agat_convert_sp_gxf2gxf/nextflow.config index bb2085eb..18b64ccd 100644 --- a/target/nextflow/agat/agat_convert_sp_gxf2gxf/nextflow.config +++ b/target/nextflow/agat/agat_convert_sp_gxf2gxf/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'agat/agat_convert_sp_gxf2gxf' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.2' + version = '0.2.0' description = 'This script fixes and/or standardizes any GTF/GFF file into full sorted\nGTF/GFF file. It AGAT parser removes duplicate features, fixes\nduplicated IDs, adds missing ID and/or Parent attributes, deflates\nfactorized attributes (attributes with several parents are duplicated\nwith uniq ID), add missing features when possible (e.g. add exon if only\nCDS described, add UTR if CDS and exon described), fix feature locations\n(e.g. check exon is embedded in the parent features mRNA, gene), etc...\n\nAll AGAT\'s scripts with the _sp_ prefix use the AGAT parser, before to\nperform any supplementary task. So, it is not necessary to run this\nscript prior the use of any other _sp_ script.\n' author = 'Leïla Paquay' } diff --git a/target/nextflow/arriba/.config.vsh.yaml b/target/nextflow/arriba/.config.vsh.yaml index 895c9556..8217fd3e 100644 --- a/target/nextflow/arriba/.config.vsh.yaml +++ b/target/nextflow/arriba/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "arriba" -version: "v0.2" +version: "0.2.0" authors: - name: "Robrecht Cannoodt" roles: @@ -688,7 +688,7 @@ engines: id: "docker" image: "quay.io/biocontainers/arriba:2.4.0--h0033a41_2" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -705,22 +705,22 @@ build_info: engine: "docker|native" output: "target/nextflow/arriba" executable: "target/nextflow/arriba/main.nf" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/arriba/main.nf b/target/nextflow/arriba/main.nf index 241de40d..5ee98bcc 100644 --- a/target/nextflow/arriba/main.nf +++ b/target/nextflow/arriba/main.nf @@ -1,8 +1,8 @@ -// arriba v0.2 +// arriba 0.2.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such @@ -1731,7 +1731,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1802,7 +1804,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1844,7 +1848,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2802,7 +2808,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "arriba", - "version" : "v0.2", + "version" : "0.2.0", "authors" : [ { "name" : "Robrecht Cannoodt", @@ -3564,7 +3570,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/arriba:2.4.0--h0033a41_2", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.2", + "target_tag" : "0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3585,22 +3591,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/arriba", - "viash_version" : "0.9.0-RC7", - "git_commit" : "f22ab0eab58dcd6bff89d8d73fe951953ff1260f", + "viash_version" : "0.9.0", + "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.2", + "version" : "0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.0-RC7", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.2'" + ".engines[.type == 'docker'].target_tag := '0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3817,7 +3823,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -3948,7 +3958,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -3956,8 +3967,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -3994,6 +4005,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -4005,10 +4017,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -4093,7 +4104,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/arriba", - "tag" : "v0.2" + "tag" : "0.2.0" }, "cpus" : 1, "tag" : "$id" diff --git a/target/nextflow/arriba/nextflow.config b/target/nextflow/arriba/nextflow.config index 2c609571..826ff39a 100644 --- a/target/nextflow/arriba/nextflow.config +++ b/target/nextflow/arriba/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'arriba' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.2' + version = '0.2.0' description = 'Detect gene fusions from RNA-Seq data' author = 'Robrecht Cannoodt' } diff --git a/target/nextflow/bcftools/bcftools_sort/.config.vsh.yaml b/target/nextflow/bcftools/bcftools_sort/.config.vsh.yaml index bbb66518..0354f8c4 100644 --- a/target/nextflow/bcftools/bcftools_sort/.config.vsh.yaml +++ b/target/nextflow/bcftools/bcftools_sort/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bcftools_sort" namespace: "bcftools" -version: "v0.2" +version: "0.2.0" authors: - name: "Theodoro Gasperin Terra Camargo" roles: @@ -162,7 +162,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -184,22 +184,22 @@ build_info: engine: "docker|native" output: "target/nextflow/bcftools/bcftools_sort" executable: "target/nextflow/bcftools/bcftools_sort/main.nf" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bcftools/bcftools_sort/main.nf b/target/nextflow/bcftools/bcftools_sort/main.nf index 46ea5236..62e80ab8 100644 --- a/target/nextflow/bcftools/bcftools_sort/main.nf +++ b/target/nextflow/bcftools/bcftools_sort/main.nf @@ -1,8 +1,8 @@ -// bcftools_sort v0.2 +// bcftools_sort 0.2.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such @@ -1731,7 +1731,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1802,7 +1804,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1844,7 +1848,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2803,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "bcftools_sort", "namespace" : "bcftools", - "version" : "v0.2", + "version" : "0.2.0", "authors" : [ { "name" : "Theodoro Gasperin Terra Camargo", @@ -3012,7 +3018,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.2", + "target_tag" : "0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3041,22 +3047,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/bcftools/bcftools_sort", - "viash_version" : "0.9.0-RC7", - "git_commit" : "f22ab0eab58dcd6bff89d8d73fe951953ff1260f", + "viash_version" : "0.9.0", + "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.2", + "version" : "0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.0-RC7", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.2'" + ".engines[.type == 'docker'].target_tag := '0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3200,7 +3206,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -3331,7 +3341,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -3339,8 +3350,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -3377,6 +3388,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -3388,10 +3400,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -3476,7 +3487,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/bcftools/bcftools_sort", - "tag" : "v0.2" + "tag" : "0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/bcftools/bcftools_sort/nextflow.config b/target/nextflow/bcftools/bcftools_sort/nextflow.config index 8a2a3b23..eb45701b 100644 --- a/target/nextflow/bcftools/bcftools_sort/nextflow.config +++ b/target/nextflow/bcftools/bcftools_sort/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'bcftools/bcftools_sort' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.2' + version = '0.2.0' description = 'Sorts VCF/BCF files.\n' author = 'Theodoro Gasperin Terra Camargo' } diff --git a/target/nextflow/bcl_convert/.config.vsh.yaml b/target/nextflow/bcl_convert/.config.vsh.yaml index 54775a48..6aba9f98 100644 --- a/target/nextflow/bcl_convert/.config.vsh.yaml +++ b/target/nextflow/bcl_convert/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "bcl_convert" -version: "v0.2" +version: "0.2.0" authors: - name: "Toni Verbeiren" roles: @@ -386,7 +386,7 @@ engines: id: "docker" image: "debian:trixie-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -417,22 +417,22 @@ build_info: engine: "docker|native" output: "target/nextflow/bcl_convert" executable: "target/nextflow/bcl_convert/main.nf" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bcl_convert/main.nf b/target/nextflow/bcl_convert/main.nf index 2009d44d..eb1c214c 100644 --- a/target/nextflow/bcl_convert/main.nf +++ b/target/nextflow/bcl_convert/main.nf @@ -1,8 +1,8 @@ -// bcl_convert v0.2 +// bcl_convert 0.2.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such @@ -1732,7 +1732,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1803,7 +1805,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1845,7 +1849,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2803,7 +2809,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "bcl_convert", - "version" : "v0.2", + "version" : "0.2.0", "authors" : [ { "name" : "Toni Verbeiren", @@ -3283,7 +3289,7 @@ meta = [ "id" : "docker", "image" : "debian:trixie-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.2", + "target_tag" : "0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3322,22 +3328,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/bcl_convert", - "viash_version" : "0.9.0-RC7", - "git_commit" : "f22ab0eab58dcd6bff89d8d73fe951953ff1260f", + "viash_version" : "0.9.0", + "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.2", + "version" : "0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.0-RC7", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.2'" + ".engines[.type == 'docker'].target_tag := '0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3528,7 +3534,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -3659,7 +3669,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -3667,8 +3678,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -3705,6 +3716,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -3716,10 +3728,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -3804,7 +3815,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/bcl_convert", - "tag" : "v0.2" + "tag" : "0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/bcl_convert/nextflow.config b/target/nextflow/bcl_convert/nextflow.config index 1ce501ec..0f8797a3 100644 --- a/target/nextflow/bcl_convert/nextflow.config +++ b/target/nextflow/bcl_convert/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'bcl_convert' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.2' + version = '0.2.0' description = 'Convert bcl files to fastq files using bcl-convert.\nInformation about upgrading from bcl2fastq via\n[Upgrading from bcl2fastq to BCL Convert](https://emea.support.illumina.com/bulletins/2020/10/upgrading-from-bcl2fastq-to-bcl-convert.html)\nand [BCL Convert Compatible Products](https://support.illumina.com/sequencing/sequencing_software/bcl-convert/compatibility.html)\n' author = 'Toni Verbeiren, Dorien Roosen' } diff --git a/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml b/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml index 00ecdd30..bfe7e16e 100644 --- a/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml +++ b/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bd_rhapsody_make_reference" namespace: "bd_rhapsody" -version: "v0.2" +version: "0.2.0" authors: - name: "Robrecht Cannoodt" roles: @@ -243,7 +243,7 @@ engines: id: "docker" image: "bdgenomics/rhapsody:2.2.1" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -269,22 +269,22 @@ build_info: engine: "docker|native" output: "target/nextflow/bd_rhapsody/bd_rhapsody_make_reference" executable: "target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf b/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf index cdf120db..295ad3bb 100644 --- a/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf +++ b/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf @@ -1,8 +1,8 @@ -// bd_rhapsody_make_reference v0.2 +// bd_rhapsody_make_reference 0.2.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such @@ -1732,7 +1732,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1803,7 +1805,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1845,7 +1849,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2804,7 +2810,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "bd_rhapsody_make_reference", "namespace" : "bd_rhapsody", - "version" : "v0.2", + "version" : "0.2.0", "authors" : [ { "name" : "Robrecht Cannoodt", @@ -3098,7 +3104,7 @@ meta = [ "id" : "docker", "image" : "bdgenomics/rhapsody:2.2.1", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.2", + "target_tag" : "0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3135,22 +3141,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/bd_rhapsody/bd_rhapsody_make_reference", - "viash_version" : "0.9.0-RC7", - "git_commit" : "f22ab0eab58dcd6bff89d8d73fe951953ff1260f", + "viash_version" : "0.9.0", + "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.2", + "version" : "0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.0-RC7", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.2'" + ".engines[.type == 'docker'].target_tag := '0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3435,7 +3441,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -3566,7 +3576,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -3574,8 +3585,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -3612,6 +3623,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -3623,10 +3635,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -3711,7 +3722,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/bd_rhapsody/bd_rhapsody_make_reference", - "tag" : "v0.2" + "tag" : "0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/nextflow.config b/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/nextflow.config index acf448b8..365dc66f 100644 --- a/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/nextflow.config +++ b/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'bd_rhapsody/bd_rhapsody_make_reference' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.2' + version = '0.2.0' description = 'The Reference Files Generator creates an archive containing Genome Index\nand Transcriptome annotation files needed for the BD Rhapsody Sequencing\nAnalysis Pipeline. The app takes as input one or more FASTA and GTF files\nand produces a compressed archive in the form of a tar.gz file. The \narchive contains:\n\n- STAR index\n- Filtered GTF file\n' author = 'Robrecht Cannoodt, Weiwei Schultz' } diff --git a/target/nextflow/bedtools/bedtools_bamtofastq/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_bamtofastq/.config.vsh.yaml index 717f0f24..ca6fe156 100644 --- a/target/nextflow/bedtools/bedtools_bamtofastq/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_bamtofastq/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bedtools_bamtofastq" namespace: "bedtools" -version: "v0.2" +version: "0.2.0" authors: - name: "Theodoro Gasperin Terra Camargo" roles: @@ -164,7 +164,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -186,22 +186,22 @@ build_info: engine: "docker|native" output: "target/nextflow/bedtools/bedtools_bamtofastq" executable: "target/nextflow/bedtools/bedtools_bamtofastq/main.nf" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_bamtofastq/main.nf b/target/nextflow/bedtools/bedtools_bamtofastq/main.nf index a8044ebc..0a531f3a 100644 --- a/target/nextflow/bedtools/bedtools_bamtofastq/main.nf +++ b/target/nextflow/bedtools/bedtools_bamtofastq/main.nf @@ -1,8 +1,8 @@ -// bedtools_bamtofastq v0.2 +// bedtools_bamtofastq 0.2.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such @@ -1731,7 +1731,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1802,7 +1804,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1844,7 +1848,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2803,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "bedtools_bamtofastq", "namespace" : "bedtools", - "version" : "v0.2", + "version" : "0.2.0", "authors" : [ { "name" : "Theodoro Gasperin Terra Camargo", @@ -3014,7 +3020,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.2", + "target_tag" : "0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3043,22 +3049,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_bamtofastq", - "viash_version" : "0.9.0-RC7", - "git_commit" : "f22ab0eab58dcd6bff89d8d73fe951953ff1260f", + "viash_version" : "0.9.0", + "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.2", + "version" : "0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.0-RC7", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.2'" + ".engines[.type == 'docker'].target_tag := '0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3206,7 +3212,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -3337,7 +3347,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -3345,8 +3356,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -3383,6 +3394,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -3394,10 +3406,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -3482,7 +3493,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/bedtools/bedtools_bamtofastq", - "tag" : "v0.2" + "tag" : "0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/bedtools/bedtools_bamtofastq/nextflow.config b/target/nextflow/bedtools/bedtools_bamtofastq/nextflow.config index e56faa26..0fd48169 100644 --- a/target/nextflow/bedtools/bedtools_bamtofastq/nextflow.config +++ b/target/nextflow/bedtools/bedtools_bamtofastq/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'bedtools/bedtools_bamtofastq' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.2' + version = '0.2.0' description = 'Conversion tool for extracting FASTQ records from sequence alignments in BAM format.\n' author = 'Theodoro Gasperin Terra Camargo' } diff --git a/target/nextflow/bedtools/bedtools_bed12tobed6/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_bed12tobed6/.config.vsh.yaml index 2df37159..32069829 100644 --- a/target/nextflow/bedtools/bedtools_bed12tobed6/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_bed12tobed6/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bedtools_bed12tobed6" namespace: "bedtools" -version: "v0.2" +version: "0.2.0" authors: - name: "Theodoro Gasperin Terra Camargo" roles: @@ -153,7 +153,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -175,22 +175,22 @@ build_info: engine: "docker|native" output: "target/nextflow/bedtools/bedtools_bed12tobed6" executable: "target/nextflow/bedtools/bedtools_bed12tobed6/main.nf" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_bed12tobed6/main.nf b/target/nextflow/bedtools/bedtools_bed12tobed6/main.nf index 69bf1d17..6f037a8e 100644 --- a/target/nextflow/bedtools/bedtools_bed12tobed6/main.nf +++ b/target/nextflow/bedtools/bedtools_bed12tobed6/main.nf @@ -1,8 +1,8 @@ -// bedtools_bed12tobed6 v0.2 +// bedtools_bed12tobed6 0.2.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such @@ -1731,7 +1731,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1802,7 +1804,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1844,7 +1848,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2803,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "bedtools_bed12tobed6", "namespace" : "bedtools", - "version" : "v0.2", + "version" : "0.2.0", "authors" : [ { "name" : "Theodoro Gasperin Terra Camargo", @@ -2999,7 +3005,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.2", + "target_tag" : "0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3028,22 +3034,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_bed12tobed6", - "viash_version" : "0.9.0-RC7", - "git_commit" : "f22ab0eab58dcd6bff89d8d73fe951953ff1260f", + "viash_version" : "0.9.0", + "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.2", + "version" : "0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.0-RC7", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.2'" + ".engines[.type == 'docker'].target_tag := '0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3187,7 +3193,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -3318,7 +3328,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -3326,8 +3337,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -3364,6 +3375,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -3375,10 +3387,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -3463,7 +3474,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/bedtools/bedtools_bed12tobed6", - "tag" : "v0.2" + "tag" : "0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/bedtools/bedtools_bed12tobed6/nextflow.config b/target/nextflow/bedtools/bedtools_bed12tobed6/nextflow.config index 505a2468..014a4714 100644 --- a/target/nextflow/bedtools/bedtools_bed12tobed6/nextflow.config +++ b/target/nextflow/bedtools/bedtools_bed12tobed6/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'bedtools/bedtools_bed12tobed6' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.2' + version = '0.2.0' description = 'Converts BED features in BED12 (a.k.a. “blocked” BED features such as genes) to discrete BED6 features.\nFor example, in the case of a gene with six exons, bed12ToBed6 would create six separate BED6 features (i.e., one for each exon).\n' author = 'Theodoro Gasperin Terra Camargo' } diff --git a/target/nextflow/bedtools/bedtools_bedtobam/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_bedtobam/.config.vsh.yaml index 52b2611b..4e2e9304 100644 --- a/target/nextflow/bedtools/bedtools_bedtobam/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_bedtobam/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bedtools_bedtobam" namespace: "bedtools" -version: "v0.2" +version: "0.2.0" authors: - name: "Theodoro Gasperin Terra Camargo" roles: @@ -186,7 +186,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -213,22 +213,22 @@ build_info: engine: "docker|native" output: "target/nextflow/bedtools/bedtools_bedtobam" executable: "target/nextflow/bedtools/bedtools_bedtobam/main.nf" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_bedtobam/main.nf b/target/nextflow/bedtools/bedtools_bedtobam/main.nf index e759d11d..0154fffb 100644 --- a/target/nextflow/bedtools/bedtools_bedtobam/main.nf +++ b/target/nextflow/bedtools/bedtools_bedtobam/main.nf @@ -1,8 +1,8 @@ -// bedtools_bedtobam v0.2 +// bedtools_bedtobam 0.2.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such @@ -1731,7 +1731,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1802,7 +1804,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1844,7 +1848,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2803,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "bedtools_bedtobam", "namespace" : "bedtools", - "version" : "v0.2", + "version" : "0.2.0", "authors" : [ { "name" : "Theodoro Gasperin Terra Camargo", @@ -3038,7 +3044,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.2", + "target_tag" : "0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3076,22 +3082,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_bedtobam", - "viash_version" : "0.9.0-RC7", - "git_commit" : "f22ab0eab58dcd6bff89d8d73fe951953ff1260f", + "viash_version" : "0.9.0", + "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.2", + "version" : "0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.0-RC7", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.2'" + ".engines[.type == 'docker'].target_tag := '0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3242,7 +3248,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -3373,7 +3383,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -3381,8 +3392,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -3419,6 +3430,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -3430,10 +3442,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -3518,7 +3529,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/bedtools/bedtools_bedtobam", - "tag" : "v0.2" + "tag" : "0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/bedtools/bedtools_bedtobam/nextflow.config b/target/nextflow/bedtools/bedtools_bedtobam/nextflow.config index 2ff898f9..661578e0 100644 --- a/target/nextflow/bedtools/bedtools_bedtobam/nextflow.config +++ b/target/nextflow/bedtools/bedtools_bedtobam/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'bedtools/bedtools_bedtobam' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.2' + version = '0.2.0' description = 'Converts feature records (bed/gff/vcf) to BAM format.' author = 'Theodoro Gasperin Terra Camargo' } diff --git a/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml index 8f5ae24a..173d9a32 100644 --- a/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bedtools_getfasta" namespace: "bedtools" -version: "v0.2" +version: "0.2.0" authors: - name: "Dries Schaumont" roles: @@ -209,7 +209,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -231,22 +231,22 @@ build_info: engine: "docker|native" output: "target/nextflow/bedtools/bedtools_getfasta" executable: "target/nextflow/bedtools/bedtools_getfasta/main.nf" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_getfasta/main.nf b/target/nextflow/bedtools/bedtools_getfasta/main.nf index 763327d8..00de8d13 100644 --- a/target/nextflow/bedtools/bedtools_getfasta/main.nf +++ b/target/nextflow/bedtools/bedtools_getfasta/main.nf @@ -1,8 +1,8 @@ -// bedtools_getfasta v0.2 +// bedtools_getfasta 0.2.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such @@ -1731,7 +1731,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1802,7 +1804,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1844,7 +1848,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2803,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "bedtools_getfasta", "namespace" : "bedtools", - "version" : "v0.2", + "version" : "0.2.0", "authors" : [ { "name" : "Dries Schaumont", @@ -3050,7 +3056,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.2", + "target_tag" : "0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3079,22 +3085,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_getfasta", - "viash_version" : "0.9.0-RC7", - "git_commit" : "f22ab0eab58dcd6bff89d8d73fe951953ff1260f", + "viash_version" : "0.9.0", + "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.2", + "version" : "0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.0-RC7", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.2'" + ".engines[.type == 'docker'].target_tag := '0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3254,7 +3260,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -3385,7 +3395,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -3393,8 +3404,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -3431,6 +3442,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -3442,10 +3454,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -3530,7 +3541,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/bedtools/bedtools_getfasta", - "tag" : "v0.2" + "tag" : "0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/bedtools/bedtools_getfasta/nextflow.config b/target/nextflow/bedtools/bedtools_getfasta/nextflow.config index 01f9db9c..f61b17d2 100644 --- a/target/nextflow/bedtools/bedtools_getfasta/nextflow.config +++ b/target/nextflow/bedtools/bedtools_getfasta/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'bedtools/bedtools_getfasta' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.2' + version = '0.2.0' description = 'Extract sequences from a FASTA file for each of the intervals defined in a BED/GFF/VCF file.' author = 'Dries Schaumont' } diff --git a/target/nextflow/bedtools/bedtools_groupby/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_groupby/.config.vsh.yaml index bd7e9a6c..c606163f 100644 --- a/target/nextflow/bedtools/bedtools_groupby/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_groupby/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bedtools_groupby" namespace: "bedtools" -version: "v0.2" +version: "0.2.0" authors: - name: "Theodoro Gasperin Terra Camargo" roles: @@ -250,7 +250,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -272,22 +272,22 @@ build_info: engine: "docker|native" output: "target/nextflow/bedtools/bedtools_groupby" executable: "target/nextflow/bedtools/bedtools_groupby/main.nf" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_groupby/main.nf b/target/nextflow/bedtools/bedtools_groupby/main.nf index be704769..08eaacb7 100644 --- a/target/nextflow/bedtools/bedtools_groupby/main.nf +++ b/target/nextflow/bedtools/bedtools_groupby/main.nf @@ -1,8 +1,8 @@ -// bedtools_groupby v0.2 +// bedtools_groupby 0.2.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such @@ -1731,7 +1731,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1802,7 +1804,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1844,7 +1848,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2803,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "bedtools_groupby", "namespace" : "bedtools", - "version" : "v0.2", + "version" : "0.2.0", "authors" : [ { "name" : "Theodoro Gasperin Terra Camargo", @@ -3094,7 +3100,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.2", + "target_tag" : "0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3123,22 +3129,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_groupby", - "viash_version" : "0.9.0-RC7", - "git_commit" : "f22ab0eab58dcd6bff89d8d73fe951953ff1260f", + "viash_version" : "0.9.0", + "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.2", + "version" : "0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.0-RC7", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.2'" + ".engines[.type == 'docker'].target_tag := '0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3312,7 +3318,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -3443,7 +3453,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -3451,8 +3462,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -3489,6 +3500,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -3500,10 +3512,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -3588,7 +3599,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/bedtools/bedtools_groupby", - "tag" : "v0.2" + "tag" : "0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/bedtools/bedtools_groupby/nextflow.config b/target/nextflow/bedtools/bedtools_groupby/nextflow.config index 09caaa59..c4a24801 100644 --- a/target/nextflow/bedtools/bedtools_groupby/nextflow.config +++ b/target/nextflow/bedtools/bedtools_groupby/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'bedtools/bedtools_groupby' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.2' + version = '0.2.0' description = 'Summarizes a dataset column based upon common column groupings. \nAkin to the SQL "group by" command.\n' author = 'Theodoro Gasperin Terra Camargo' } diff --git a/target/nextflow/bedtools/bedtools_intersect/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_intersect/.config.vsh.yaml index fc7f1ad2..16cda546 100644 --- a/target/nextflow/bedtools/bedtools_intersect/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_intersect/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bedtools_intersect" namespace: "bedtools" -version: "v0.2" +version: "0.2.0" authors: - name: "Theodoro Gasperin Terra Camargo" roles: @@ -387,7 +387,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -409,22 +409,22 @@ build_info: engine: "docker|native" output: "target/nextflow/bedtools/bedtools_intersect" executable: "target/nextflow/bedtools/bedtools_intersect/main.nf" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_intersect/main.nf b/target/nextflow/bedtools/bedtools_intersect/main.nf index f1432170..0a2c9580 100644 --- a/target/nextflow/bedtools/bedtools_intersect/main.nf +++ b/target/nextflow/bedtools/bedtools_intersect/main.nf @@ -1,8 +1,8 @@ -// bedtools_intersect v0.2 +// bedtools_intersect 0.2.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such @@ -1731,7 +1731,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1802,7 +1804,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1844,7 +1848,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2803,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "bedtools_intersect", "namespace" : "bedtools", - "version" : "v0.2", + "version" : "0.2.0", "authors" : [ { "name" : "Theodoro Gasperin Terra Camargo", @@ -3246,7 +3252,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.2", + "target_tag" : "0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3275,22 +3281,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_intersect", - "viash_version" : "0.9.0-RC7", - "git_commit" : "f22ab0eab58dcd6bff89d8d73fe951953ff1260f", + "viash_version" : "0.9.0", + "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.2", + "version" : "0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.0-RC7", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.2'" + ".engines[.type == 'docker'].target_tag := '0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3514,7 +3520,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -3645,7 +3655,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -3653,8 +3664,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -3691,6 +3702,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -3702,10 +3714,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -3790,7 +3801,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/bedtools/bedtools_intersect", - "tag" : "v0.2" + "tag" : "0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/bedtools/bedtools_intersect/nextflow.config b/target/nextflow/bedtools/bedtools_intersect/nextflow.config index 3a6de324..1b08d2b2 100644 --- a/target/nextflow/bedtools/bedtools_intersect/nextflow.config +++ b/target/nextflow/bedtools/bedtools_intersect/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'bedtools/bedtools_intersect' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.2' + version = '0.2.0' description = 'bedtools intersect allows one to screen for overlaps between two sets of genomic features. \nMoreover, it allows one to have fine control as to how the intersections are reported. \nbedtools intersect works with both BED/GFF/VCF and BAM files as input.\n' author = 'Theodoro Gasperin Terra Camargo' } diff --git a/target/nextflow/bedtools/bedtools_links/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_links/.config.vsh.yaml index 806737b3..b9d4b930 100644 --- a/target/nextflow/bedtools/bedtools_links/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_links/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bedtools_links" namespace: "bedtools" -version: "v0.2" +version: "0.2.0" authors: - name: "Theodoro Gasperin Terra Camargo" roles: @@ -187,7 +187,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -209,22 +209,22 @@ build_info: engine: "docker|native" output: "target/nextflow/bedtools/bedtools_links" executable: "target/nextflow/bedtools/bedtools_links/main.nf" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_links/main.nf b/target/nextflow/bedtools/bedtools_links/main.nf index cc87cf88..ea91e5f5 100644 --- a/target/nextflow/bedtools/bedtools_links/main.nf +++ b/target/nextflow/bedtools/bedtools_links/main.nf @@ -1,8 +1,8 @@ -// bedtools_links v0.2 +// bedtools_links 0.2.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such @@ -1731,7 +1731,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1802,7 +1804,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1844,7 +1848,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2803,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "bedtools_links", "namespace" : "bedtools", - "version" : "v0.2", + "version" : "0.2.0", "authors" : [ { "name" : "Theodoro Gasperin Terra Camargo", @@ -3037,7 +3043,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.2", + "target_tag" : "0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3066,22 +3072,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_links", - "viash_version" : "0.9.0-RC7", - "git_commit" : "f22ab0eab58dcd6bff89d8d73fe951953ff1260f", + "viash_version" : "0.9.0", + "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.2", + "version" : "0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.0-RC7", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.2'" + ".engines[.type == 'docker'].target_tag := '0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3226,7 +3232,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -3357,7 +3367,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -3365,8 +3376,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -3403,6 +3414,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -3414,10 +3426,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -3502,7 +3513,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/bedtools/bedtools_links", - "tag" : "v0.2" + "tag" : "0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/bedtools/bedtools_links/nextflow.config b/target/nextflow/bedtools/bedtools_links/nextflow.config index 3d3c14a9..33eb36ff 100644 --- a/target/nextflow/bedtools/bedtools_links/nextflow.config +++ b/target/nextflow/bedtools/bedtools_links/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'bedtools/bedtools_links' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.2' + version = '0.2.0' description = 'Creates an HTML file with links to an instance of the UCSC Genome Browser for all features / intervals in a file. \nThis is useful for cases when one wants to manually inspect through a large set of annotations or features.\n' author = 'Theodoro Gasperin Terra Camargo' } diff --git a/target/nextflow/bedtools/bedtools_merge/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_merge/.config.vsh.yaml index 7e743428..1f3fa6de 100644 --- a/target/nextflow/bedtools/bedtools_merge/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_merge/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bedtools_merge" namespace: "bedtools" -version: "v0.2" +version: "0.2.0" authors: - name: "Theodoro Gasperin Terra Camargo" roles: @@ -256,7 +256,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -278,22 +278,22 @@ build_info: engine: "docker|native" output: "target/nextflow/bedtools/bedtools_merge" executable: "target/nextflow/bedtools/bedtools_merge/main.nf" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_merge/main.nf b/target/nextflow/bedtools/bedtools_merge/main.nf index 3d010580..6cd59548 100644 --- a/target/nextflow/bedtools/bedtools_merge/main.nf +++ b/target/nextflow/bedtools/bedtools_merge/main.nf @@ -1,8 +1,8 @@ -// bedtools_merge v0.2 +// bedtools_merge 0.2.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such @@ -1731,7 +1731,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1802,7 +1804,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1844,7 +1848,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2803,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "bedtools_merge", "namespace" : "bedtools", - "version" : "v0.2", + "version" : "0.2.0", "authors" : [ { "name" : "Theodoro Gasperin Terra Camargo", @@ -3098,7 +3104,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.2", + "target_tag" : "0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3127,22 +3133,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_merge", - "viash_version" : "0.9.0-RC7", - "git_commit" : "f22ab0eab58dcd6bff89d8d73fe951953ff1260f", + "viash_version" : "0.9.0", + "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.2", + "version" : "0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.0-RC7", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.2'" + ".engines[.type == 'docker'].target_tag := '0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3315,7 +3321,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -3446,7 +3456,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -3454,8 +3465,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -3492,6 +3503,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -3503,10 +3515,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -3591,7 +3602,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/bedtools/bedtools_merge", - "tag" : "v0.2" + "tag" : "0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/bedtools/bedtools_merge/nextflow.config b/target/nextflow/bedtools/bedtools_merge/nextflow.config index 4fb0e662..a7523a1c 100644 --- a/target/nextflow/bedtools/bedtools_merge/nextflow.config +++ b/target/nextflow/bedtools/bedtools_merge/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'bedtools/bedtools_merge' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.2' + version = '0.2.0' description = 'Merges overlapping BED/GFF/VCF entries into a single interval.\n' author = 'Theodoro Gasperin Terra Camargo' } diff --git a/target/nextflow/bedtools/bedtools_sort/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_sort/.config.vsh.yaml index 36652804..a5240910 100644 --- a/target/nextflow/bedtools/bedtools_sort/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_sort/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bedtools_sort" namespace: "bedtools" -version: "v0.2" +version: "0.2.0" authors: - name: "Theodoro Gasperin Terra Camargo" roles: @@ -199,7 +199,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -221,22 +221,22 @@ build_info: engine: "docker|native" output: "target/nextflow/bedtools/bedtools_sort" executable: "target/nextflow/bedtools/bedtools_sort/main.nf" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_sort/main.nf b/target/nextflow/bedtools/bedtools_sort/main.nf index 917d4094..156f6127 100644 --- a/target/nextflow/bedtools/bedtools_sort/main.nf +++ b/target/nextflow/bedtools/bedtools_sort/main.nf @@ -1,8 +1,8 @@ -// bedtools_sort v0.2 +// bedtools_sort 0.2.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such @@ -1731,7 +1731,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1802,7 +1804,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1844,7 +1848,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2803,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "bedtools_sort", "namespace" : "bedtools", - "version" : "v0.2", + "version" : "0.2.0", "authors" : [ { "name" : "Theodoro Gasperin Terra Camargo", @@ -3056,7 +3062,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.2", + "target_tag" : "0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3085,22 +3091,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_sort", - "viash_version" : "0.9.0-RC7", - "git_commit" : "f22ab0eab58dcd6bff89d8d73fe951953ff1260f", + "viash_version" : "0.9.0", + "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.2", + "version" : "0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.0-RC7", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.2'" + ".engines[.type == 'docker'].target_tag := '0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3271,7 +3277,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -3402,7 +3412,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -3410,8 +3421,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -3448,6 +3459,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -3459,10 +3471,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -3547,7 +3558,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/bedtools/bedtools_sort", - "tag" : "v0.2" + "tag" : "0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/bedtools/bedtools_sort/nextflow.config b/target/nextflow/bedtools/bedtools_sort/nextflow.config index 54e075fa..81c566cf 100644 --- a/target/nextflow/bedtools/bedtools_sort/nextflow.config +++ b/target/nextflow/bedtools/bedtools_sort/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'bedtools/bedtools_sort' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.2' + version = '0.2.0' description = 'Sorts a feature file (bed/gff/vcf) by chromosome and other criteria.' author = 'Theodoro Gasperin Terra Camargo' } diff --git a/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml b/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml index 6576a6e6..04b03d38 100644 --- a/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml +++ b/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "busco_download_datasets" namespace: "busco" -version: "v0.2" +version: "0.2.0" authors: - name: "Dorien Roosen" roles: @@ -141,7 +141,7 @@ engines: id: "docker" image: "quay.io/biocontainers/busco:5.7.1--pyhdfd78af_0" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -157,22 +157,22 @@ build_info: engine: "docker|native" output: "target/nextflow/busco/busco_download_datasets" executable: "target/nextflow/busco/busco_download_datasets/main.nf" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/busco/busco_download_datasets/main.nf b/target/nextflow/busco/busco_download_datasets/main.nf index f398aad5..9e13a282 100644 --- a/target/nextflow/busco/busco_download_datasets/main.nf +++ b/target/nextflow/busco/busco_download_datasets/main.nf @@ -1,8 +1,8 @@ -// busco_download_datasets v0.2 +// busco_download_datasets 0.2.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such @@ -1731,7 +1731,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1802,7 +1804,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1844,7 +1848,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2803,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "busco_download_datasets", "namespace" : "busco", - "version" : "v0.2", + "version" : "0.2.0", "authors" : [ { "name" : "Dorien Roosen", @@ -2983,7 +2989,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/busco:5.7.1--pyhdfd78af_0", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.2", + "target_tag" : "0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3004,22 +3010,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/busco/busco_download_datasets", - "viash_version" : "0.9.0-RC7", - "git_commit" : "f22ab0eab58dcd6bff89d8d73fe951953ff1260f", + "viash_version" : "0.9.0", + "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.2", + "version" : "0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.0-RC7", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.2'" + ".engines[.type == 'docker'].target_tag := '0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3161,7 +3167,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -3292,7 +3302,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -3300,8 +3311,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -3338,6 +3349,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -3349,10 +3361,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -3437,7 +3448,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/busco/busco_download_datasets", - "tag" : "v0.2" + "tag" : "0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/busco/busco_download_datasets/nextflow.config b/target/nextflow/busco/busco_download_datasets/nextflow.config index 255e3d4b..98e282f1 100644 --- a/target/nextflow/busco/busco_download_datasets/nextflow.config +++ b/target/nextflow/busco/busco_download_datasets/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'busco/busco_download_datasets' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.2' + version = '0.2.0' description = 'Downloads available busco datasets' author = 'Dorien Roosen' } diff --git a/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml b/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml index 0bb38659..4632e840 100644 --- a/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml +++ b/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "busco_list_datasets" namespace: "busco" -version: "v0.2" +version: "0.2.0" authors: - name: "Dorien Roosen" roles: @@ -128,7 +128,7 @@ engines: id: "docker" image: "quay.io/biocontainers/busco:5.7.1--pyhdfd78af_0" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -144,22 +144,22 @@ build_info: engine: "docker|native" output: "target/nextflow/busco/busco_list_datasets" executable: "target/nextflow/busco/busco_list_datasets/main.nf" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/busco/busco_list_datasets/main.nf b/target/nextflow/busco/busco_list_datasets/main.nf index c2b2f2ab..b077980e 100644 --- a/target/nextflow/busco/busco_list_datasets/main.nf +++ b/target/nextflow/busco/busco_list_datasets/main.nf @@ -1,8 +1,8 @@ -// busco_list_datasets v0.2 +// busco_list_datasets 0.2.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such @@ -1731,7 +1731,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1802,7 +1804,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1844,7 +1848,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2803,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "busco_list_datasets", "namespace" : "busco", - "version" : "v0.2", + "version" : "0.2.0", "authors" : [ { "name" : "Dorien Roosen", @@ -2969,7 +2975,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/busco:5.7.1--pyhdfd78af_0", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.2", + "target_tag" : "0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -2990,22 +2996,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/busco/busco_list_datasets", - "viash_version" : "0.9.0-RC7", - "git_commit" : "f22ab0eab58dcd6bff89d8d73fe951953ff1260f", + "viash_version" : "0.9.0", + "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.2", + "version" : "0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.0-RC7", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.2'" + ".engines[.type == 'docker'].target_tag := '0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3138,7 +3144,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -3269,7 +3279,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -3277,8 +3288,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -3315,6 +3326,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -3326,10 +3338,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -3414,7 +3425,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/busco/busco_list_datasets", - "tag" : "v0.2" + "tag" : "0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/busco/busco_list_datasets/nextflow.config b/target/nextflow/busco/busco_list_datasets/nextflow.config index 88679c47..c41da094 100644 --- a/target/nextflow/busco/busco_list_datasets/nextflow.config +++ b/target/nextflow/busco/busco_list_datasets/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'busco/busco_list_datasets' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.2' + version = '0.2.0' description = 'Lists the available busco datasets' author = 'Dorien Roosen' } diff --git a/target/nextflow/busco/busco_run/.config.vsh.yaml b/target/nextflow/busco/busco_run/.config.vsh.yaml index f4cec20e..893c319a 100644 --- a/target/nextflow/busco/busco_run/.config.vsh.yaml +++ b/target/nextflow/busco/busco_run/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "busco_run" namespace: "busco" -version: "v0.2" +version: "0.2.0" authors: - name: "Dorien Roosen" roles: @@ -406,7 +406,7 @@ engines: id: "docker" image: "quay.io/biocontainers/busco:5.7.1--pyhdfd78af_0" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -422,22 +422,22 @@ build_info: engine: "docker|native" output: "target/nextflow/busco/busco_run" executable: "target/nextflow/busco/busco_run/main.nf" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/busco/busco_run/main.nf b/target/nextflow/busco/busco_run/main.nf index 3bf457fd..438de8c2 100644 --- a/target/nextflow/busco/busco_run/main.nf +++ b/target/nextflow/busco/busco_run/main.nf @@ -1,8 +1,8 @@ -// busco_run v0.2 +// busco_run 0.2.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such @@ -1731,7 +1731,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1802,7 +1804,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1844,7 +1848,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2803,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "busco_run", "namespace" : "busco", - "version" : "v0.2", + "version" : "0.2.0", "authors" : [ { "name" : "Dorien Roosen", @@ -3281,7 +3287,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/busco:5.7.1--pyhdfd78af_0", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.2", + "target_tag" : "0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3302,22 +3308,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/busco/busco_run", - "viash_version" : "0.9.0-RC7", - "git_commit" : "f22ab0eab58dcd6bff89d8d73fe951953ff1260f", + "viash_version" : "0.9.0", + "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.2", + "version" : "0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.0-RC7", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.2'" + ".engines[.type == 'docker'].target_tag := '0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3548,7 +3554,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -3679,7 +3689,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -3687,8 +3698,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -3725,6 +3736,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -3736,10 +3748,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -3824,7 +3835,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/busco/busco_run", - "tag" : "v0.2" + "tag" : "0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/busco/busco_run/nextflow.config b/target/nextflow/busco/busco_run/nextflow.config index 75ddd636..93634eaf 100644 --- a/target/nextflow/busco/busco_run/nextflow.config +++ b/target/nextflow/busco/busco_run/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'busco/busco_run' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.2' + version = '0.2.0' description = 'Assessment of genome assembly and annotation completeness with single copy orthologs' author = 'Dorien Roosen' } diff --git a/target/nextflow/cutadapt/.config.vsh.yaml b/target/nextflow/cutadapt/.config.vsh.yaml index efca3dd8..259949cd 100644 --- a/target/nextflow/cutadapt/.config.vsh.yaml +++ b/target/nextflow/cutadapt/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "cutadapt" -version: "v0.2" +version: "0.2.0" authors: - name: "Toni Verbeiren" roles: @@ -718,7 +718,7 @@ engines: id: "docker" image: "python:3.12" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "python" @@ -739,22 +739,22 @@ build_info: engine: "docker|native" output: "target/nextflow/cutadapt" executable: "target/nextflow/cutadapt/main.nf" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/cutadapt/main.nf b/target/nextflow/cutadapt/main.nf index 1f356c4e..4468bef5 100644 --- a/target/nextflow/cutadapt/main.nf +++ b/target/nextflow/cutadapt/main.nf @@ -1,8 +1,8 @@ -// cutadapt v0.2 +// cutadapt 0.2.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such @@ -1731,7 +1731,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1802,7 +1804,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1844,7 +1848,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2802,7 +2808,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "cutadapt", - "version" : "v0.2", + "version" : "0.2.0", "authors" : [ { "name" : "Toni Verbeiren", @@ -3583,7 +3589,7 @@ meta = [ "id" : "docker", "image" : "python:3.12", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.2", + "target_tag" : "0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3612,22 +3618,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/cutadapt", - "viash_version" : "0.9.0-RC7", - "git_commit" : "f22ab0eab58dcd6bff89d8d73fe951953ff1260f", + "viash_version" : "0.9.0", + "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.2", + "version" : "0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.0-RC7", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.2'" + ".engines[.type == 'docker'].target_tag := '0.2.0'" ], "keywords" : [ "bioinformatics", @@ -4059,7 +4065,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -4190,7 +4200,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -4198,8 +4209,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -4236,6 +4247,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -4247,10 +4259,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -4335,7 +4346,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/cutadapt", - "tag" : "v0.2" + "tag" : "0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/cutadapt/nextflow.config b/target/nextflow/cutadapt/nextflow.config index 4969fe47..2aa5ef3b 100644 --- a/target/nextflow/cutadapt/nextflow.config +++ b/target/nextflow/cutadapt/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'cutadapt' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.2' + version = '0.2.0' description = 'Cutadapt removes adapter sequences from high-throughput sequencing reads.\n' author = 'Toni Verbeiren' } diff --git a/target/nextflow/falco/.config.vsh.yaml b/target/nextflow/falco/.config.vsh.yaml index 729286b0..71b2d68f 100644 --- a/target/nextflow/falco/.config.vsh.yaml +++ b/target/nextflow/falco/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "falco" -version: "v0.2" +version: "0.2.0" authors: - name: "Toni Verbeiren" roles: @@ -287,7 +287,7 @@ engines: id: "docker" image: "debian:trixie-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -316,22 +316,22 @@ build_info: engine: "docker|native" output: "target/nextflow/falco" executable: "target/nextflow/falco/main.nf" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/falco/main.nf b/target/nextflow/falco/main.nf index d3a4203b..b0bdf8e2 100644 --- a/target/nextflow/falco/main.nf +++ b/target/nextflow/falco/main.nf @@ -1,8 +1,8 @@ -// falco v0.2 +// falco 0.2.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such @@ -1731,7 +1731,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1802,7 +1804,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1844,7 +1848,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2802,7 +2808,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "falco", - "version" : "v0.2", + "version" : "0.2.0", "authors" : [ { "name" : "Toni Verbeiren", @@ -3125,7 +3131,7 @@ meta = [ "id" : "docker", "image" : "debian:trixie-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.2", + "target_tag" : "0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3163,22 +3169,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/falco", - "viash_version" : "0.9.0-RC7", - "git_commit" : "f22ab0eab58dcd6bff89d8d73fe951953ff1260f", + "viash_version" : "0.9.0", + "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.2", + "version" : "0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.0-RC7", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.2'" + ".engines[.type == 'docker'].target_tag := '0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3343,7 +3349,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -3474,7 +3484,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -3482,8 +3493,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -3520,6 +3531,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -3531,10 +3543,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -3619,7 +3630,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/falco", - "tag" : "v0.2" + "tag" : "0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/falco/nextflow.config b/target/nextflow/falco/nextflow.config index 4b131f2a..9251d236 100644 --- a/target/nextflow/falco/nextflow.config +++ b/target/nextflow/falco/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'falco' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.2' + version = '0.2.0' description = 'A C++ drop-in replacement of FastQC to assess the quality of sequence read data' author = 'Toni Verbeiren' } diff --git a/target/nextflow/fastp/.config.vsh.yaml b/target/nextflow/fastp/.config.vsh.yaml index 9b91ebce..401926d6 100644 --- a/target/nextflow/fastp/.config.vsh.yaml +++ b/target/nextflow/fastp/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "fastp" -version: "v0.2" +version: "0.2.0" authors: - name: "Robrecht Cannoodt" roles: @@ -1066,7 +1066,7 @@ engines: id: "docker" image: "quay.io/biocontainers/fastp:0.23.4--hadf994f_2" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -1082,22 +1082,22 @@ build_info: engine: "docker|native" output: "target/nextflow/fastp" executable: "target/nextflow/fastp/main.nf" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/fastp/main.nf b/target/nextflow/fastp/main.nf index 828ce870..571d8b58 100644 --- a/target/nextflow/fastp/main.nf +++ b/target/nextflow/fastp/main.nf @@ -1,8 +1,8 @@ -// fastp v0.2 +// fastp 0.2.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such @@ -1731,7 +1731,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1802,7 +1804,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1844,7 +1848,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2802,7 +2808,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "fastp", - "version" : "v0.2", + "version" : "0.2.0", "authors" : [ { "name" : "Robrecht Cannoodt", @@ -3995,7 +4001,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/fastp:0.23.4--hadf994f_2", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.2", + "target_tag" : "0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -4016,22 +4022,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/fastp", - "viash_version" : "0.9.0-RC7", - "git_commit" : "f22ab0eab58dcd6bff89d8d73fe951953ff1260f", + "viash_version" : "0.9.0", + "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.2", + "version" : "0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.0-RC7", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.2'" + ".engines[.type == 'docker'].target_tag := '0.2.0'" ], "keywords" : [ "bioinformatics", @@ -4345,7 +4351,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -4476,7 +4486,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -4484,8 +4495,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -4522,6 +4533,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -4533,10 +4545,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -4621,7 +4632,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/fastp", - "tag" : "v0.2" + "tag" : "0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/fastp/nextflow.config b/target/nextflow/fastp/nextflow.config index 451714f0..3e1cb67e 100644 --- a/target/nextflow/fastp/nextflow.config +++ b/target/nextflow/fastp/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'fastp' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.2' + version = '0.2.0' description = 'An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...).\n\nFeatures:\n\n - comprehensive quality profiling for both before and after filtering data (quality curves, base contents, KMER, Q20/Q30, GC Ratio, duplication, adapter contents...)\n - filter out bad reads (too low quality, too short, or too many N...)\n - cut low quality bases for per read in its 5\' and 3\' by evaluating the mean quality from a sliding window (like Trimmomatic but faster).\n - trim all reads in front and tail\n - cut adapters. Adapter sequences can be automatically detected, which means you don\'t have to input the adapter sequences to trim them.\n - correct mismatched base pairs in overlapped regions of paired end reads, if one base is with high quality while the other is with ultra low quality\n - trim polyG in 3\' ends, which is commonly seen in NovaSeq/NextSeq data. Trim polyX in 3\' ends to remove unwanted polyX tailing (i.e. polyA tailing for mRNA-Seq data)\n - preprocess unique molecular identifier (UMI) enabled data, shift UMI to sequence name.\n - report JSON format result for further interpreting.\n - visualize quality control and filtering results on a single HTML page (like FASTQC but faster and more informative).\n - split the output to multiple files (0001.R1.gz, 0002.R1.gz...) to support parallel processing. Two modes can be used, limiting the total split file number, or limitting the lines of each split file.\n - support long reads (data from PacBio / Nanopore devices).\n - support reading from STDIN and writing to STDOUT\n - support interleaved input\n - support ultra-fast FASTQ-level deduplication\n' author = 'Robrecht Cannoodt' } diff --git a/target/nextflow/fastqc/.config.vsh.yaml b/target/nextflow/fastqc/.config.vsh.yaml index 3e9253c2..eae52449 100644 --- a/target/nextflow/fastqc/.config.vsh.yaml +++ b/target/nextflow/fastqc/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "fastqc" -version: "v0.2" +version: "0.2.0" authors: - name: "Theodoro Gasperin Terra Camargo" roles: @@ -323,7 +323,7 @@ engines: id: "docker" image: "biocontainers/fastqc:v0.11.9_cv8" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -339,22 +339,22 @@ build_info: engine: "docker|native" output: "target/nextflow/fastqc" executable: "target/nextflow/fastqc/main.nf" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/fastqc/main.nf b/target/nextflow/fastqc/main.nf index 5d69b70f..8949a8b2 100644 --- a/target/nextflow/fastqc/main.nf +++ b/target/nextflow/fastqc/main.nf @@ -1,8 +1,8 @@ -// fastqc v0.2 +// fastqc 0.2.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such @@ -1731,7 +1731,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1802,7 +1804,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1844,7 +1848,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2802,7 +2808,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "fastqc", - "version" : "v0.2", + "version" : "0.2.0", "authors" : [ { "name" : "Theodoro Gasperin Terra Camargo", @@ -3154,7 +3160,7 @@ meta = [ "id" : "docker", "image" : "biocontainers/fastqc:v0.11.9_cv8", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.2", + "target_tag" : "0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3175,22 +3181,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/fastqc", - "viash_version" : "0.9.0-RC7", - "git_commit" : "f22ab0eab58dcd6bff89d8d73fe951953ff1260f", + "viash_version" : "0.9.0", + "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.2", + "version" : "0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.0-RC7", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.2'" + ".engines[.type == 'docker'].target_tag := '0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3417,7 +3423,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -3548,7 +3558,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -3556,8 +3567,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -3594,6 +3605,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -3605,10 +3617,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -3693,7 +3704,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/fastqc", - "tag" : "v0.2" + "tag" : "0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/fastqc/nextflow.config b/target/nextflow/fastqc/nextflow.config index 146c3d6b..780f1235 100644 --- a/target/nextflow/fastqc/nextflow.config +++ b/target/nextflow/fastqc/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'fastqc' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.2' + version = '0.2.0' description = 'FastQC - A high throughput sequence QC analysis tool.' author = 'Theodoro Gasperin Terra Camargo' } diff --git a/target/nextflow/featurecounts/.config.vsh.yaml b/target/nextflow/featurecounts/.config.vsh.yaml index 158a3c74..79e96a83 100644 --- a/target/nextflow/featurecounts/.config.vsh.yaml +++ b/target/nextflow/featurecounts/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "featurecounts" -version: "v0.2" +version: "0.2.0" authors: - name: "Sai Nirmayi Yasa" roles: @@ -627,7 +627,7 @@ engines: id: "docker" image: "quay.io/biocontainers/subread:2.0.6--he4a0461_0" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -644,22 +644,22 @@ build_info: engine: "docker|native" output: "target/nextflow/featurecounts" executable: "target/nextflow/featurecounts/main.nf" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/featurecounts/main.nf b/target/nextflow/featurecounts/main.nf index 1a8ddc90..f39e7133 100644 --- a/target/nextflow/featurecounts/main.nf +++ b/target/nextflow/featurecounts/main.nf @@ -1,8 +1,8 @@ -// featurecounts v0.2 +// featurecounts 0.2.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such @@ -1731,7 +1731,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1802,7 +1804,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1844,7 +1848,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2802,7 +2808,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "featurecounts", - "version" : "v0.2", + "version" : "0.2.0", "authors" : [ { "name" : "Sai Nirmayi Yasa", @@ -3521,7 +3527,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/subread:2.0.6--he4a0461_0", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.2", + "target_tag" : "0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3542,22 +3548,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/featurecounts", - "viash_version" : "0.9.0-RC7", - "git_commit" : "f22ab0eab58dcd6bff89d8d73fe951953ff1260f", + "viash_version" : "0.9.0", + "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.2", + "version" : "0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.0-RC7", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.2'" + ".engines[.type == 'docker'].target_tag := '0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3828,7 +3834,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -3959,7 +3969,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -3967,8 +3978,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -4005,6 +4016,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -4016,10 +4028,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -4104,7 +4115,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/featurecounts", - "tag" : "v0.2" + "tag" : "0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/featurecounts/nextflow.config b/target/nextflow/featurecounts/nextflow.config index 055ec1df..346054a3 100644 --- a/target/nextflow/featurecounts/nextflow.config +++ b/target/nextflow/featurecounts/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'featurecounts' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.2' + version = '0.2.0' description = 'featureCounts is a read summarization program for counting reads generated from either RNA or genomic DNA sequencing experiments by implementing highly efficient chromosome hashing and feature blocking techniques. It works with either single or paired-end reads and provides a wide range of options appropriate for different sequencing applications.\n' author = 'Sai Nirmayi Yasa' } diff --git a/target/nextflow/gffread/.config.vsh.yaml b/target/nextflow/gffread/.config.vsh.yaml index c61daefb..8fdae94e 100644 --- a/target/nextflow/gffread/.config.vsh.yaml +++ b/target/nextflow/gffread/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "gffread" -version: "v0.2" +version: "0.2.0" authors: - name: "Emma Rousseau" roles: @@ -668,7 +668,7 @@ engines: id: "docker" image: "quay.io/biocontainers/gffread:0.12.7--hdcf5f25_3" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -684,22 +684,22 @@ build_info: engine: "docker|native" output: "target/nextflow/gffread" executable: "target/nextflow/gffread/main.nf" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/gffread/main.nf b/target/nextflow/gffread/main.nf index 05da776e..4fa0e80f 100644 --- a/target/nextflow/gffread/main.nf +++ b/target/nextflow/gffread/main.nf @@ -1,8 +1,8 @@ -// gffread v0.2 +// gffread 0.2.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such @@ -1731,7 +1731,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1802,7 +1804,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1844,7 +1848,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2802,7 +2808,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "gffread", - "version" : "v0.2", + "version" : "0.2.0", "authors" : [ { "name" : "Emma Rousseau", @@ -3578,7 +3584,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/gffread:0.12.7--hdcf5f25_3", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.2", + "target_tag" : "0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3599,22 +3605,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/gffread", - "viash_version" : "0.9.0-RC7", - "git_commit" : "f22ab0eab58dcd6bff89d8d73fe951953ff1260f", + "viash_version" : "0.9.0", + "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.2", + "version" : "0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.0-RC7", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.2'" + ".engines[.type == 'docker'].target_tag := '0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3931,7 +3937,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -4062,7 +4072,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -4070,8 +4081,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -4108,6 +4119,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -4119,10 +4131,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -4207,7 +4218,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/gffread", - "tag" : "v0.2" + "tag" : "0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/gffread/nextflow.config b/target/nextflow/gffread/nextflow.config index 556496a5..18606584 100644 --- a/target/nextflow/gffread/nextflow.config +++ b/target/nextflow/gffread/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'gffread' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.2' + version = '0.2.0' description = 'Validate, filter, convert and perform various other operations on GFF files.' author = 'Emma Rousseau' } diff --git a/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml b/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml index 7ee3e79e..e2d38a49 100644 --- a/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml +++ b/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "lofreq_call" namespace: "lofreq" -version: "v0.2" +version: "0.2.0" authors: - name: "Kai Waldrant" roles: @@ -489,7 +489,7 @@ engines: id: "docker" image: "quay.io/biocontainers/lofreq:2.1.5--py38h794fc9e_10" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -506,22 +506,22 @@ build_info: engine: "docker|native" output: "target/nextflow/lofreq/lofreq_call" executable: "target/nextflow/lofreq/lofreq_call/main.nf" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/lofreq/lofreq_call/main.nf b/target/nextflow/lofreq/lofreq_call/main.nf index a998efba..f35859df 100644 --- a/target/nextflow/lofreq/lofreq_call/main.nf +++ b/target/nextflow/lofreq/lofreq_call/main.nf @@ -1,8 +1,8 @@ -// lofreq_call v0.2 +// lofreq_call 0.2.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such @@ -1731,7 +1731,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1802,7 +1804,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1844,7 +1848,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2803,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "lofreq_call", "namespace" : "lofreq", - "version" : "v0.2", + "version" : "0.2.0", "authors" : [ { "name" : "Kai Waldrant", @@ -3386,7 +3392,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/lofreq:2.1.5--py38h794fc9e_10", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.2", + "target_tag" : "0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3407,22 +3413,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/lofreq/lofreq_call", - "viash_version" : "0.9.0-RC7", - "git_commit" : "f22ab0eab58dcd6bff89d8d73fe951953ff1260f", + "viash_version" : "0.9.0", + "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.2", + "version" : "0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.0-RC7", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.2'" + ".engines[.type == 'docker'].target_tag := '0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3647,7 +3653,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -3778,7 +3788,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -3786,8 +3797,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -3824,6 +3835,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -3835,10 +3847,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -3923,7 +3934,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/lofreq/lofreq_call", - "tag" : "v0.2" + "tag" : "0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/lofreq/lofreq_call/nextflow.config b/target/nextflow/lofreq/lofreq_call/nextflow.config index 8a6c0aa1..d424c8ec 100644 --- a/target/nextflow/lofreq/lofreq_call/nextflow.config +++ b/target/nextflow/lofreq/lofreq_call/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'lofreq/lofreq_call' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.2' + version = '0.2.0' description = 'Call variants from a BAM file.\n\nLoFreq* (i.e. LoFreq version 2) is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call qualities and other sources of errors inherent in sequencing (e.g. mapping or base/indel alignment uncertainty), which are usually ignored by other methods or only used for filtering.\n\nLoFreq* can run on almost any type of aligned sequencing data (e.g. Illumina, IonTorrent or Pacbio) since no machine- or sequencing-technology dependent thresholds are used. It automatically adapts to changes in coverage and sequencing quality and can therefore be applied to a variety of data-sets e.g. viral/quasispecies, bacterial, metagenomics or somatic data.\n\nLoFreq* is very sensitive; most notably, it is able to predict variants below the average base-call quality (i.e. sequencing error rate). Each variant call is assigned a p-value which allows for rigorous false positive control. Even though it uses no approximations or heuristics, it is very efficient due to several runtime optimizations and also provides a (pseudo-)parallel implementation. LoFreq* is generic and fast enough to be applied to high-coverage data and large genomes. On a single processor it takes a minute to analyze Dengue genome sequencing data with nearly 4000X coverage, roughly one hour to call SNVs on a 600X coverage E.coli genome and also roughly an hour to run on a 100X coverage human exome dataset.\n' author = 'Kai Waldrant' } diff --git a/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml b/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml index b3c04e9e..5a4f21b5 100644 --- a/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml +++ b/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "lofreq_indelqual" namespace: "lofreq" -version: "v0.2" +version: "0.2.0" authors: - name: "Kai Waldrant" roles: @@ -197,7 +197,7 @@ engines: id: "docker" image: "quay.io/biocontainers/lofreq:2.1.5--py38h794fc9e_10" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -214,22 +214,22 @@ build_info: engine: "docker|native" output: "target/nextflow/lofreq/lofreq_indelqual" executable: "target/nextflow/lofreq/lofreq_indelqual/main.nf" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/lofreq/lofreq_indelqual/main.nf b/target/nextflow/lofreq/lofreq_indelqual/main.nf index 96aff370..7c8bb8ce 100644 --- a/target/nextflow/lofreq/lofreq_indelqual/main.nf +++ b/target/nextflow/lofreq/lofreq_indelqual/main.nf @@ -1,8 +1,8 @@ -// lofreq_indelqual v0.2 +// lofreq_indelqual 0.2.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such @@ -1731,7 +1731,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1802,7 +1804,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1844,7 +1848,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2803,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "lofreq_indelqual", "namespace" : "lofreq", - "version" : "v0.2", + "version" : "0.2.0", "authors" : [ { "name" : "Kai Waldrant", @@ -3049,7 +3055,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/lofreq:2.1.5--py38h794fc9e_10", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.2", + "target_tag" : "0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3070,22 +3076,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/lofreq/lofreq_indelqual", - "viash_version" : "0.9.0-RC7", - "git_commit" : "f22ab0eab58dcd6bff89d8d73fe951953ff1260f", + "viash_version" : "0.9.0", + "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.2", + "version" : "0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.0-RC7", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.2'" + ".engines[.type == 'docker'].target_tag := '0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3234,7 +3240,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -3365,7 +3375,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -3373,8 +3384,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -3411,6 +3422,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -3422,10 +3434,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -3510,7 +3521,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/lofreq/lofreq_indelqual", - "tag" : "v0.2" + "tag" : "0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/lofreq/lofreq_indelqual/nextflow.config b/target/nextflow/lofreq/lofreq_indelqual/nextflow.config index 4a4c8206..4a81e6c2 100644 --- a/target/nextflow/lofreq/lofreq_indelqual/nextflow.config +++ b/target/nextflow/lofreq/lofreq_indelqual/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'lofreq/lofreq_indelqual' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.2' + version = '0.2.0' description = 'Insert indel qualities into BAM file (required for indel predictions).\n\nThe preferred way of inserting indel qualities should be via GATK\'s BQSR (>=2) If that\'s not possible, use this subcommand.\nThe command has two modes: \'uniform\' and \'dindel\':\n- \'uniform\' will assign a given value uniformly, whereas\n- \'dindel\' will insert indel qualities based on Dindel (PMID 20980555).\nBoth will overwrite any existing values.\nDo not realign your BAM file afterwards!\n' author = 'Kai Waldrant' } diff --git a/target/nextflow/multiqc/.config.vsh.yaml b/target/nextflow/multiqc/.config.vsh.yaml index 2d440791..245ef5c6 100644 --- a/target/nextflow/multiqc/.config.vsh.yaml +++ b/target/nextflow/multiqc/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "multiqc" -version: "v0.2" +version: "0.2.0" authors: - name: "Dorien Roosen" roles: @@ -433,7 +433,7 @@ engines: id: "docker" image: "quay.io/biocontainers/multiqc:1.21--pyhdfd78af_0" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -455,22 +455,22 @@ build_info: engine: "docker|native" output: "target/nextflow/multiqc" executable: "target/nextflow/multiqc/main.nf" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/multiqc/main.nf b/target/nextflow/multiqc/main.nf index 3233fd42..7e0282b5 100644 --- a/target/nextflow/multiqc/main.nf +++ b/target/nextflow/multiqc/main.nf @@ -1,8 +1,8 @@ -// multiqc v0.2 +// multiqc 0.2.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such @@ -1731,7 +1731,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1802,7 +1804,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1844,7 +1848,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2802,7 +2808,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "multiqc", - "version" : "v0.2", + "version" : "0.2.0", "authors" : [ { "name" : "Dorien Roosen", @@ -3329,7 +3335,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/multiqc:1.21--pyhdfd78af_0", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.2", + "target_tag" : "0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3359,22 +3365,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/multiqc", - "viash_version" : "0.9.0-RC7", - "git_commit" : "f22ab0eab58dcd6bff89d8d73fe951953ff1260f", + "viash_version" : "0.9.0", + "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.2", + "version" : "0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.0-RC7", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.2'" + ".engines[.type == 'docker'].target_tag := '0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3674,7 +3680,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -3805,7 +3815,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -3813,8 +3824,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -3851,6 +3862,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -3862,10 +3874,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -3950,7 +3961,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/multiqc", - "tag" : "v0.2" + "tag" : "0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/multiqc/nextflow.config b/target/nextflow/multiqc/nextflow.config index ac3218cf..2fe3a6a0 100644 --- a/target/nextflow/multiqc/nextflow.config +++ b/target/nextflow/multiqc/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'multiqc' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.2' + version = '0.2.0' description = 'MultiQC aggregates results from bioinformatics analyses across many samples into a single report.\nIt searches a given directory for analysis logs and compiles a HTML report. It\'s a general use tool, perfect for summarising the output from numerous bioinformatics tools.\n' author = 'Dorien Roosen' } diff --git a/target/nextflow/pear/.config.vsh.yaml b/target/nextflow/pear/.config.vsh.yaml index 67ca5271..a825f32e 100644 --- a/target/nextflow/pear/.config.vsh.yaml +++ b/target/nextflow/pear/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "pear" -version: "v0.2" +version: "0.2.0" authors: - name: "Kai Waldrant" roles: @@ -380,7 +380,7 @@ engines: id: "docker" image: "quay.io/biocontainers/pear:0.9.6--h9d449c0_10" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -397,22 +397,22 @@ build_info: engine: "docker|native" output: "target/nextflow/pear" executable: "target/nextflow/pear/main.nf" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/pear/main.nf b/target/nextflow/pear/main.nf index 0ec5329a..2b8ae602 100644 --- a/target/nextflow/pear/main.nf +++ b/target/nextflow/pear/main.nf @@ -1,8 +1,8 @@ -// pear v0.2 +// pear 0.2.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such @@ -1731,7 +1731,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1802,7 +1804,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1844,7 +1848,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2802,7 +2808,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "pear", - "version" : "v0.2", + "version" : "0.2.0", "authors" : [ { "name" : "Kai Waldrant", @@ -3231,7 +3237,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/pear:0.9.6--h9d449c0_10", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.2", + "target_tag" : "0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3252,22 +3258,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/pear", - "viash_version" : "0.9.0-RC7", - "git_commit" : "f22ab0eab58dcd6bff89d8d73fe951953ff1260f", + "viash_version" : "0.9.0", + "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.2", + "version" : "0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.0-RC7", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.2'" + ".engines[.type == 'docker'].target_tag := '0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3477,7 +3483,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -3608,7 +3618,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -3616,8 +3627,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -3654,6 +3665,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -3665,10 +3677,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -3753,7 +3764,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/pear", - "tag" : "v0.2" + "tag" : "0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/pear/nextflow.config b/target/nextflow/pear/nextflow.config index f78e6201..e4633bd2 100644 --- a/target/nextflow/pear/nextflow.config +++ b/target/nextflow/pear/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'pear' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.2' + version = '0.2.0' description = 'PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory.\n\nPEAR evaluates all possible paired-end read overlaps and without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results. Together with a highly optimized implementation, it can merge millions of paired end reads within a couple of minutes on a standard desktop computer.\n' author = 'Kai Waldrant' } diff --git a/target/nextflow/qualimap/qualimap_rnaseq/.config.vsh.yaml b/target/nextflow/qualimap/qualimap_rnaseq/.config.vsh.yaml index 326e584f..29bdd909 100644 --- a/target/nextflow/qualimap/qualimap_rnaseq/.config.vsh.yaml +++ b/target/nextflow/qualimap/qualimap_rnaseq/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "qualimap_rnaseq" namespace: "qualimap" -version: "v0.2" +version: "0.2.0" authors: - name: "Dorien Roosen" roles: @@ -247,7 +247,7 @@ engines: id: "docker" image: "quay.io/biocontainers/qualimap:2.3--hdfd78af_0" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -263,22 +263,22 @@ build_info: engine: "docker|native" output: "target/nextflow/qualimap/qualimap_rnaseq" executable: "target/nextflow/qualimap/qualimap_rnaseq/main.nf" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/qualimap/qualimap_rnaseq/main.nf b/target/nextflow/qualimap/qualimap_rnaseq/main.nf index 58cb6f0b..b2cb1e41 100644 --- a/target/nextflow/qualimap/qualimap_rnaseq/main.nf +++ b/target/nextflow/qualimap/qualimap_rnaseq/main.nf @@ -1,8 +1,8 @@ -// qualimap_rnaseq v0.2 +// qualimap_rnaseq 0.2.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such @@ -1731,7 +1731,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1802,7 +1804,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1844,7 +1848,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2803,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "qualimap_rnaseq", "namespace" : "qualimap", - "version" : "v0.2", + "version" : "0.2.0", "authors" : [ { "name" : "Dorien Roosen", @@ -3101,7 +3107,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/qualimap:2.3--hdfd78af_0", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.2", + "target_tag" : "0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3122,22 +3128,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/qualimap/qualimap_rnaseq", - "viash_version" : "0.9.0-RC7", - "git_commit" : "f22ab0eab58dcd6bff89d8d73fe951953ff1260f", + "viash_version" : "0.9.0", + "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.2", + "version" : "0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.0-RC7", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.2'" + ".engines[.type == 'docker'].target_tag := '0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3327,7 +3333,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -3458,7 +3468,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -3466,8 +3477,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -3504,6 +3515,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -3515,10 +3527,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -3603,7 +3614,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/qualimap/qualimap_rnaseq", - "tag" : "v0.2" + "tag" : "0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/qualimap/qualimap_rnaseq/nextflow.config b/target/nextflow/qualimap/qualimap_rnaseq/nextflow.config index ff01c7be..906a2486 100644 --- a/target/nextflow/qualimap/qualimap_rnaseq/nextflow.config +++ b/target/nextflow/qualimap/qualimap_rnaseq/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'qualimap/qualimap_rnaseq' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.2' + version = '0.2.0' description = 'Qualimap RNA-seq QC reports quality control metrics and bias estimations \nwhich are specific for whole transcriptome sequencing, including reads genomic \norigin, junction analysis, transcript coverage and 5’-3’ bias computation.\n' author = 'Dorien Roosen' } diff --git a/target/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml b/target/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml index 858cdccb..76883ee3 100644 --- a/target/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml +++ b/target/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "rsem_prepare_reference" namespace: "rsem" -version: "v0.2" +version: "0.2.0" authors: - name: "Sai Nirmayi Yasa" roles: @@ -352,7 +352,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -415,22 +415,22 @@ build_info: engine: "docker|native" output: "target/nextflow/rsem/rsem_prepare_reference" executable: "target/nextflow/rsem/rsem_prepare_reference/main.nf" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/rsem/rsem_prepare_reference/main.nf b/target/nextflow/rsem/rsem_prepare_reference/main.nf index f186ce74..3fd602ed 100644 --- a/target/nextflow/rsem/rsem_prepare_reference/main.nf +++ b/target/nextflow/rsem/rsem_prepare_reference/main.nf @@ -1,8 +1,8 @@ -// rsem_prepare_reference v0.2 +// rsem_prepare_reference 0.2.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such @@ -1731,7 +1731,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1802,7 +1804,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1844,7 +1848,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2803,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "rsem_prepare_reference", "namespace" : "rsem", - "version" : "v0.2", + "version" : "0.2.0", "authors" : [ { "name" : "Sai Nirmayi Yasa", @@ -3179,7 +3185,7 @@ meta = [ "id" : "docker", "image" : "ubuntu:22.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.2", + "target_tag" : "0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3238,22 +3244,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/rsem/rsem_prepare_reference", - "viash_version" : "0.9.0-RC7", - "git_commit" : "f22ab0eab58dcd6bff89d8d73fe951953ff1260f", + "viash_version" : "0.9.0", + "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.2", + "version" : "0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.0-RC7", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.2'" + ".engines[.type == 'docker'].target_tag := '0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3444,7 +3450,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -3575,7 +3585,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -3583,8 +3594,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -3621,6 +3632,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -3632,10 +3644,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -3720,7 +3731,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/rsem/rsem_prepare_reference", - "tag" : "v0.2" + "tag" : "0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/rsem/rsem_prepare_reference/nextflow.config b/target/nextflow/rsem/rsem_prepare_reference/nextflow.config index 1a40bbac..02146110 100644 --- a/target/nextflow/rsem/rsem_prepare_reference/nextflow.config +++ b/target/nextflow/rsem/rsem_prepare_reference/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'rsem/rsem_prepare_reference' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.2' + version = '0.2.0' description = 'RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. This component prepares transcript references for RSEM.\n' author = 'Sai Nirmayi Yasa' } diff --git a/target/nextflow/salmon/salmon_index/.config.vsh.yaml b/target/nextflow/salmon/salmon_index/.config.vsh.yaml index 87dc34d3..f4b3e353 100644 --- a/target/nextflow/salmon/salmon_index/.config.vsh.yaml +++ b/target/nextflow/salmon/salmon_index/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "salmon_index" namespace: "salmon" -version: "v0.2" +version: "0.2.0" authors: - name: "Sai Nirmayi Yasa" roles: @@ -260,7 +260,7 @@ engines: id: "docker" image: "quay.io/biocontainers/salmon:1.10.2--hecfa306_0" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -276,22 +276,22 @@ build_info: engine: "docker|native" output: "target/nextflow/salmon/salmon_index" executable: "target/nextflow/salmon/salmon_index/main.nf" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/salmon/salmon_index/main.nf b/target/nextflow/salmon/salmon_index/main.nf index 177977e2..6633d73b 100644 --- a/target/nextflow/salmon/salmon_index/main.nf +++ b/target/nextflow/salmon/salmon_index/main.nf @@ -1,8 +1,8 @@ -// salmon_index v0.2 +// salmon_index 0.2.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such @@ -1731,7 +1731,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1802,7 +1804,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1844,7 +1848,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2803,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "salmon_index", "namespace" : "salmon", - "version" : "v0.2", + "version" : "0.2.0", "authors" : [ { "name" : "Sai Nirmayi Yasa", @@ -3101,7 +3107,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/salmon:1.10.2--hecfa306_0", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.2", + "target_tag" : "0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3122,22 +3128,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/salmon/salmon_index", - "viash_version" : "0.9.0-RC7", - "git_commit" : "f22ab0eab58dcd6bff89d8d73fe951953ff1260f", + "viash_version" : "0.9.0", + "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.2", + "version" : "0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.0-RC7", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.2'" + ".engines[.type == 'docker'].target_tag := '0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3332,7 +3338,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -3463,7 +3473,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -3471,8 +3482,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -3509,6 +3520,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -3520,10 +3532,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -3608,7 +3619,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/salmon/salmon_index", - "tag" : "v0.2" + "tag" : "0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/salmon/salmon_index/nextflow.config b/target/nextflow/salmon/salmon_index/nextflow.config index 7de93132..d036a17d 100644 --- a/target/nextflow/salmon/salmon_index/nextflow.config +++ b/target/nextflow/salmon/salmon_index/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'salmon/salmon_index' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.2' + version = '0.2.0' 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. This component creates a salmon index for the transcriptome to use Salmon in the mapping-based mode. It is generally recommend that you build a decoy-aware transcriptome file. This is done using the entire genome of the organism as the decoy sequence by concatenating the genome to the end of the transcriptome to be indexed and populating the decoys.txt file with the chromosome names.\n' author = 'Sai Nirmayi Yasa' } diff --git a/target/nextflow/salmon/salmon_quant/.config.vsh.yaml b/target/nextflow/salmon/salmon_quant/.config.vsh.yaml index 1839f6a0..2e84d6c5 100644 --- a/target/nextflow/salmon/salmon_quant/.config.vsh.yaml +++ b/target/nextflow/salmon/salmon_quant/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "salmon_quant" namespace: "salmon" -version: "v0.2" +version: "0.2.0" authors: - name: "Sai Nirmayi Yasa" roles: @@ -1156,7 +1156,7 @@ engines: id: "docker" image: "quay.io/biocontainers/salmon:1.10.2--hecfa306_0" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -1172,22 +1172,22 @@ build_info: engine: "docker|native" output: "target/nextflow/salmon/salmon_quant" executable: "target/nextflow/salmon/salmon_quant/main.nf" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/salmon/salmon_quant/main.nf b/target/nextflow/salmon/salmon_quant/main.nf index a9a8e46c..4c415267 100644 --- a/target/nextflow/salmon/salmon_quant/main.nf +++ b/target/nextflow/salmon/salmon_quant/main.nf @@ -1,8 +1,8 @@ -// salmon_quant v0.2 +// salmon_quant 0.2.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such @@ -1731,7 +1731,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1802,7 +1804,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1844,7 +1848,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2803,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "salmon_quant", "namespace" : "salmon", - "version" : "v0.2", + "version" : "0.2.0", "authors" : [ { "name" : "Sai Nirmayi Yasa", @@ -3936,7 +3942,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/salmon:1.10.2--hecfa306_0", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.2", + "target_tag" : "0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3957,22 +3963,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/salmon/salmon_quant", - "viash_version" : "0.9.0-RC7", - "git_commit" : "f22ab0eab58dcd6bff89d8d73fe951953ff1260f", + "viash_version" : "0.9.0", + "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.2", + "version" : "0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.0-RC7", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.2'" + ".engines[.type == 'docker'].target_tag := '0.2.0'" ], "keywords" : [ "bioinformatics", @@ -4347,7 +4353,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -4478,7 +4488,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -4486,8 +4497,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -4524,6 +4535,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -4535,10 +4547,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -4623,7 +4634,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/salmon/salmon_quant", - "tag" : "v0.2" + "tag" : "0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/salmon/salmon_quant/nextflow.config b/target/nextflow/salmon/salmon_quant/nextflow.config index 31f73b40..34252791 100644 --- a/target/nextflow/salmon/salmon_quant/nextflow.config +++ b/target/nextflow/salmon/salmon_quant/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'salmon/salmon_quant' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.2' + version = '0.2.0' 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' author = 'Sai Nirmayi Yasa' } diff --git a/target/nextflow/samtools/samtools_collate/.config.vsh.yaml b/target/nextflow/samtools/samtools_collate/.config.vsh.yaml index f7324a76..8907edb3 100644 --- a/target/nextflow/samtools/samtools_collate/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_collate/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "samtools_collate" namespace: "samtools" -version: "v0.2" +version: "0.2.0" authors: - name: "Emma Rousseau" roles: @@ -246,7 +246,7 @@ engines: id: "docker" image: "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -263,22 +263,22 @@ build_info: engine: "docker|native" output: "target/nextflow/samtools/samtools_collate" executable: "target/nextflow/samtools/samtools_collate/main.nf" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/samtools/samtools_collate/main.nf b/target/nextflow/samtools/samtools_collate/main.nf index ccd4f389..60b6acd3 100644 --- a/target/nextflow/samtools/samtools_collate/main.nf +++ b/target/nextflow/samtools/samtools_collate/main.nf @@ -1,8 +1,8 @@ -// samtools_collate v0.2 +// samtools_collate 0.2.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such @@ -1731,7 +1731,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1802,7 +1804,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1844,7 +1848,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2803,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "samtools_collate", "namespace" : "samtools", - "version" : "v0.2", + "version" : "0.2.0", "authors" : [ { "name" : "Emma Rousseau", @@ -3112,7 +3118,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.2", + "target_tag" : "0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3133,22 +3139,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_collate", - "viash_version" : "0.9.0-RC7", - "git_commit" : "f22ab0eab58dcd6bff89d8d73fe951953ff1260f", + "viash_version" : "0.9.0", + "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.2", + "version" : "0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.0-RC7", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.2'" + ".engines[.type == 'docker'].target_tag := '0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3314,7 +3320,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -3445,7 +3455,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -3453,8 +3464,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -3491,6 +3502,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -3502,10 +3514,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -3590,7 +3601,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/samtools/samtools_collate", - "tag" : "v0.2" + "tag" : "0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/samtools/samtools_collate/nextflow.config b/target/nextflow/samtools/samtools_collate/nextflow.config index cc61016a..29f6c620 100644 --- a/target/nextflow/samtools/samtools_collate/nextflow.config +++ b/target/nextflow/samtools/samtools_collate/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'samtools/samtools_collate' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.2' + version = '0.2.0' description = 'Shuffles and groups reads in SAM/BAM/CRAM files together by their names.' author = 'Emma Rousseau' } diff --git a/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml b/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml index d6b710a8..721d15f3 100644 --- a/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "samtools_faidx" namespace: "samtools" -version: "v0.2" +version: "0.2.0" authors: - name: "Emma Rousseau" roles: @@ -225,7 +225,7 @@ engines: id: "docker" image: "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -242,22 +242,22 @@ build_info: engine: "docker|native" output: "target/nextflow/samtools/samtools_faidx" executable: "target/nextflow/samtools/samtools_faidx/main.nf" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/samtools/samtools_faidx/main.nf b/target/nextflow/samtools/samtools_faidx/main.nf index 34f3fd1f..201839f3 100644 --- a/target/nextflow/samtools/samtools_faidx/main.nf +++ b/target/nextflow/samtools/samtools_faidx/main.nf @@ -1,8 +1,8 @@ -// samtools_faidx v0.2 +// samtools_faidx 0.2.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such @@ -1731,7 +1731,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1802,7 +1804,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1844,7 +1848,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2803,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "samtools_faidx", "namespace" : "samtools", - "version" : "v0.2", + "version" : "0.2.0", "authors" : [ { "name" : "Emma Rousseau", @@ -3084,7 +3090,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.2", + "target_tag" : "0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3105,22 +3111,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_faidx", - "viash_version" : "0.9.0-RC7", - "git_commit" : "f22ab0eab58dcd6bff89d8d73fe951953ff1260f", + "viash_version" : "0.9.0", + "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.2", + "version" : "0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.0-RC7", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.2'" + ".engines[.type == 'docker'].target_tag := '0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3280,7 +3286,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -3411,7 +3421,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -3419,8 +3430,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -3457,6 +3468,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -3468,10 +3480,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -3556,7 +3567,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/samtools/samtools_faidx", - "tag" : "v0.2" + "tag" : "0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/samtools/samtools_faidx/nextflow.config b/target/nextflow/samtools/samtools_faidx/nextflow.config index 73492a58..5955ef93 100644 --- a/target/nextflow/samtools/samtools_faidx/nextflow.config +++ b/target/nextflow/samtools/samtools_faidx/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'samtools/samtools_faidx' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.2' + version = '0.2.0' description = 'Indexes FASTA files to enable random access to fasta and fastq files.' author = 'Emma Rousseau' } diff --git a/target/nextflow/samtools/samtools_fasta/.config.vsh.yaml b/target/nextflow/samtools/samtools_fasta/.config.vsh.yaml index 988e42fe..5f15bdda 100644 --- a/target/nextflow/samtools/samtools_fasta/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_fasta/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "samtools_fasta" namespace: "samtools" -version: "v0.2" +version: "0.2.0" authors: - name: "Emma Rousseau" roles: @@ -415,7 +415,7 @@ engines: id: "docker" image: "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -432,22 +432,22 @@ build_info: engine: "docker|native" output: "target/nextflow/samtools/samtools_fasta" executable: "target/nextflow/samtools/samtools_fasta/main.nf" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/samtools/samtools_fasta/main.nf b/target/nextflow/samtools/samtools_fasta/main.nf index 768c37fe..10bba4d7 100644 --- a/target/nextflow/samtools/samtools_fasta/main.nf +++ b/target/nextflow/samtools/samtools_fasta/main.nf @@ -1,8 +1,8 @@ -// samtools_fasta v0.2 +// samtools_fasta 0.2.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such @@ -1731,7 +1731,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1802,7 +1804,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1844,7 +1848,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2803,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "samtools_fasta", "namespace" : "samtools", - "version" : "v0.2", + "version" : "0.2.0", "authors" : [ { "name" : "Emma Rousseau", @@ -3276,7 +3282,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.2", + "target_tag" : "0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3297,22 +3303,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_fasta", - "viash_version" : "0.9.0-RC7", - "git_commit" : "f22ab0eab58dcd6bff89d8d73fe951953ff1260f", + "viash_version" : "0.9.0", + "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.2", + "version" : "0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.0-RC7", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.2'" + ".engines[.type == 'docker'].target_tag := '0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3516,7 +3522,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -3647,7 +3657,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -3655,8 +3666,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -3693,6 +3704,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -3704,10 +3716,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -3792,7 +3803,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/samtools/samtools_fasta", - "tag" : "v0.2" + "tag" : "0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/samtools/samtools_fasta/nextflow.config b/target/nextflow/samtools/samtools_fasta/nextflow.config index 95895b7c..1d278ef7 100644 --- a/target/nextflow/samtools/samtools_fasta/nextflow.config +++ b/target/nextflow/samtools/samtools_fasta/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'samtools/samtools_fasta' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.2' + version = '0.2.0' description = 'Converts a SAM, BAM or CRAM to FASTA format.' author = 'Emma Rousseau' } diff --git a/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml b/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml index 89312f62..ba2532e3 100644 --- a/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "samtools_fastq" namespace: "samtools" -version: "v0.2" +version: "0.2.0" authors: - name: "Emma Rousseau" roles: @@ -415,7 +415,7 @@ engines: id: "docker" image: "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -432,22 +432,22 @@ build_info: engine: "docker|native" output: "target/nextflow/samtools/samtools_fastq" executable: "target/nextflow/samtools/samtools_fastq/main.nf" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/samtools/samtools_fastq/main.nf b/target/nextflow/samtools/samtools_fastq/main.nf index 853f1991..fd4314fe 100644 --- a/target/nextflow/samtools/samtools_fastq/main.nf +++ b/target/nextflow/samtools/samtools_fastq/main.nf @@ -1,8 +1,8 @@ -// samtools_fastq v0.2 +// samtools_fastq 0.2.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such @@ -1731,7 +1731,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1802,7 +1804,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1844,7 +1848,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2803,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "samtools_fastq", "namespace" : "samtools", - "version" : "v0.2", + "version" : "0.2.0", "authors" : [ { "name" : "Emma Rousseau", @@ -3276,7 +3282,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.2", + "target_tag" : "0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3297,22 +3303,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_fastq", - "viash_version" : "0.9.0-RC7", - "git_commit" : "f22ab0eab58dcd6bff89d8d73fe951953ff1260f", + "viash_version" : "0.9.0", + "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.2", + "version" : "0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.0-RC7", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.2'" + ".engines[.type == 'docker'].target_tag := '0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3516,7 +3522,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -3647,7 +3657,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -3655,8 +3666,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -3693,6 +3704,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -3704,10 +3716,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -3792,7 +3803,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/samtools/samtools_fastq", - "tag" : "v0.2" + "tag" : "0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/samtools/samtools_fastq/nextflow.config b/target/nextflow/samtools/samtools_fastq/nextflow.config index 36280170..9fff574e 100644 --- a/target/nextflow/samtools/samtools_fastq/nextflow.config +++ b/target/nextflow/samtools/samtools_fastq/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'samtools/samtools_fastq' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.2' + version = '0.2.0' description = 'Converts a SAM, BAM or CRAM to FASTQ format.' author = 'Emma Rousseau' } diff --git a/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml b/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml index 01e86e57..85c50eac 100644 --- a/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "samtools_flagstat" namespace: "samtools" -version: "v0.2" +version: "0.2.0" authors: - name: "Emma Rousseau" roles: @@ -155,7 +155,7 @@ engines: id: "docker" image: "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -172,22 +172,22 @@ build_info: engine: "docker|native" output: "target/nextflow/samtools/samtools_flagstat" executable: "target/nextflow/samtools/samtools_flagstat/main.nf" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/samtools/samtools_flagstat/main.nf b/target/nextflow/samtools/samtools_flagstat/main.nf index 18ee4ad6..4e8d8e99 100644 --- a/target/nextflow/samtools/samtools_flagstat/main.nf +++ b/target/nextflow/samtools/samtools_flagstat/main.nf @@ -1,8 +1,8 @@ -// samtools_flagstat v0.2 +// samtools_flagstat 0.2.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such @@ -1731,7 +1731,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1802,7 +1804,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1844,7 +1848,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2803,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "samtools_flagstat", "namespace" : "samtools", - "version" : "v0.2", + "version" : "0.2.0", "authors" : [ { "name" : "Emma Rousseau", @@ -3000,7 +3006,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.2", + "target_tag" : "0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3021,22 +3027,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_flagstat", - "viash_version" : "0.9.0-RC7", - "git_commit" : "f22ab0eab58dcd6bff89d8d73fe951953ff1260f", + "viash_version" : "0.9.0", + "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.2", + "version" : "0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.0-RC7", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.2'" + ".engines[.type == 'docker'].target_tag := '0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3176,7 +3182,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -3307,7 +3317,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -3315,8 +3326,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -3353,6 +3364,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -3364,10 +3376,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -3452,7 +3463,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/samtools/samtools_flagstat", - "tag" : "v0.2" + "tag" : "0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/samtools/samtools_flagstat/nextflow.config b/target/nextflow/samtools/samtools_flagstat/nextflow.config index 4799619e..17007f7c 100644 --- a/target/nextflow/samtools/samtools_flagstat/nextflow.config +++ b/target/nextflow/samtools/samtools_flagstat/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'samtools/samtools_flagstat' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.2' + version = '0.2.0' description = 'Counts the number of alignments in SAM/BAM/CRAM files for each FLAG type.' author = 'Emma Rousseau' } diff --git a/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml b/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml index 918c14f3..48743292 100644 --- a/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "samtools_idxstats" namespace: "samtools" -version: "v0.2" +version: "0.2.0" authors: - name: "Emma Rousseau" roles: @@ -165,7 +165,7 @@ engines: id: "docker" image: "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -182,22 +182,22 @@ build_info: engine: "docker|native" output: "target/nextflow/samtools/samtools_idxstats" executable: "target/nextflow/samtools/samtools_idxstats/main.nf" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/samtools/samtools_idxstats/main.nf b/target/nextflow/samtools/samtools_idxstats/main.nf index a7c9ae12..15ce9495 100644 --- a/target/nextflow/samtools/samtools_idxstats/main.nf +++ b/target/nextflow/samtools/samtools_idxstats/main.nf @@ -1,8 +1,8 @@ -// samtools_idxstats v0.2 +// samtools_idxstats 0.2.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such @@ -1731,7 +1731,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1802,7 +1804,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1844,7 +1848,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2803,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "samtools_idxstats", "namespace" : "samtools", - "version" : "v0.2", + "version" : "0.2.0", "authors" : [ { "name" : "Emma Rousseau", @@ -3012,7 +3018,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.2", + "target_tag" : "0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3033,22 +3039,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_idxstats", - "viash_version" : "0.9.0-RC7", - "git_commit" : "f22ab0eab58dcd6bff89d8d73fe951953ff1260f", + "viash_version" : "0.9.0", + "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.2", + "version" : "0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.0-RC7", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.2'" + ".engines[.type == 'docker'].target_tag := '0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3186,7 +3192,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -3317,7 +3327,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -3325,8 +3336,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -3363,6 +3374,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -3374,10 +3386,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -3462,7 +3473,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/samtools/samtools_idxstats", - "tag" : "v0.2" + "tag" : "0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/samtools/samtools_idxstats/nextflow.config b/target/nextflow/samtools/samtools_idxstats/nextflow.config index b0c480a4..c53aaa5d 100644 --- a/target/nextflow/samtools/samtools_idxstats/nextflow.config +++ b/target/nextflow/samtools/samtools_idxstats/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'samtools/samtools_idxstats' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.2' + version = '0.2.0' description = 'Reports alignment summary statistics for a BAM file.' author = 'Emma Rousseau' } diff --git a/target/nextflow/samtools/samtools_index/.config.vsh.yaml b/target/nextflow/samtools/samtools_index/.config.vsh.yaml index 6d7eb220..36e112f3 100644 --- a/target/nextflow/samtools/samtools_index/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_index/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "samtools_index" namespace: "samtools" -version: "v0.2" +version: "0.2.0" authors: - name: "Emma Rousseau" roles: @@ -171,7 +171,7 @@ engines: id: "docker" image: "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -188,22 +188,22 @@ build_info: engine: "docker|native" output: "target/nextflow/samtools/samtools_index" executable: "target/nextflow/samtools/samtools_index/main.nf" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/samtools/samtools_index/main.nf b/target/nextflow/samtools/samtools_index/main.nf index a6d94d28..d8b6b241 100644 --- a/target/nextflow/samtools/samtools_index/main.nf +++ b/target/nextflow/samtools/samtools_index/main.nf @@ -1,8 +1,8 @@ -// samtools_index v0.2 +// samtools_index 0.2.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such @@ -1731,7 +1731,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1802,7 +1804,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1844,7 +1848,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2803,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "samtools_index", "namespace" : "samtools", - "version" : "v0.2", + "version" : "0.2.0", "authors" : [ { "name" : "Emma Rousseau", @@ -3025,7 +3031,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.2", + "target_tag" : "0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3046,22 +3052,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_index", - "viash_version" : "0.9.0-RC7", - "git_commit" : "f22ab0eab58dcd6bff89d8d73fe951953ff1260f", + "viash_version" : "0.9.0", + "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.2", + "version" : "0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.0-RC7", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.2'" + ".engines[.type == 'docker'].target_tag := '0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3210,7 +3216,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -3341,7 +3351,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -3349,8 +3360,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -3387,6 +3398,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -3398,10 +3410,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -3486,7 +3497,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/samtools/samtools_index", - "tag" : "v0.2" + "tag" : "0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/samtools/samtools_index/nextflow.config b/target/nextflow/samtools/samtools_index/nextflow.config index 862c7aea..0ce06ea1 100644 --- a/target/nextflow/samtools/samtools_index/nextflow.config +++ b/target/nextflow/samtools/samtools_index/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'samtools/samtools_index' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.2' + version = '0.2.0' description = 'Index SAM/BAM/CRAM files.' author = 'Emma Rousseau' } diff --git a/target/nextflow/samtools/samtools_sort/.config.vsh.yaml b/target/nextflow/samtools/samtools_sort/.config.vsh.yaml index f372951b..a37efeb4 100644 --- a/target/nextflow/samtools/samtools_sort/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_sort/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "samtools_sort" namespace: "samtools" -version: "v0.2" +version: "0.2.0" authors: - name: "Emma Rousseau" roles: @@ -314,7 +314,7 @@ engines: id: "docker" image: "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -331,22 +331,22 @@ build_info: engine: "docker|native" output: "target/nextflow/samtools/samtools_sort" executable: "target/nextflow/samtools/samtools_sort/main.nf" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/samtools/samtools_sort/main.nf b/target/nextflow/samtools/samtools_sort/main.nf index a7562cbd..7525e025 100644 --- a/target/nextflow/samtools/samtools_sort/main.nf +++ b/target/nextflow/samtools/samtools_sort/main.nf @@ -1,8 +1,8 @@ -// samtools_sort v0.2 +// samtools_sort 0.2.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such @@ -1731,7 +1731,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1802,7 +1804,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1844,7 +1848,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2803,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "samtools_sort", "namespace" : "samtools", - "version" : "v0.2", + "version" : "0.2.0", "authors" : [ { "name" : "Emma Rousseau", @@ -3197,7 +3203,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.2", + "target_tag" : "0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3218,22 +3224,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_sort", - "viash_version" : "0.9.0-RC7", - "git_commit" : "f22ab0eab58dcd6bff89d8d73fe951953ff1260f", + "viash_version" : "0.9.0", + "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.2", + "version" : "0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.0-RC7", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.2'" + ".engines[.type == 'docker'].target_tag := '0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3430,7 +3436,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -3561,7 +3571,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -3569,8 +3580,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -3607,6 +3618,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -3618,10 +3630,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -3706,7 +3717,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/samtools/samtools_sort", - "tag" : "v0.2" + "tag" : "0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/samtools/samtools_sort/nextflow.config b/target/nextflow/samtools/samtools_sort/nextflow.config index 60bd4dbc..ea64c8c9 100644 --- a/target/nextflow/samtools/samtools_sort/nextflow.config +++ b/target/nextflow/samtools/samtools_sort/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'samtools/samtools_sort' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.2' + version = '0.2.0' description = 'Sort SAM/BAM/CRAM file.' author = 'Emma Rousseau' } diff --git a/target/nextflow/samtools/samtools_stats/.config.vsh.yaml b/target/nextflow/samtools/samtools_stats/.config.vsh.yaml index 782fb790..ee7dd489 100644 --- a/target/nextflow/samtools/samtools_stats/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_stats/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "samtools_stats" namespace: "samtools" -version: "v0.2" +version: "0.2.0" authors: - name: "Emma Rousseau" roles: @@ -383,7 +383,7 @@ engines: id: "docker" image: "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -400,22 +400,22 @@ build_info: engine: "docker|native" output: "target/nextflow/samtools/samtools_stats" executable: "target/nextflow/samtools/samtools_stats/main.nf" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/samtools/samtools_stats/main.nf b/target/nextflow/samtools/samtools_stats/main.nf index d1a21470..1f8595f4 100644 --- a/target/nextflow/samtools/samtools_stats/main.nf +++ b/target/nextflow/samtools/samtools_stats/main.nf @@ -1,8 +1,8 @@ -// samtools_stats v0.2 +// samtools_stats 0.2.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such @@ -1731,7 +1731,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1802,7 +1804,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1844,7 +1848,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2803,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "samtools_stats", "namespace" : "samtools", - "version" : "v0.2", + "version" : "0.2.0", "authors" : [ { "name" : "Emma Rousseau", @@ -3267,7 +3273,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.2", + "target_tag" : "0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3288,22 +3294,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_stats", - "viash_version" : "0.9.0-RC7", - "git_commit" : "f22ab0eab58dcd6bff89d8d73fe951953ff1260f", + "viash_version" : "0.9.0", + "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.2", + "version" : "0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.0-RC7", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.2'" + ".engines[.type == 'docker'].target_tag := '0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3492,7 +3498,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -3623,7 +3633,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -3631,8 +3642,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -3669,6 +3680,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -3680,10 +3692,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -3768,7 +3779,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/samtools/samtools_stats", - "tag" : "v0.2" + "tag" : "0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/samtools/samtools_stats/nextflow.config b/target/nextflow/samtools/samtools_stats/nextflow.config index d658458e..8b99052a 100644 --- a/target/nextflow/samtools/samtools_stats/nextflow.config +++ b/target/nextflow/samtools/samtools_stats/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'samtools/samtools_stats' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.2' + version = '0.2.0' description = 'Reports alignment summary statistics for a BAM file.' author = 'Emma Rousseau' } diff --git a/target/nextflow/samtools/samtools_view/.config.vsh.yaml b/target/nextflow/samtools/samtools_view/.config.vsh.yaml index 37b7925e..0c2c0ad4 100644 --- a/target/nextflow/samtools/samtools_view/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_view/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "samtools_view" namespace: "samtools" -version: "v0.2" +version: "0.2.0" authors: - name: "Emma Rousseau" roles: @@ -647,7 +647,7 @@ engines: id: "docker" image: "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -664,22 +664,22 @@ build_info: engine: "docker|native" output: "target/nextflow/samtools/samtools_view" executable: "target/nextflow/samtools/samtools_view/main.nf" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/samtools/samtools_view/main.nf b/target/nextflow/samtools/samtools_view/main.nf index b3997501..db7caab5 100644 --- a/target/nextflow/samtools/samtools_view/main.nf +++ b/target/nextflow/samtools/samtools_view/main.nf @@ -1,8 +1,8 @@ -// samtools_view v0.2 +// samtools_view 0.2.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such @@ -1731,7 +1731,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1802,7 +1804,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1844,7 +1848,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2803,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "samtools_view", "namespace" : "samtools", - "version" : "v0.2", + "version" : "0.2.0", "authors" : [ { "name" : "Emma Rousseau", @@ -3448,7 +3454,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.2", + "target_tag" : "0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3469,22 +3475,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_view", - "viash_version" : "0.9.0-RC7", - "git_commit" : "f22ab0eab58dcd6bff89d8d73fe951953ff1260f", + "viash_version" : "0.9.0", + "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.2", + "version" : "0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.0-RC7", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.2'" + ".engines[.type == 'docker'].target_tag := '0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3734,7 +3740,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -3865,7 +3875,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -3873,8 +3884,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -3911,6 +3922,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -3922,10 +3934,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -4010,7 +4021,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/samtools/samtools_view", - "tag" : "v0.2" + "tag" : "0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/samtools/samtools_view/nextflow.config b/target/nextflow/samtools/samtools_view/nextflow.config index bfa815ad..d8931428 100644 --- a/target/nextflow/samtools/samtools_view/nextflow.config +++ b/target/nextflow/samtools/samtools_view/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'samtools/samtools_view' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.2' + version = '0.2.0' description = 'Views and converts SAM/BAM/CRAM files.' author = 'Emma Rousseau' } diff --git a/target/nextflow/seqtk/seqtk_sample/.config.vsh.yaml b/target/nextflow/seqtk/seqtk_sample/.config.vsh.yaml index ae2be056..6cf7ed30 100644 --- a/target/nextflow/seqtk/seqtk_sample/.config.vsh.yaml +++ b/target/nextflow/seqtk/seqtk_sample/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "seqtk_sample" namespace: "seqtk" -version: "v0.2" +version: "0.2.0" authors: - name: "Jakub Majercik" roles: @@ -160,7 +160,7 @@ engines: id: "docker" image: "quay.io/biocontainers/seqtk:1.4--he4a0461_2" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" entrypoint: [] cmd: null @@ -172,22 +172,22 @@ build_info: engine: "docker|native" output: "target/nextflow/seqtk/seqtk_sample" executable: "target/nextflow/seqtk/seqtk_sample/main.nf" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/seqtk/seqtk_sample/main.nf b/target/nextflow/seqtk/seqtk_sample/main.nf index dbc084ad..2170955f 100644 --- a/target/nextflow/seqtk/seqtk_sample/main.nf +++ b/target/nextflow/seqtk/seqtk_sample/main.nf @@ -1,8 +1,8 @@ -// seqtk_sample v0.2 +// seqtk_sample 0.2.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such @@ -1731,7 +1731,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1802,7 +1804,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1844,7 +1848,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2803,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "seqtk_sample", "namespace" : "seqtk", - "version" : "v0.2", + "version" : "0.2.0", "authors" : [ { "name" : "Jakub Majercik", @@ -3010,7 +3016,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/seqtk:1.4--he4a0461_2", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.2", + "target_tag" : "0.2.0", "namespace_separator" : "/" }, { @@ -3023,22 +3029,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/seqtk/seqtk_sample", - "viash_version" : "0.9.0-RC7", - "git_commit" : "f22ab0eab58dcd6bff89d8d73fe951953ff1260f", + "viash_version" : "0.9.0", + "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.2", + "version" : "0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.0-RC7", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.2'" + ".engines[.type == 'docker'].target_tag := '0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3180,7 +3186,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -3311,7 +3321,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -3319,8 +3330,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -3357,6 +3368,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -3368,10 +3380,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -3456,7 +3467,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/seqtk/seqtk_sample", - "tag" : "v0.2" + "tag" : "0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/seqtk/seqtk_sample/nextflow.config b/target/nextflow/seqtk/seqtk_sample/nextflow.config index b81fb900..abd614f8 100644 --- a/target/nextflow/seqtk/seqtk_sample/nextflow.config +++ b/target/nextflow/seqtk/seqtk_sample/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'seqtk/seqtk_sample' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.2' + version = '0.2.0' description = 'Subsamples sequences from FASTA/Q files.' author = 'Jakub Majercik' } diff --git a/target/nextflow/seqtk/seqtk_subseq/.config.vsh.yaml b/target/nextflow/seqtk/seqtk_subseq/.config.vsh.yaml index 5b8755a2..115571b9 100644 --- a/target/nextflow/seqtk/seqtk_subseq/.config.vsh.yaml +++ b/target/nextflow/seqtk/seqtk_subseq/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "seqtk_subseq" namespace: "seqtk" -version: "v0.2" +version: "0.2.0" authors: - name: "Theodoro Gasperin Terra Camargo" roles: @@ -179,7 +179,7 @@ engines: id: "docker" image: "quay.io/biocontainers/seqtk:1.4--he4a0461_2" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -195,22 +195,22 @@ build_info: engine: "docker|native" output: "target/nextflow/seqtk/seqtk_subseq" executable: "target/nextflow/seqtk/seqtk_subseq/main.nf" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/seqtk/seqtk_subseq/main.nf b/target/nextflow/seqtk/seqtk_subseq/main.nf index 199991a5..a2554f16 100644 --- a/target/nextflow/seqtk/seqtk_subseq/main.nf +++ b/target/nextflow/seqtk/seqtk_subseq/main.nf @@ -1,8 +1,8 @@ -// seqtk_subseq v0.2 +// seqtk_subseq 0.2.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such @@ -1731,7 +1731,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1802,7 +1804,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1844,7 +1848,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2803,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "seqtk_subseq", "namespace" : "seqtk", - "version" : "v0.2", + "version" : "0.2.0", "authors" : [ { "name" : "Theodoro Gasperin Terra Camargo", @@ -3032,7 +3038,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/seqtk:1.4--he4a0461_2", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.2", + "target_tag" : "0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3053,22 +3059,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/seqtk/seqtk_subseq", - "viash_version" : "0.9.0-RC7", - "git_commit" : "f22ab0eab58dcd6bff89d8d73fe951953ff1260f", + "viash_version" : "0.9.0", + "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.2", + "version" : "0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.0-RC7", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.2'" + ".engines[.type == 'docker'].target_tag := '0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3215,7 +3221,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -3346,7 +3356,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -3354,8 +3365,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -3392,6 +3403,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -3403,10 +3415,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -3491,7 +3502,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/seqtk/seqtk_subseq", - "tag" : "v0.2" + "tag" : "0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/seqtk/seqtk_subseq/nextflow.config b/target/nextflow/seqtk/seqtk_subseq/nextflow.config index 56a42af1..20088033 100644 --- a/target/nextflow/seqtk/seqtk_subseq/nextflow.config +++ b/target/nextflow/seqtk/seqtk_subseq/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'seqtk/seqtk_subseq' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.2' + version = '0.2.0' description = 'Extract subsequences from FASTA/Q files. Takes as input a FASTA/Q file and a name.lst (sequence ids file) or a reg.bed (genomic regions file).\n' author = 'Theodoro Gasperin Terra Camargo' } diff --git a/target/nextflow/star/star_align_reads/.config.vsh.yaml b/target/nextflow/star/star_align_reads/.config.vsh.yaml index 1156321a..caf1001d 100644 --- a/target/nextflow/star/star_align_reads/.config.vsh.yaml +++ b/target/nextflow/star/star_align_reads/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "star_align_reads" namespace: "star" -version: "v0.2" +version: "0.2.0" authors: - name: "Angela Oliveira Pisco" roles: @@ -2624,7 +2624,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -2662,22 +2662,22 @@ build_info: engine: "docker|native" output: "target/nextflow/star/star_align_reads" executable: "target/nextflow/star/star_align_reads/main.nf" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/star/star_align_reads/main.nf b/target/nextflow/star/star_align_reads/main.nf index d94c1ec4..a205d8a2 100644 --- a/target/nextflow/star/star_align_reads/main.nf +++ b/target/nextflow/star/star_align_reads/main.nf @@ -1,8 +1,8 @@ -// star_align_reads v0.2 +// star_align_reads 0.2.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such @@ -1732,7 +1732,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1803,7 +1805,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1845,7 +1849,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2804,7 +2810,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "star_align_reads", "namespace" : "star", - "version" : "v0.2", + "version" : "0.2.0", "authors" : [ { "name" : "Angela Oliveira Pisco", @@ -4564,7 +4570,7 @@ meta = [ { "type" : "integer", "name" : "--seed_split_min", - "description" : "min length of the seed sequen''' + '''ces split by Ns or mate gap", + "description" : "min length of the seed seque''' + '''nces split by Ns or mate gap", "info" : { "orig_name" : "--seedSplitMin" }, @@ -5888,7 +5894,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.2", + "target_tag" : "0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -5936,22 +5942,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/star/star_align_reads", - "viash_version" : "0.9.0-RC7", - "git_commit" : "f22ab0eab58dcd6bff89d8d73fe951953ff1260f", + "viash_version" : "0.9.0", + "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.2", + "version" : "0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.0-RC7", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.2'" + ".engines[.type == 'docker'].target_tag := '0.2.0'" ], "keywords" : [ "bioinformatics", @@ -6384,7 +6390,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -6515,7 +6525,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -6523,8 +6534,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -6561,6 +6572,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -6572,10 +6584,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -6660,7 +6671,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/star/star_align_reads", - "tag" : "v0.2" + "tag" : "0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/star/star_align_reads/nextflow.config b/target/nextflow/star/star_align_reads/nextflow.config index 540ee070..9406e869 100644 --- a/target/nextflow/star/star_align_reads/nextflow.config +++ b/target/nextflow/star/star_align_reads/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'star/star_align_reads' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.2' + version = '0.2.0' description = 'Aligns reads to a reference genome using STAR.\n' author = 'Angela Oliveira Pisco, Robrecht Cannoodt' } diff --git a/target/nextflow/star/star_genome_generate/.config.vsh.yaml b/target/nextflow/star/star_genome_generate/.config.vsh.yaml index bb0db735..0280082e 100644 --- a/target/nextflow/star/star_genome_generate/.config.vsh.yaml +++ b/target/nextflow/star/star_genome_generate/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "star_genome_generate" namespace: "star" -version: "v0.2" +version: "0.2.0" authors: - name: "Sai Nirmayi Yasa" roles: @@ -305,7 +305,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -332,22 +332,22 @@ build_info: engine: "docker|native" output: "target/nextflow/star/star_genome_generate" executable: "target/nextflow/star/star_genome_generate/main.nf" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/star/star_genome_generate/main.nf b/target/nextflow/star/star_genome_generate/main.nf index 02ce1e24..68618010 100644 --- a/target/nextflow/star/star_genome_generate/main.nf +++ b/target/nextflow/star/star_genome_generate/main.nf @@ -1,8 +1,8 @@ -// star_genome_generate v0.2 +// star_genome_generate 0.2.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such @@ -1731,7 +1731,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1802,7 +1804,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1844,7 +1848,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2803,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "star_genome_generate", "namespace" : "star", - "version" : "v0.2", + "version" : "0.2.0", "authors" : [ { "name" : "Sai Nirmayi Yasa", @@ -3157,7 +3163,7 @@ meta = [ "id" : "docker", "image" : "ubuntu:22.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.2", + "target_tag" : "0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3188,22 +3194,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/star/star_genome_generate", - "viash_version" : "0.9.0-RC7", - "git_commit" : "f22ab0eab58dcd6bff89d8d73fe951953ff1260f", + "viash_version" : "0.9.0", + "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.2", + "version" : "0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.0-RC7", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.2'" + ".engines[.type == 'docker'].target_tag := '0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3375,7 +3381,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -3506,7 +3516,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -3514,8 +3525,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -3552,6 +3563,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -3563,10 +3575,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -3651,7 +3662,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/star/star_genome_generate", - "tag" : "v0.2" + "tag" : "0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/star/star_genome_generate/nextflow.config b/target/nextflow/star/star_genome_generate/nextflow.config index c95e860f..19e916a3 100644 --- a/target/nextflow/star/star_genome_generate/nextflow.config +++ b/target/nextflow/star/star_genome_generate/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'star/star_genome_generate' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.2' + version = '0.2.0' description = 'Create index for STAR\n' author = 'Sai Nirmayi Yasa' } diff --git a/target/nextflow/umi_tools/umi_tools_dedup/.config.vsh.yaml b/target/nextflow/umi_tools/umi_tools_dedup/.config.vsh.yaml index 6c3d3b2e..f7d709cd 100644 --- a/target/nextflow/umi_tools/umi_tools_dedup/.config.vsh.yaml +++ b/target/nextflow/umi_tools/umi_tools_dedup/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "umi_tools_dedup" namespace: "umi_tools" -version: "v0.2" +version: "0.2.0" authors: - name: "Emma Rousseau" roles: @@ -594,7 +594,7 @@ engines: id: "docker" image: "quay.io/biocontainers/umi_tools:1.1.5--py39hf95cd2a_1" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -610,22 +610,22 @@ build_info: engine: "docker|native" output: "target/nextflow/umi_tools/umi_tools_dedup" executable: "target/nextflow/umi_tools/umi_tools_dedup/main.nf" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/umi_tools/umi_tools_dedup/main.nf b/target/nextflow/umi_tools/umi_tools_dedup/main.nf index 6b14392f..8e92cce9 100644 --- a/target/nextflow/umi_tools/umi_tools_dedup/main.nf +++ b/target/nextflow/umi_tools/umi_tools_dedup/main.nf @@ -1,8 +1,8 @@ -// umi_tools_dedup v0.2 +// umi_tools_dedup 0.2.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such @@ -1731,7 +1731,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1802,7 +1804,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1844,7 +1848,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2803,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "umi_tools_dedup", "namespace" : "umi_tools", - "version" : "v0.2", + "version" : "0.2.0", "authors" : [ { "name" : "Emma Rousseau", @@ -3459,7 +3465,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/umi_tools:1.1.5--py39hf95cd2a_1", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.2", + "target_tag" : "0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3480,22 +3486,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/umi_tools/umi_tools_dedup", - "viash_version" : "0.9.0-RC7", - "git_commit" : "f22ab0eab58dcd6bff89d8d73fe951953ff1260f", + "viash_version" : "0.9.0", + "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.2", + "version" : "0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.0-RC7", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.2'" + ".engines[.type == 'docker'].target_tag := '0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3747,7 +3753,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -3878,7 +3888,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -3886,8 +3897,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -3924,6 +3935,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -3935,10 +3947,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -4023,7 +4034,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/umi_tools/umi_tools_dedup", - "tag" : "v0.2" + "tag" : "0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/umi_tools/umi_tools_dedup/nextflow.config b/target/nextflow/umi_tools/umi_tools_dedup/nextflow.config index 35e6f3b4..4a9124a0 100644 --- a/target/nextflow/umi_tools/umi_tools_dedup/nextflow.config +++ b/target/nextflow/umi_tools/umi_tools_dedup/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'umi_tools/umi_tools_dedup' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.2' + version = '0.2.0' description = 'Deduplicate reads based on the mapping co-ordinate and the UMI attached to the read.\n' author = 'Emma Rousseau' } diff --git a/target/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml b/target/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml index b56f0211..5807149d 100644 --- a/target/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml +++ b/target/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "umi_tools_extract" namespace: "umi_tools" -version: "v0.2" +version: "0.2.0" argument_groups: - name: "Input" arguments: @@ -432,7 +432,7 @@ engines: id: "docker" image: "quay.io/biocontainers/umi_tools:1.1.4--py310h4b81fae_2" target_registry: "images.viash-hub.com" - target_tag: "v0.2" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -448,22 +448,22 @@ build_info: engine: "docker|native" output: "target/nextflow/umi_tools/umi_tools_extract" executable: "target/nextflow/umi_tools/umi_tools_extract/main.nf" - viash_version: "0.9.0-RC7" - git_commit: "f22ab0eab58dcd6bff89d8d73fe951953ff1260f" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.2" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.2'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/umi_tools/umi_tools_extract/main.nf b/target/nextflow/umi_tools/umi_tools_extract/main.nf index f9b5d96e..6bc9d6a0 100644 --- a/target/nextflow/umi_tools/umi_tools_extract/main.nf +++ b/target/nextflow/umi_tools/umi_tools_extract/main.nf @@ -1,8 +1,8 @@ -// umi_tools_extract v0.2 +// umi_tools_extract 0.2.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such @@ -1728,7 +1728,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1799,7 +1801,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1841,7 +1845,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2800,7 +2806,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "umi_tools_extract", "namespace" : "umi_tools", - "version" : "v0.2", + "version" : "0.2.0", "argument_groups" : [ { "name" : "Input", @@ -3288,7 +3294,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/umi_tools:1.1.4--py310h4b81fae_2", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.2", + "target_tag" : "0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3309,22 +3315,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/umi_tools/umi_tools_extract", - "viash_version" : "0.9.0-RC7", - "git_commit" : "f22ab0eab58dcd6bff89d8d73fe951953ff1260f", + "viash_version" : "0.9.0", + "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.2", + "version" : "0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.0-RC7", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.2'" + ".engines[.type == 'docker'].target_tag := '0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3574,7 +3580,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -3705,7 +3715,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -3713,8 +3724,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -3751,6 +3762,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -3762,10 +3774,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -3850,7 +3861,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/umi_tools/umi_tools_extract", - "tag" : "v0.2" + "tag" : "0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/umi_tools/umi_tools_extract/nextflow.config b/target/nextflow/umi_tools/umi_tools_extract/nextflow.config index af78aaea..d1ede51c 100644 --- a/target/nextflow/umi_tools/umi_tools_extract/nextflow.config +++ b/target/nextflow/umi_tools/umi_tools_extract/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'umi_tools/umi_tools_extract' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.2' + version = '0.2.0' description = 'Flexible removal of UMI sequences from fastq reads.\nUMIs are removed and appended to the read name. Any other barcode, for example a library barcode,\nis left on the read. Can also filter reads by quality or against a whitelist.\n' }