From 5817caa0f2ea6b5de3560f050b3ee9322913ae47 Mon Sep 17 00:00:00 2001 From: CI Date: Wed, 21 Aug 2024 07:17:31 +0000 Subject: [PATCH] Build branch qualimap with version qualimap (c407a88) Build pipeline: viash-hub.biobox.qualimap-qd5rq Source commit: https://github.com/viash-hub/biobox/commit/c407a88b173a2a25054ac2ee7e2abdd639d7efc4 Source message: update version and container image --- src/qualimap/qualimap_rnaseq/config.vsh.yaml | 19 +- .../agat_convert_bed2gff/.config.vsh.yaml | 2 +- .../agat_convert_bed2gff/agat_convert_bed2gff | 4 +- .../agat_convert_embl2gff/.config.vsh.yaml | 2 +- .../agat_convert_embl2gff | 4 +- .../agat_convert_sp_gff2gtf/.config.vsh.yaml | 2 +- .../agat_convert_sp_gff2gtf | 4 +- .../agat_convert_sp_gff2tsv/.config.vsh.yaml | 2 +- .../agat_convert_sp_gff2tsv | 4 +- .../agat_convert_sp_gxf2gxf/.config.vsh.yaml | 2 +- .../agat_convert_sp_gxf2gxf | 4 +- target/executable/arriba/.config.vsh.yaml | 2 +- target/executable/arriba/arriba | 4 +- .../executable/bcl_convert/.config.vsh.yaml | 2 +- target/executable/bcl_convert/bcl_convert | 4 +- .../.config.vsh.yaml | 2 +- .../bd_rhapsody_make_reference | 4 +- .../bedtools_bamtofastq/.config.vsh.yaml | 2 +- .../bedtools_bamtofastq/bedtools_bamtofastq | 4 +- .../bedtools_bedtobam/.config.vsh.yaml | 2 +- .../bedtools_bedtobam/bedtools_bedtobam | 4 +- .../bedtools_getfasta/.config.vsh.yaml | 2 +- .../bedtools_getfasta/bedtools_getfasta | 4 +- .../bedtools_intersect/.config.vsh.yaml | 2 +- .../bedtools_intersect/bedtools_intersect | 4 +- .../bedtools/bedtools_sort/.config.vsh.yaml | 2 +- .../bedtools/bedtools_sort/bedtools_sort | 4 +- .../busco_download_datasets/.config.vsh.yaml | 2 +- .../busco_download_datasets | 4 +- .../busco_list_datasets/.config.vsh.yaml | 2 +- .../busco_list_datasets/busco_list_datasets | 4 +- .../busco/busco_run/.config.vsh.yaml | 2 +- target/executable/busco/busco_run/busco_run | 4 +- target/executable/cutadapt/.config.vsh.yaml | 2 +- target/executable/cutadapt/cutadapt | 4 +- target/executable/falco/.config.vsh.yaml | 2 +- target/executable/falco/falco | 4 +- target/executable/fastp/.config.vsh.yaml | 2 +- target/executable/fastp/fastp | 4 +- .../executable/featurecounts/.config.vsh.yaml | 2 +- target/executable/featurecounts/featurecounts | 4 +- target/executable/gffread/.config.vsh.yaml | 2 +- target/executable/gffread/gffread | 4 +- .../lofreq/lofreq_call/.config.vsh.yaml | 2 +- .../executable/lofreq/lofreq_call/lofreq_call | 4 +- .../lofreq/lofreq_indelqual/.config.vsh.yaml | 2 +- .../lofreq/lofreq_indelqual/lofreq_indelqual | 4 +- target/executable/multiqc/.config.vsh.yaml | 2 +- target/executable/multiqc/multiqc | 4 +- target/executable/pear/.config.vsh.yaml | 2 +- target/executable/pear/pear | 4 +- .../{ => qualimap_rnaseq}/.config.vsh.yaml | 31 +- .../qualimap_rnaseq} | 39 +- .../salmon/salmon_index/.config.vsh.yaml | 2 +- .../salmon/salmon_index/salmon_index | 4 +- .../salmon/salmon_quant/.config.vsh.yaml | 2 +- .../salmon/salmon_quant/salmon_quant | 4 +- .../samtools_collate/.config.vsh.yaml | 2 +- .../samtools_collate/samtools_collate | 4 +- .../samtools/samtools_faidx/.config.vsh.yaml | 2 +- .../samtools/samtools_faidx/samtools_faidx | 4 +- .../samtools/samtools_fasta/.config.vsh.yaml | 2 +- .../samtools/samtools_fasta/samtools_fasta | 4 +- .../samtools/samtools_fastq/.config.vsh.yaml | 2 +- .../samtools/samtools_fastq/samtools_fastq | 4 +- .../samtools_flagstat/.config.vsh.yaml | 2 +- .../samtools_flagstat/samtools_flagstat | 4 +- .../samtools_idxstats/.config.vsh.yaml | 2 +- .../samtools_idxstats/samtools_idxstats | 4 +- .../samtools/samtools_index/.config.vsh.yaml | 2 +- .../samtools/samtools_index/samtools_index | 4 +- .../samtools/samtools_sort/.config.vsh.yaml | 2 +- .../samtools/samtools_sort/samtools_sort | 4 +- .../samtools/samtools_stats/.config.vsh.yaml | 2 +- .../samtools/samtools_stats/samtools_stats | 4 +- .../samtools/samtools_view/.config.vsh.yaml | 2 +- .../samtools/samtools_view/samtools_view | 4 +- .../seqtk/seqtk_sample/.config.vsh.yaml | 2 +- .../seqtk/seqtk_sample/seqtk_sample | 4 +- .../seqtk/seqtk_subseq/.config.vsh.yaml | 2 +- .../seqtk/seqtk_subseq/seqtk_subseq | 4 +- .../star/star_align_reads/.config.vsh.yaml | 2 +- .../star/star_align_reads/star_align_reads | 4 +- .../star_genome_generate/.config.vsh.yaml | 2 +- .../star_genome_generate/star_genome_generate | 4 +- .../umi_tools_dedup/.config.vsh.yaml | 2 +- .../umi_tools/umi_tools_dedup/umi_tools_dedup | 4 +- .../umi_tools_extract/.config.vsh.yaml | 2 +- .../umi_tools_extract/umi_tools_extract | 4 +- .../agat_convert_bed2gff/.config.vsh.yaml | 2 +- .../agat/agat_convert_bed2gff/main.nf | 2 +- .../agat_convert_embl2gff/.config.vsh.yaml | 2 +- .../agat/agat_convert_embl2gff/main.nf | 2 +- .../agat_convert_sp_gff2gtf/.config.vsh.yaml | 2 +- .../agat/agat_convert_sp_gff2gtf/main.nf | 2 +- .../agat_convert_sp_gff2tsv/.config.vsh.yaml | 2 +- .../agat/agat_convert_sp_gff2tsv/main.nf | 2 +- .../agat_convert_sp_gxf2gxf/.config.vsh.yaml | 2 +- .../agat/agat_convert_sp_gxf2gxf/main.nf | 2 +- target/nextflow/arriba/.config.vsh.yaml | 2 +- target/nextflow/arriba/main.nf | 2 +- target/nextflow/bcl_convert/.config.vsh.yaml | 2 +- target/nextflow/bcl_convert/main.nf | 2 +- .../.config.vsh.yaml | 2 +- .../bd_rhapsody_make_reference/main.nf | 2 +- .../bedtools_bamtofastq/.config.vsh.yaml | 2 +- .../bedtools/bedtools_bamtofastq/main.nf | 2 +- .../bedtools_bedtobam/.config.vsh.yaml | 2 +- .../bedtools/bedtools_bedtobam/main.nf | 2 +- .../bedtools_getfasta/.config.vsh.yaml | 2 +- .../bedtools/bedtools_getfasta/main.nf | 2 +- .../bedtools_intersect/.config.vsh.yaml | 2 +- .../bedtools/bedtools_intersect/main.nf | 2 +- .../bedtools/bedtools_sort/.config.vsh.yaml | 2 +- .../nextflow/bedtools/bedtools_sort/main.nf | 2 +- .../busco_download_datasets/.config.vsh.yaml | 2 +- .../busco/busco_download_datasets/main.nf | 2 +- .../busco_list_datasets/.config.vsh.yaml | 2 +- .../busco/busco_list_datasets/main.nf | 2 +- .../nextflow/busco/busco_run/.config.vsh.yaml | 2 +- target/nextflow/busco/busco_run/main.nf | 2 +- .../busco/busco_run/nextflow_schema.json | 471 ------------------ target/nextflow/cutadapt/.config.vsh.yaml | 2 +- target/nextflow/cutadapt/main.nf | 2 +- target/nextflow/falco/.config.vsh.yaml | 2 +- target/nextflow/falco/main.nf | 2 +- target/nextflow/fastp/.config.vsh.yaml | 2 +- target/nextflow/fastp/main.nf | 2 +- .../nextflow/featurecounts/.config.vsh.yaml | 2 +- target/nextflow/featurecounts/main.nf | 2 +- target/nextflow/gffread/.config.vsh.yaml | 2 +- target/nextflow/gffread/main.nf | 2 +- .../lofreq/lofreq_call/.config.vsh.yaml | 2 +- target/nextflow/lofreq/lofreq_call/main.nf | 2 +- .../lofreq/lofreq_indelqual/.config.vsh.yaml | 2 +- .../nextflow/lofreq/lofreq_indelqual/main.nf | 2 +- .../lofreq_indelqual/nextflow_schema.json | 151 ------ target/nextflow/multiqc/.config.vsh.yaml | 2 +- target/nextflow/multiqc/main.nf | 2 +- target/nextflow/pear/.config.vsh.yaml | 2 +- target/nextflow/pear/main.nf | 2 +- .../{ => qualimap_rnaseq}/.config.vsh.yaml | 31 +- .../qualimap/{ => qualimap_rnaseq}/main.nf | 37 +- .../{ => qualimap_rnaseq}/nextflow.config | 2 +- .../nextflow_schema.json | 2 +- .../salmon/salmon_index/.config.vsh.yaml | 2 +- target/nextflow/salmon/salmon_index/main.nf | 2 +- .../salmon/salmon_quant/.config.vsh.yaml | 2 +- target/nextflow/salmon/salmon_quant/main.nf | 2 +- .../samtools_collate/.config.vsh.yaml | 2 +- .../samtools/samtools_collate/main.nf | 2 +- .../samtools/samtools_faidx/.config.vsh.yaml | 2 +- .../nextflow/samtools/samtools_faidx/main.nf | 2 +- .../samtools/samtools_fasta/.config.vsh.yaml | 2 +- .../nextflow/samtools/samtools_fasta/main.nf | 2 +- .../samtools/samtools_fastq/.config.vsh.yaml | 2 +- .../nextflow/samtools/samtools_fastq/main.nf | 2 +- .../samtools_flagstat/.config.vsh.yaml | 2 +- .../samtools/samtools_flagstat/main.nf | 2 +- .../samtools_idxstats/.config.vsh.yaml | 2 +- .../samtools/samtools_idxstats/main.nf | 2 +- .../samtools/samtools_index/.config.vsh.yaml | 2 +- .../nextflow/samtools/samtools_index/main.nf | 2 +- .../samtools/samtools_sort/.config.vsh.yaml | 2 +- .../nextflow/samtools/samtools_sort/main.nf | 2 +- .../samtools/samtools_stats/.config.vsh.yaml | 2 +- .../nextflow/samtools/samtools_stats/main.nf | 2 +- .../samtools/samtools_view/.config.vsh.yaml | 2 +- .../nextflow/samtools/samtools_view/main.nf | 2 +- .../seqtk/seqtk_sample/.config.vsh.yaml | 2 +- target/nextflow/seqtk/seqtk_sample/main.nf | 2 +- .../seqtk/seqtk_subseq/.config.vsh.yaml | 2 +- target/nextflow/seqtk/seqtk_subseq/main.nf | 2 +- .../star/star_align_reads/.config.vsh.yaml | 2 +- target/nextflow/star/star_align_reads/main.nf | 2 +- .../star_genome_generate/.config.vsh.yaml | 2 +- .../star/star_genome_generate/main.nf | 2 +- .../umi_tools_dedup/.config.vsh.yaml | 2 +- .../umi_tools/umi_tools_dedup/main.nf | 2 +- .../umi_tools_extract/.config.vsh.yaml | 2 +- .../umi_tools/umi_tools_extract/main.nf | 2 +- 181 files changed, 255 insertions(+), 958 deletions(-) rename target/executable/qualimap/{ => qualimap_rnaseq}/.config.vsh.yaml (91%) rename target/executable/qualimap/{qualimap => qualimap_rnaseq/qualimap_rnaseq} (97%) delete mode 100644 target/nextflow/busco/busco_run/nextflow_schema.json delete mode 100644 target/nextflow/lofreq/lofreq_indelqual/nextflow_schema.json rename target/nextflow/qualimap/{ => qualimap_rnaseq}/.config.vsh.yaml (91%) rename target/nextflow/qualimap/{ => qualimap_rnaseq}/main.nf (99%) rename target/nextflow/qualimap/{ => qualimap_rnaseq}/nextflow.config (99%) rename target/nextflow/qualimap/{ => qualimap_rnaseq}/nextflow_schema.json (99%) diff --git a/src/qualimap/qualimap_rnaseq/config.vsh.yaml b/src/qualimap/qualimap_rnaseq/config.vsh.yaml index 7988ae27..35e8c6ff 100644 --- a/src/qualimap/qualimap_rnaseq/config.vsh.yaml +++ b/src/qualimap/qualimap_rnaseq/config.vsh.yaml @@ -1,4 +1,5 @@ -name: "qualimap" +name: qualimap_rnaseq +namespace: qualimap keywords: [RNA-seq, quality control, QC Report] description: | Qualimap RNA-seq QC reports quality control metrics and bias estimations @@ -92,23 +93,11 @@ test_resources: engines: - type: docker - image: ubuntu:22.04 + image: quay.io/biocontainers/qualimap:2.3--hdfd78af_0 setup: - - type: apt - packages: [ r-base, unzip, wget, openjdk-8-jdk, libxml2-dev, libcurl4-openssl-dev ] - type: docker run: | - wget https://bitbucket.org/kokonech/qualimap/downloads/qualimap_v2.3.zip && \ - unzip qualimap_v2.3.zip && \ - cp -a qualimap_v2.3/. usr/bin && \ - unset DISPLAY && \ - mkdir -p tmp && \ - export _JAVA_OPTIONS=-Djava.io.tmpdir=./tmp && \ - echo "qualimap: v2.3" > /var/software_versions.txt - - - type: r - bioc: [ NOISeqr ] - cran: [ optparse ] + echo QualiMap: $(qualimap 2>&1 | grep QualiMap | sed 's/^.*QualiMap//') runners: - type: executable - type: nextflow diff --git a/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml b/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml index ed69faf9..1902895f 100644 --- a/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml +++ b/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml @@ -235,7 +235,7 @@ build_info: output: "target/executable/agat/agat_convert_bed2gff" executable: "target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff b/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff index 5ff35fb9..7de36b7f 100755 --- a/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff +++ b/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff @@ -514,9 +514,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t LABEL org.opencontainers.image.authors="Leïla Paquay" LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_bed2gff" -LABEL org.opencontainers.image.created="2024-08-20T21:05:02Z" +LABEL org.opencontainers.image.created="2024-08-21T07:00:57Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" +LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER diff --git a/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml b/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml index dfb70eb1..151039f6 100644 --- a/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml +++ b/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml @@ -225,7 +225,7 @@ build_info: output: "target/executable/agat/agat_convert_embl2gff" executable: "target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff b/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff index 5274c8f7..8816dd20 100755 --- a/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff +++ b/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff @@ -504,9 +504,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t LABEL org.opencontainers.image.authors="Leïla Paquay" LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_embl2gff" -LABEL org.opencontainers.image.created="2024-08-20T21:05:01Z" +LABEL org.opencontainers.image.created="2024-08-21T07:00:57Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" +LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER 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 f55ef9be..798fc3b4 100644 --- a/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml +++ b/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml @@ -228,7 +228,7 @@ build_info: output: "target/executable/agat/agat_convert_sp_gff2gtf" executable: "target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" 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 8c5f2744..17c42535 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 @@ -518,9 +518,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t LABEL org.opencontainers.image.authors="Leïla Paquay" LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_sp_gff2gtf" -LABEL org.opencontainers.image.created="2024-08-20T21:05:02Z" +LABEL org.opencontainers.image.created="2024-08-21T07:00:58Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" +LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER 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 044931a1..3ca74b75 100644 --- a/target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml +++ b/target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml @@ -188,7 +188,7 @@ build_info: output: "target/executable/agat/agat_convert_sp_gff2tsv" executable: "target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" 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 5fa528ad..d33a63a2 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 @@ -483,9 +483,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t LABEL org.opencontainers.image.authors="Leïla Paquay" LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_sp_gff2tsv" -LABEL org.opencontainers.image.created="2024-08-20T21:05:01Z" +LABEL org.opencontainers.image.created="2024-08-21T07:00:57Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" +LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER 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 6a79153b..85174ce6 100644 --- a/target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml +++ b/target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml @@ -195,7 +195,7 @@ build_info: output: "target/executable/agat/agat_convert_sp_gxf2gxf" executable: "target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" 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 8f012352..f4c4179b 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 @@ -492,9 +492,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t LABEL org.opencontainers.image.authors="Leïla Paquay" LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_sp_gxf2gxf" -LABEL org.opencontainers.image.created="2024-08-20T21:05:01Z" +LABEL org.opencontainers.image.created="2024-08-21T07:00:56Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" +LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER diff --git a/target/executable/arriba/.config.vsh.yaml b/target/executable/arriba/.config.vsh.yaml index cfd5fdfb..d480984c 100644 --- a/target/executable/arriba/.config.vsh.yaml +++ b/target/executable/arriba/.config.vsh.yaml @@ -706,7 +706,7 @@ build_info: output: "target/executable/arriba" executable: "target/executable/arriba/arriba" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/arriba/arriba b/target/executable/arriba/arriba index fb519183..2a37ebf9 100755 --- a/target/executable/arriba/arriba +++ b/target/executable/arriba/arriba @@ -753,9 +753,9 @@ 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="2024-08-20T21:05:03Z" +LABEL org.opencontainers.image.created="2024-08-21T07:00:59Z" LABEL org.opencontainers.image.source="https://github.com/suhrig/arriba" -LABEL org.opencontainers.image.revision="d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" +LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER diff --git a/target/executable/bcl_convert/.config.vsh.yaml b/target/executable/bcl_convert/.config.vsh.yaml index 19887fe5..1190e893 100644 --- a/target/executable/bcl_convert/.config.vsh.yaml +++ b/target/executable/bcl_convert/.config.vsh.yaml @@ -418,7 +418,7 @@ build_info: output: "target/executable/bcl_convert" executable: "target/executable/bcl_convert/bcl_convert" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/bcl_convert/bcl_convert b/target/executable/bcl_convert/bcl_convert index 000d5a57..ae15aa0c 100755 --- a/target/executable/bcl_convert/bcl_convert +++ b/target/executable/bcl_convert/bcl_convert @@ -598,9 +598,9 @@ RUN echo "bcl-convert: \"$(bcl-convert -V 2>&1 >/dev/null | sed -n '/Version/ s/ LABEL org.opencontainers.image.authors="Toni Verbeiren, Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component bcl_convert" -LABEL org.opencontainers.image.created="2024-08-20T21:05:03Z" +LABEL org.opencontainers.image.created="2024-08-21T07:00:58Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox" -LABEL org.opencontainers.image.revision="d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" +LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER diff --git a/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml b/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml index 93fb7239..3930ee93 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 @@ -270,7 +270,7 @@ build_info: output: "target/executable/bd_rhapsody/bd_rhapsody_make_reference" executable: "target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" 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 5058de07..9d3abcaf 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 @@ -548,9 +548,9 @@ 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="2024-08-20T21:05:07Z" +LABEL org.opencontainers.image.created="2024-08-21T07:01:01Z" LABEL org.opencontainers.image.source="https://bitbucket.org/CRSwDev/cwl/src/master/v2.2.1/Extra_Utilities/" -LABEL org.opencontainers.image.revision="d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" +LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER diff --git a/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml b/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml index 96271e26..1eee8649 100644 --- a/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml @@ -187,7 +187,7 @@ build_info: output: "target/executable/bedtools/bedtools_bamtofastq" executable: "target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq b/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq index 891015ac..b1207775 100755 --- a/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq +++ b/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq @@ -482,9 +482,9 @@ 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="2024-08-20T21:04:51Z" +LABEL org.opencontainers.image.created="2024-08-21T07:00:47Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" +LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER diff --git a/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml b/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml index 3c259cd4..4d20fca3 100644 --- a/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml @@ -214,7 +214,7 @@ build_info: output: "target/executable/bedtools/bedtools_bedtobam" executable: "target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam b/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam index e6be00bd..3706e934 100755 --- a/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam +++ b/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam @@ -495,9 +495,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bedtobam" -LABEL org.opencontainers.image.created="2024-08-20T21:04:52Z" +LABEL org.opencontainers.image.created="2024-08-21T07:00:48Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" +LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER diff --git a/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml b/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml index dc45156e..2bc7b389 100644 --- a/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml @@ -232,7 +232,7 @@ build_info: output: "target/executable/bedtools/bedtools_getfasta" executable: "target/executable/bedtools/bedtools_getfasta/bedtools_getfasta" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta b/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta index cd3b584c..5a8625d7 100755 --- a/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta +++ b/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta @@ -525,9 +525,9 @@ RUN echo "bedtools: \"$(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="2024-08-20T21:04:51Z" +LABEL org.opencontainers.image.created="2024-08-21T07:00:47Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" +LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER diff --git a/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml b/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml index ce8a0c3d..a8efae55 100644 --- a/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml @@ -410,7 +410,7 @@ build_info: output: "target/executable/bedtools/bedtools_intersect" executable: "target/executable/bedtools/bedtools_intersect/bedtools_intersect" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/bedtools/bedtools_intersect/bedtools_intersect b/target/executable/bedtools/bedtools_intersect/bedtools_intersect index 3dda0002..030ffe0c 100755 --- a/target/executable/bedtools/bedtools_intersect/bedtools_intersect +++ b/target/executable/bedtools/bedtools_intersect/bedtools_intersect @@ -632,9 +632,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_intersect" -LABEL org.opencontainers.image.created="2024-08-20T21:04:51Z" +LABEL org.opencontainers.image.created="2024-08-21T07:00:47Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" +LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER diff --git a/target/executable/bedtools/bedtools_sort/.config.vsh.yaml b/target/executable/bedtools/bedtools_sort/.config.vsh.yaml index d5e8e238..768db3d4 100644 --- a/target/executable/bedtools/bedtools_sort/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_sort/.config.vsh.yaml @@ -222,7 +222,7 @@ build_info: output: "target/executable/bedtools/bedtools_sort" executable: "target/executable/bedtools/bedtools_sort/bedtools_sort" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/bedtools/bedtools_sort/bedtools_sort b/target/executable/bedtools/bedtools_sort/bedtools_sort index 66d87f5b..c0a6f3e1 100755 --- a/target/executable/bedtools/bedtools_sort/bedtools_sort +++ b/target/executable/bedtools/bedtools_sort/bedtools_sort @@ -508,9 +508,9 @@ RUN echo "bedtools: \"$(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="2024-08-20T21:04:52Z" +LABEL org.opencontainers.image.created="2024-08-21T07:00:48Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" +LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER diff --git a/target/executable/busco/busco_download_datasets/.config.vsh.yaml b/target/executable/busco/busco_download_datasets/.config.vsh.yaml index 7bfd3ea3..e6cb3450 100644 --- a/target/executable/busco/busco_download_datasets/.config.vsh.yaml +++ b/target/executable/busco/busco_download_datasets/.config.vsh.yaml @@ -158,7 +158,7 @@ build_info: output: "target/executable/busco/busco_download_datasets" executable: "target/executable/busco/busco_download_datasets/busco_download_datasets" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/busco/busco_download_datasets/busco_download_datasets b/target/executable/busco/busco_download_datasets/busco_download_datasets index b723f968..c1a242bf 100755 --- a/target/executable/busco/busco_download_datasets/busco_download_datasets +++ b/target/executable/busco/busco_download_datasets/busco_download_datasets @@ -474,9 +474,9 @@ RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_version LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component busco busco_download_datasets" -LABEL org.opencontainers.image.created="2024-08-20T21:05:00Z" +LABEL org.opencontainers.image.created="2024-08-21T07:00:55Z" LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco" -LABEL org.opencontainers.image.revision="d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" +LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER diff --git a/target/executable/busco/busco_list_datasets/.config.vsh.yaml b/target/executable/busco/busco_list_datasets/.config.vsh.yaml index 82103a46..d009328d 100644 --- a/target/executable/busco/busco_list_datasets/.config.vsh.yaml +++ b/target/executable/busco/busco_list_datasets/.config.vsh.yaml @@ -145,7 +145,7 @@ build_info: output: "target/executable/busco/busco_list_datasets" executable: "target/executable/busco/busco_list_datasets/busco_list_datasets" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/busco/busco_list_datasets/busco_list_datasets b/target/executable/busco/busco_list_datasets/busco_list_datasets index a9341137..482d02f4 100755 --- a/target/executable/busco/busco_list_datasets/busco_list_datasets +++ b/target/executable/busco/busco_list_datasets/busco_list_datasets @@ -464,9 +464,9 @@ RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_version LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component busco busco_list_datasets" -LABEL org.opencontainers.image.created="2024-08-20T21:05:00Z" +LABEL org.opencontainers.image.created="2024-08-21T07:00:56Z" LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco" -LABEL org.opencontainers.image.revision="d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" +LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER diff --git a/target/executable/busco/busco_run/.config.vsh.yaml b/target/executable/busco/busco_run/.config.vsh.yaml index c3fd7140..c2fcd66c 100644 --- a/target/executable/busco/busco_run/.config.vsh.yaml +++ b/target/executable/busco/busco_run/.config.vsh.yaml @@ -423,7 +423,7 @@ build_info: output: "target/executable/busco/busco_run" executable: "target/executable/busco/busco_run/busco_run" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/busco/busco_run/busco_run b/target/executable/busco/busco_run/busco_run index fcb7a0e3..819827a9 100755 --- a/target/executable/busco/busco_run/busco_run +++ b/target/executable/busco/busco_run/busco_run @@ -631,9 +631,9 @@ RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_version LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component busco busco_run" -LABEL org.opencontainers.image.created="2024-08-20T21:05:00Z" +LABEL org.opencontainers.image.created="2024-08-21T07:00:56Z" LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco" -LABEL org.opencontainers.image.revision="d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" +LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER diff --git a/target/executable/cutadapt/.config.vsh.yaml b/target/executable/cutadapt/.config.vsh.yaml index e4915197..856c83f7 100644 --- a/target/executable/cutadapt/.config.vsh.yaml +++ b/target/executable/cutadapt/.config.vsh.yaml @@ -740,7 +740,7 @@ build_info: output: "target/executable/cutadapt" executable: "target/executable/cutadapt/cutadapt" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/cutadapt/cutadapt b/target/executable/cutadapt/cutadapt index 6999553e..4793903a 100755 --- a/target/executable/cutadapt/cutadapt +++ b/target/executable/cutadapt/cutadapt @@ -830,9 +830,9 @@ RUN cutadapt --version | sed 's/\(.*\)/cutadapt: "\1"/' > /var/software_versions LABEL org.opencontainers.image.authors="Toni Verbeiren" LABEL org.opencontainers.image.description="Companion container for running component cutadapt" -LABEL org.opencontainers.image.created="2024-08-20T21:05:05Z" +LABEL org.opencontainers.image.created="2024-08-21T07:01:00Z" LABEL org.opencontainers.image.source="https://github.com/marcelm/cutadapt" -LABEL org.opencontainers.image.revision="d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" +LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER diff --git a/target/executable/falco/.config.vsh.yaml b/target/executable/falco/.config.vsh.yaml index 7315c0cd..30fb22da 100644 --- a/target/executable/falco/.config.vsh.yaml +++ b/target/executable/falco/.config.vsh.yaml @@ -317,7 +317,7 @@ build_info: output: "target/executable/falco" executable: "target/executable/falco/falco" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/falco/falco b/target/executable/falco/falco index be6289c1..21866b3f 100755 --- a/target/executable/falco/falco +++ b/target/executable/falco/falco @@ -588,9 +588,9 @@ RUN echo "falco: \"$(falco -v | sed -n 's/^falco //p')\"" > /var/software_versio LABEL org.opencontainers.image.authors="Toni Verbeiren" LABEL org.opencontainers.image.description="Companion container for running component falco" -LABEL org.opencontainers.image.created="2024-08-20T21:05:06Z" +LABEL org.opencontainers.image.created="2024-08-21T07:01:01Z" LABEL org.opencontainers.image.source="https://github.com/smithlabcode/falco" -LABEL org.opencontainers.image.revision="d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" +LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER diff --git a/target/executable/fastp/.config.vsh.yaml b/target/executable/fastp/.config.vsh.yaml index 6846d8d3..b1277bf7 100644 --- a/target/executable/fastp/.config.vsh.yaml +++ b/target/executable/fastp/.config.vsh.yaml @@ -1083,7 +1083,7 @@ build_info: output: "target/executable/fastp" executable: "target/executable/fastp/fastp" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/fastp/fastp b/target/executable/fastp/fastp index 54d3f876..f4c1dbd5 100755 --- a/target/executable/fastp/fastp +++ b/target/executable/fastp/fastp @@ -1027,9 +1027,9 @@ RUN fastp --version 2>&1 | sed 's# #: "#;s#$#"#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component fastp" -LABEL org.opencontainers.image.created="2024-08-20T21:05:02Z" +LABEL org.opencontainers.image.created="2024-08-21T07:00:58Z" LABEL org.opencontainers.image.source="https://github.com/OpenGene/fastp" -LABEL org.opencontainers.image.revision="d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" +LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER diff --git a/target/executable/featurecounts/.config.vsh.yaml b/target/executable/featurecounts/.config.vsh.yaml index f504e053..ee3d3d39 100644 --- a/target/executable/featurecounts/.config.vsh.yaml +++ b/target/executable/featurecounts/.config.vsh.yaml @@ -645,7 +645,7 @@ build_info: output: "target/executable/featurecounts" executable: "target/executable/featurecounts/featurecounts" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/featurecounts/featurecounts b/target/executable/featurecounts/featurecounts index 97c16547..bfb22b6d 100755 --- a/target/executable/featurecounts/featurecounts +++ b/target/executable/featurecounts/featurecounts @@ -753,9 +753,9 @@ RUN featureCounts -v 2>&1 | sed 's/featureCounts v\([0-9.]*\)/featureCounts: \1/ LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa" LABEL org.opencontainers.image.description="Companion container for running component featurecounts" -LABEL org.opencontainers.image.created="2024-08-20T21:04:58Z" +LABEL org.opencontainers.image.created="2024-08-21T07:00:54Z" LABEL org.opencontainers.image.source="https://github.com/ShiLab-Bioinformatics/subread" -LABEL org.opencontainers.image.revision="d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" +LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER diff --git a/target/executable/gffread/.config.vsh.yaml b/target/executable/gffread/.config.vsh.yaml index 1a0b51f5..bab2933c 100644 --- a/target/executable/gffread/.config.vsh.yaml +++ b/target/executable/gffread/.config.vsh.yaml @@ -685,7 +685,7 @@ build_info: output: "target/executable/gffread" executable: "target/executable/gffread/gffread" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/gffread/gffread b/target/executable/gffread/gffread index a2ae3c15..acb36c40 100755 --- a/target/executable/gffread/gffread +++ b/target/executable/gffread/gffread @@ -806,9 +806,9 @@ RUN echo "gffread: \"$(gffread --version 2>&1)\"" > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component gffread" -LABEL org.opencontainers.image.created="2024-08-20T21:04:50Z" +LABEL org.opencontainers.image.created="2024-08-21T07:00:46Z" LABEL org.opencontainers.image.source="https://github.com/gpertea/gffread" -LABEL org.opencontainers.image.revision="d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" +LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER diff --git a/target/executable/lofreq/lofreq_call/.config.vsh.yaml b/target/executable/lofreq/lofreq_call/.config.vsh.yaml index 65870256..5a48e737 100644 --- a/target/executable/lofreq/lofreq_call/.config.vsh.yaml +++ b/target/executable/lofreq/lofreq_call/.config.vsh.yaml @@ -507,7 +507,7 @@ build_info: output: "target/executable/lofreq/lofreq_call" executable: "target/executable/lofreq/lofreq_call/lofreq_call" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/lofreq/lofreq_call/lofreq_call b/target/executable/lofreq/lofreq_call/lofreq_call index 9a5cb337..25d387c3 100755 --- a/target/executable/lofreq/lofreq_call/lofreq_call +++ b/target/executable/lofreq/lofreq_call/lofreq_call @@ -655,9 +655,9 @@ echo "lofreq: $version" > /var/software_versions.txt LABEL org.opencontainers.image.authors="Kai Waldrant" LABEL org.opencontainers.image.description="Companion container for running component lofreq lofreq_call" -LABEL org.opencontainers.image.created="2024-08-20T21:04:58Z" +LABEL org.opencontainers.image.created="2024-08-21T07:00:53Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox" -LABEL org.opencontainers.image.revision="d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" +LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER diff --git a/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml b/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml index c7b9da24..ae4650c3 100644 --- a/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml +++ b/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml @@ -215,7 +215,7 @@ build_info: output: "target/executable/lofreq/lofreq_indelqual" executable: "target/executable/lofreq/lofreq_indelqual/lofreq_indelqual" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual b/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual index cf5b3386..dd103e44 100755 --- a/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual +++ b/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual @@ -500,9 +500,9 @@ echo "lofreq: $version" > /var/software_versions.txt LABEL org.opencontainers.image.authors="Kai Waldrant" LABEL org.opencontainers.image.description="Companion container for running component lofreq lofreq_indelqual" -LABEL org.opencontainers.image.created="2024-08-20T21:04:57Z" +LABEL org.opencontainers.image.created="2024-08-21T07:00:53Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox" -LABEL org.opencontainers.image.revision="d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" +LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER diff --git a/target/executable/multiqc/.config.vsh.yaml b/target/executable/multiqc/.config.vsh.yaml index d86606ee..42cdb1e6 100644 --- a/target/executable/multiqc/.config.vsh.yaml +++ b/target/executable/multiqc/.config.vsh.yaml @@ -456,7 +456,7 @@ build_info: output: "target/executable/multiqc" executable: "target/executable/multiqc/multiqc" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/multiqc/multiqc b/target/executable/multiqc/multiqc index d7b8ffdc..bc018937 100755 --- a/target/executable/multiqc/multiqc +++ b/target/executable/multiqc/multiqc @@ -636,9 +636,9 @@ RUN multiqc --version | sed 's/multiqc, version\s\(.*\)/multiqc: "\1"/' > /var/s LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component multiqc" -LABEL org.opencontainers.image.created="2024-08-20T21:05:06Z" +LABEL org.opencontainers.image.created="2024-08-21T07:01:00Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox" -LABEL org.opencontainers.image.revision="d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" +LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER diff --git a/target/executable/pear/.config.vsh.yaml b/target/executable/pear/.config.vsh.yaml index 9f1fefcb..eca540df 100644 --- a/target/executable/pear/.config.vsh.yaml +++ b/target/executable/pear/.config.vsh.yaml @@ -398,7 +398,7 @@ build_info: output: "target/executable/pear" executable: "target/executable/pear/pear" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/pear/pear b/target/executable/pear/pear index 4f78ad99..e935c57d 100755 --- a/target/executable/pear/pear +++ b/target/executable/pear/pear @@ -596,9 +596,9 @@ echo "pear: $version" > /var/software_versions.txt LABEL org.opencontainers.image.authors="Kai Waldrant" LABEL org.opencontainers.image.description="Companion container for running component pear" -LABEL org.opencontainers.image.created="2024-08-20T21:04:52Z" +LABEL org.opencontainers.image.created="2024-08-21T07:00:48Z" LABEL org.opencontainers.image.source="https://github.com/tseemann/PEAR" -LABEL org.opencontainers.image.revision="d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" +LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER diff --git a/target/executable/qualimap/.config.vsh.yaml b/target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml similarity index 91% rename from target/executable/qualimap/.config.vsh.yaml rename to target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml index 1ba49a7c..c205e499 100644 --- a/target/executable/qualimap/.config.vsh.yaml +++ b/target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml @@ -1,4 +1,5 @@ -name: "qualimap" +name: "qualimap_rnaseq" +namespace: "qualimap" version: "qualimap" authors: - name: "Dorien Roosen" @@ -244,32 +245,14 @@ runners: engines: - type: "docker" id: "docker" - image: "ubuntu:22.04" + image: "quay.io/biocontainers/qualimap:2.3--hdfd78af_0" target_registry: "images.viash-hub.com" target_tag: "qualimap" namespace_separator: "/" setup: - - type: "apt" - packages: - - "r-base" - - "unzip" - - "wget" - - "openjdk-8-jdk" - - "libxml2-dev" - - "libcurl4-openssl-dev" - interactive: false - type: "docker" run: - - "wget https://bitbucket.org/kokonech/qualimap/downloads/qualimap_v2.3.zip &&\ - \ \\\nunzip qualimap_v2.3.zip && \\\ncp -a qualimap_v2.3/. usr/bin && \\\nunset\ - \ DISPLAY && \\\nmkdir -p tmp && \\\nexport _JAVA_OPTIONS=-Djava.io.tmpdir=./tmp\ - \ && \\\necho \"qualimap: v2.3\" > /var/software_versions.txt\n" - - type: "r" - cran: - - "optparse" - bioc: - - "NOISeqr" - bioc_force_install: false + - "echo QualiMap: $(qualimap 2>&1 | grep QualiMap | sed 's/^.*QualiMap//')\n" entrypoint: [] cmd: null - type: "native" @@ -278,10 +261,10 @@ build_info: config: "src/qualimap/qualimap_rnaseq/config.vsh.yaml" runner: "executable" engine: "docker|native" - output: "target/executable/qualimap" - executable: "target/executable/qualimap/qualimap" + output: "target/executable/qualimap/qualimap_rnaseq" + executable: "target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/qualimap/qualimap b/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq similarity index 97% rename from target/executable/qualimap/qualimap rename to target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq index f02fd6c0..0383d823 100755 --- a/target/executable/qualimap/qualimap +++ b/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# qualimap qualimap +# qualimap_rnaseq qualimap # # This wrapper script is auto-generated by viash 0.9.0-RC6 and is thus a # derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from @@ -165,8 +165,8 @@ VIASH_META_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}` VIASH_TARGET_DIR=`ViashFindTargetDir $VIASH_META_RESOURCES_DIR` # define meta fields -VIASH_META_NAME="qualimap" -VIASH_META_FUNCTIONALITY_NAME="qualimap" +VIASH_META_NAME="qualimap_rnaseq" +VIASH_META_FUNCTIONALITY_NAME="qualimap_rnaseq" VIASH_META_EXECUTABLE="$VIASH_META_RESOURCES_DIR/$VIASH_META_NAME" VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml" VIASH_META_TEMP_DIR="$VIASH_TEMP" @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "qualimap qualimap" + echo "qualimap_rnaseq qualimap" echo "" echo "Qualimap RNA-seq QC reports quality control metrics and bias estimations" echo "which are specific for whole transcriptome sequencing, including reads genomic" @@ -520,30 +520,15 @@ function ViashDockerfile { if [[ "$engine_id" == "docker" ]]; then cat << 'VIASHDOCKER' -FROM ubuntu:22.04 +FROM quay.io/biocontainers/qualimap:2.3--hdfd78af_0 ENTRYPOINT [] -RUN apt-get update && \ - DEBIAN_FRONTEND=noninteractive apt-get install -y r-base unzip wget openjdk-8-jdk libxml2-dev libcurl4-openssl-dev && \ - rm -rf /var/lib/apt/lists/* - -RUN wget https://bitbucket.org/kokonech/qualimap/downloads/qualimap_v2.3.zip && \ -unzip qualimap_v2.3.zip && \ -cp -a qualimap_v2.3/. usr/bin && \ -unset DISPLAY && \ -mkdir -p tmp && \ -export _JAVA_OPTIONS=-Djava.io.tmpdir=./tmp && \ -echo "qualimap: v2.3" > /var/software_versions.txt - -RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packages("remotes")' && \ - Rscript -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")' && \ - Rscript -e 'if (!requireNamespace("NOISeqr", quietly = TRUE)) BiocManager::install("NOISeqr")' && \ - Rscript -e 'remotes::install_cran(c("optparse"), repos = "https://cran.rstudio.com")' +RUN echo QualiMap: $(qualimap 2>&1 | grep QualiMap | sed 's/^.*QualiMap//') LABEL org.opencontainers.image.authors="Dorien Roosen" -LABEL org.opencontainers.image.description="Companion container for running component qualimap" -LABEL org.opencontainers.image.created="2024-08-20T21:04:56Z" +LABEL org.opencontainers.image.description="Companion container for running component qualimap qualimap_rnaseq" +LABEL org.opencontainers.image.created="2024-08-21T07:00:52Z" LABEL org.opencontainers.image.source="https://bitbucket.org/kokonech/qualimap/commits/branch/master" -LABEL org.opencontainers.image.revision="d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" +LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER @@ -667,7 +652,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "qualimap qualimap" + echo "qualimap_rnaseq qualimap" exit ;; --bam) @@ -866,7 +851,7 @@ if [[ "$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/qualimap:qualimap' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/qualimap/qualimap_rnaseq:qualimap' fi # print dockerfile @@ -1234,7 +1219,7 @@ fi ViashDebug "Running command: $(echo $VIASH_CMD)" cat << VIASHEOF | eval $VIASH_CMD set -e -tempscript=\$(mktemp "$VIASH_META_TEMP_DIR/viash-run-qualimap-XXXXXX").sh +tempscript=\$(mktemp "$VIASH_META_TEMP_DIR/viash-run-qualimap_rnaseq-XXXXXX").sh function clean_up { rm "\$tempscript" } diff --git a/target/executable/salmon/salmon_index/.config.vsh.yaml b/target/executable/salmon/salmon_index/.config.vsh.yaml index d8fc81a2..ad7a50f9 100644 --- a/target/executable/salmon/salmon_index/.config.vsh.yaml +++ b/target/executable/salmon/salmon_index/.config.vsh.yaml @@ -277,7 +277,7 @@ build_info: output: "target/executable/salmon/salmon_index" executable: "target/executable/salmon/salmon_index/salmon_index" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/salmon/salmon_index/salmon_index b/target/executable/salmon/salmon_index/salmon_index index 144c19b7..98beb8f9 100755 --- a/target/executable/salmon/salmon_index/salmon_index +++ b/target/executable/salmon/salmon_index/salmon_index @@ -545,9 +545,9 @@ RUN salmon index -v 2>&1 | sed 's/salmon \([0-9.]*\)/salmon: \1/' > /var/softwar LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa" LABEL org.opencontainers.image.description="Companion container for running component salmon salmon_index" -LABEL org.opencontainers.image.created="2024-08-20T21:05:04Z" +LABEL org.opencontainers.image.created="2024-08-21T07:00:59Z" LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon" -LABEL org.opencontainers.image.revision="d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" +LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER diff --git a/target/executable/salmon/salmon_quant/.config.vsh.yaml b/target/executable/salmon/salmon_quant/.config.vsh.yaml index 85e47720..392db5f7 100644 --- a/target/executable/salmon/salmon_quant/.config.vsh.yaml +++ b/target/executable/salmon/salmon_quant/.config.vsh.yaml @@ -1173,7 +1173,7 @@ build_info: output: "target/executable/salmon/salmon_quant" executable: "target/executable/salmon/salmon_quant/salmon_quant" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/salmon/salmon_quant/salmon_quant b/target/executable/salmon/salmon_quant/salmon_quant index 9fc4c908..e2e2d3a0 100755 --- a/target/executable/salmon/salmon_quant/salmon_quant +++ b/target/executable/salmon/salmon_quant/salmon_quant @@ -1167,9 +1167,9 @@ RUN salmon index -v 2>&1 | sed 's/salmon \([0-9.]*\)/salmon: \1/' > /var/softwar LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa" LABEL org.opencontainers.image.description="Companion container for running component salmon salmon_quant" -LABEL org.opencontainers.image.created="2024-08-20T21:05:04Z" +LABEL org.opencontainers.image.created="2024-08-21T07:00:59Z" LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon" -LABEL org.opencontainers.image.revision="d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" +LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER diff --git a/target/executable/samtools/samtools_collate/.config.vsh.yaml b/target/executable/samtools/samtools_collate/.config.vsh.yaml index b39bf21a..65a47b1f 100644 --- a/target/executable/samtools/samtools_collate/.config.vsh.yaml +++ b/target/executable/samtools/samtools_collate/.config.vsh.yaml @@ -264,7 +264,7 @@ build_info: output: "target/executable/samtools/samtools_collate" executable: "target/executable/samtools/samtools_collate/samtools_collate" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/samtools/samtools_collate/samtools_collate b/target/executable/samtools/samtools_collate/samtools_collate index b5975577..6fa838d3 100755 --- a/target/executable/samtools/samtools_collate/samtools_collate +++ b/target/executable/samtools/samtools_collate/samtools_collate @@ -518,9 +518,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_collate" -LABEL org.opencontainers.image.created="2024-08-20T21:04:55Z" +LABEL org.opencontainers.image.created="2024-08-21T07:00:51Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" +LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER diff --git a/target/executable/samtools/samtools_faidx/.config.vsh.yaml b/target/executable/samtools/samtools_faidx/.config.vsh.yaml index dc4e4ea4..043597d3 100644 --- a/target/executable/samtools/samtools_faidx/.config.vsh.yaml +++ b/target/executable/samtools/samtools_faidx/.config.vsh.yaml @@ -243,7 +243,7 @@ build_info: output: "target/executable/samtools/samtools_faidx" executable: "target/executable/samtools/samtools_faidx/samtools_faidx" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/samtools/samtools_faidx/samtools_faidx b/target/executable/samtools/samtools_faidx/samtools_faidx index 89d45c84..5e2db129 100755 --- a/target/executable/samtools/samtools_faidx/samtools_faidx +++ b/target/executable/samtools/samtools_faidx/samtools_faidx @@ -511,9 +511,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_faidx" -LABEL org.opencontainers.image.created="2024-08-20T21:04:54Z" +LABEL org.opencontainers.image.created="2024-08-21T07:00:50Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" +LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER diff --git a/target/executable/samtools/samtools_fasta/.config.vsh.yaml b/target/executable/samtools/samtools_fasta/.config.vsh.yaml index a26c8480..cfa6d480 100644 --- a/target/executable/samtools/samtools_fasta/.config.vsh.yaml +++ b/target/executable/samtools/samtools_fasta/.config.vsh.yaml @@ -433,7 +433,7 @@ build_info: output: "target/executable/samtools/samtools_fasta" executable: "target/executable/samtools/samtools_fasta/samtools_fasta" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/samtools/samtools_fasta/samtools_fasta b/target/executable/samtools/samtools_fasta/samtools_fasta index 123c3886..ec7567de 100755 --- a/target/executable/samtools/samtools_fasta/samtools_fasta +++ b/target/executable/samtools/samtools_fasta/samtools_fasta @@ -624,9 +624,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_fasta" -LABEL org.opencontainers.image.created="2024-08-20T21:04:55Z" +LABEL org.opencontainers.image.created="2024-08-21T07:00:51Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" +LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER diff --git a/target/executable/samtools/samtools_fastq/.config.vsh.yaml b/target/executable/samtools/samtools_fastq/.config.vsh.yaml index f6c2eb33..206c1215 100644 --- a/target/executable/samtools/samtools_fastq/.config.vsh.yaml +++ b/target/executable/samtools/samtools_fastq/.config.vsh.yaml @@ -433,7 +433,7 @@ build_info: output: "target/executable/samtools/samtools_fastq" executable: "target/executable/samtools/samtools_fastq/samtools_fastq" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/samtools/samtools_fastq/samtools_fastq b/target/executable/samtools/samtools_fastq/samtools_fastq index acde271b..e9ca7f26 100755 --- a/target/executable/samtools/samtools_fastq/samtools_fastq +++ b/target/executable/samtools/samtools_fastq/samtools_fastq @@ -625,9 +625,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_fastq" -LABEL org.opencontainers.image.created="2024-08-20T21:04:54Z" +LABEL org.opencontainers.image.created="2024-08-21T07:00:50Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" +LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER diff --git a/target/executable/samtools/samtools_flagstat/.config.vsh.yaml b/target/executable/samtools/samtools_flagstat/.config.vsh.yaml index 6a8f31e1..79b1a078 100644 --- a/target/executable/samtools/samtools_flagstat/.config.vsh.yaml +++ b/target/executable/samtools/samtools_flagstat/.config.vsh.yaml @@ -173,7 +173,7 @@ build_info: output: "target/executable/samtools/samtools_flagstat" executable: "target/executable/samtools/samtools_flagstat/samtools_flagstat" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/samtools/samtools_flagstat/samtools_flagstat b/target/executable/samtools/samtools_flagstat/samtools_flagstat index a360f0fc..9575aa54 100755 --- a/target/executable/samtools/samtools_flagstat/samtools_flagstat +++ b/target/executable/samtools/samtools_flagstat/samtools_flagstat @@ -473,9 +473,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_flagstat" -LABEL org.opencontainers.image.created="2024-08-20T21:04:54Z" +LABEL org.opencontainers.image.created="2024-08-21T07:00:50Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" +LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER diff --git a/target/executable/samtools/samtools_idxstats/.config.vsh.yaml b/target/executable/samtools/samtools_idxstats/.config.vsh.yaml index eaca3632..7ecd2a05 100644 --- a/target/executable/samtools/samtools_idxstats/.config.vsh.yaml +++ b/target/executable/samtools/samtools_idxstats/.config.vsh.yaml @@ -183,7 +183,7 @@ build_info: output: "target/executable/samtools/samtools_idxstats" executable: "target/executable/samtools/samtools_idxstats/samtools_idxstats" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/samtools/samtools_idxstats/samtools_idxstats b/target/executable/samtools/samtools_idxstats/samtools_idxstats index 6879fac6..63b3828d 100755 --- a/target/executable/samtools/samtools_idxstats/samtools_idxstats +++ b/target/executable/samtools/samtools_idxstats/samtools_idxstats @@ -477,9 +477,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_idxstats" -LABEL org.opencontainers.image.created="2024-08-20T21:04:53Z" +LABEL org.opencontainers.image.created="2024-08-21T07:00:49Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" +LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER diff --git a/target/executable/samtools/samtools_index/.config.vsh.yaml b/target/executable/samtools/samtools_index/.config.vsh.yaml index e7f0ad05..3b9f0223 100644 --- a/target/executable/samtools/samtools_index/.config.vsh.yaml +++ b/target/executable/samtools/samtools_index/.config.vsh.yaml @@ -189,7 +189,7 @@ build_info: output: "target/executable/samtools/samtools_index" executable: "target/executable/samtools/samtools_index/samtools_index" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/samtools/samtools_index/samtools_index b/target/executable/samtools/samtools_index/samtools_index index dcc71fc3..0f9cfd3c 100755 --- a/target/executable/samtools/samtools_index/samtools_index +++ b/target/executable/samtools/samtools_index/samtools_index @@ -484,9 +484,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_index" -LABEL org.opencontainers.image.created="2024-08-20T21:04:53Z" +LABEL org.opencontainers.image.created="2024-08-21T07:00:49Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" +LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER diff --git a/target/executable/samtools/samtools_sort/.config.vsh.yaml b/target/executable/samtools/samtools_sort/.config.vsh.yaml index 48168420..b6977ec8 100644 --- a/target/executable/samtools/samtools_sort/.config.vsh.yaml +++ b/target/executable/samtools/samtools_sort/.config.vsh.yaml @@ -332,7 +332,7 @@ build_info: output: "target/executable/samtools/samtools_sort" executable: "target/executable/samtools/samtools_sort/samtools_sort" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/samtools/samtools_sort/samtools_sort b/target/executable/samtools/samtools_sort/samtools_sort index c7062689..b5318209 100755 --- a/target/executable/samtools/samtools_sort/samtools_sort +++ b/target/executable/samtools/samtools_sort/samtools_sort @@ -555,9 +555,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_sort" -LABEL org.opencontainers.image.created="2024-08-20T21:04:55Z" +LABEL org.opencontainers.image.created="2024-08-21T07:00:51Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" +LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER diff --git a/target/executable/samtools/samtools_stats/.config.vsh.yaml b/target/executable/samtools/samtools_stats/.config.vsh.yaml index 999b9f22..cf2c0c31 100644 --- a/target/executable/samtools/samtools_stats/.config.vsh.yaml +++ b/target/executable/samtools/samtools_stats/.config.vsh.yaml @@ -401,7 +401,7 @@ build_info: output: "target/executable/samtools/samtools_stats" executable: "target/executable/samtools/samtools_stats/samtools_stats" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/samtools/samtools_stats/samtools_stats b/target/executable/samtools/samtools_stats/samtools_stats index fb2eaac1..5aaa5912 100755 --- a/target/executable/samtools/samtools_stats/samtools_stats +++ b/target/executable/samtools/samtools_stats/samtools_stats @@ -574,9 +574,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_stats" -LABEL org.opencontainers.image.created="2024-08-20T21:04:56Z" +LABEL org.opencontainers.image.created="2024-08-21T07:00:52Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" +LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER diff --git a/target/executable/samtools/samtools_view/.config.vsh.yaml b/target/executable/samtools/samtools_view/.config.vsh.yaml index b957e10a..d5b7454e 100644 --- a/target/executable/samtools/samtools_view/.config.vsh.yaml +++ b/target/executable/samtools/samtools_view/.config.vsh.yaml @@ -665,7 +665,7 @@ build_info: output: "target/executable/samtools/samtools_view" executable: "target/executable/samtools/samtools_view/samtools_view" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/samtools/samtools_view/samtools_view b/target/executable/samtools/samtools_view/samtools_view index ba2f358c..6c41658a 100755 --- a/target/executable/samtools/samtools_view/samtools_view +++ b/target/executable/samtools/samtools_view/samtools_view @@ -824,9 +824,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_view" -LABEL org.opencontainers.image.created="2024-08-20T21:04:53Z" +LABEL org.opencontainers.image.created="2024-08-21T07:00:49Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" +LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER diff --git a/target/executable/seqtk/seqtk_sample/.config.vsh.yaml b/target/executable/seqtk/seqtk_sample/.config.vsh.yaml index 9ca08a73..7cd94c97 100644 --- a/target/executable/seqtk/seqtk_sample/.config.vsh.yaml +++ b/target/executable/seqtk/seqtk_sample/.config.vsh.yaml @@ -173,7 +173,7 @@ build_info: output: "target/executable/seqtk/seqtk_sample" executable: "target/executable/seqtk/seqtk_sample/seqtk_sample" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/seqtk/seqtk_sample/seqtk_sample b/target/executable/seqtk/seqtk_sample/seqtk_sample index ba5e96bc..62625cae 100755 --- a/target/executable/seqtk/seqtk_sample/seqtk_sample +++ b/target/executable/seqtk/seqtk_sample/seqtk_sample @@ -480,9 +480,9 @@ FROM quay.io/biocontainers/seqtk:1.4--he4a0461_2 ENTRYPOINT [] LABEL org.opencontainers.image.authors="Jakub Majercik" LABEL org.opencontainers.image.description="Companion container for running component seqtk seqtk_sample" -LABEL org.opencontainers.image.created="2024-08-20T21:05:07Z" +LABEL org.opencontainers.image.created="2024-08-21T07:01:02Z" LABEL org.opencontainers.image.source="https://github.com/lh3/seqtk/tree/v1.4" -LABEL org.opencontainers.image.revision="d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" +LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER diff --git a/target/executable/seqtk/seqtk_subseq/.config.vsh.yaml b/target/executable/seqtk/seqtk_subseq/.config.vsh.yaml index c41ce46d..fbb142e7 100644 --- a/target/executable/seqtk/seqtk_subseq/.config.vsh.yaml +++ b/target/executable/seqtk/seqtk_subseq/.config.vsh.yaml @@ -196,7 +196,7 @@ build_info: output: "target/executable/seqtk/seqtk_subseq" executable: "target/executable/seqtk/seqtk_subseq/seqtk_subseq" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/seqtk/seqtk_subseq/seqtk_subseq b/target/executable/seqtk/seqtk_subseq/seqtk_subseq index 83b0fab6..31f14049 100755 --- a/target/executable/seqtk/seqtk_subseq/seqtk_subseq +++ b/target/executable/seqtk/seqtk_subseq/seqtk_subseq @@ -490,9 +490,9 @@ RUN echo $(echo $(seqtk 2>&1) | sed -n 's/.*\(Version: [^ ]*\).*/\1/p') > /var/s LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component seqtk seqtk_subseq" -LABEL org.opencontainers.image.created="2024-08-20T21:05:07Z" +LABEL org.opencontainers.image.created="2024-08-21T07:01:01Z" LABEL org.opencontainers.image.source="https://github.com/lh3/seqtk/tree/v1.4" -LABEL org.opencontainers.image.revision="d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" +LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER diff --git a/target/executable/star/star_align_reads/.config.vsh.yaml b/target/executable/star/star_align_reads/.config.vsh.yaml index 35b63179..1682696e 100644 --- a/target/executable/star/star_align_reads/.config.vsh.yaml +++ b/target/executable/star/star_align_reads/.config.vsh.yaml @@ -2663,7 +2663,7 @@ build_info: output: "target/executable/star/star_align_reads" executable: "target/executable/star/star_align_reads/star_align_reads" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/star/star_align_reads/star_align_reads b/target/executable/star/star_align_reads/star_align_reads index 24ae4e6b..ce95ead7 100755 --- a/target/executable/star/star_align_reads/star_align_reads +++ b/target/executable/star/star_align_reads/star_align_reads @@ -1919,9 +1919,9 @@ RUN STAR --version | sed 's#\(.*\)#star: "\1"#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component star star_align_reads" -LABEL org.opencontainers.image.created="2024-08-20T21:04:59Z" +LABEL org.opencontainers.image.created="2024-08-21T07:00:55Z" LABEL org.opencontainers.image.source="https://github.com/alexdobin/STAR" -LABEL org.opencontainers.image.revision="d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" +LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER diff --git a/target/executable/star/star_genome_generate/.config.vsh.yaml b/target/executable/star/star_genome_generate/.config.vsh.yaml index e3f4bc49..c3c6e902 100644 --- a/target/executable/star/star_genome_generate/.config.vsh.yaml +++ b/target/executable/star/star_genome_generate/.config.vsh.yaml @@ -333,7 +333,7 @@ build_info: output: "target/executable/star/star_genome_generate" executable: "target/executable/star/star_genome_generate/star_genome_generate" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/star/star_genome_generate/star_genome_generate b/target/executable/star/star_genome_generate/star_genome_generate index 1d8e6ae0..ddc58a1b 100755 --- a/target/executable/star/star_genome_generate/star_genome_generate +++ b/target/executable/star/star_genome_generate/star_genome_generate @@ -576,9 +576,9 @@ RUN STAR --version | sed 's#\(.*\)#star: "\1"#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa" LABEL org.opencontainers.image.description="Companion container for running component star star_genome_generate" -LABEL org.opencontainers.image.created="2024-08-20T21:04:59Z" +LABEL org.opencontainers.image.created="2024-08-21T07:00:54Z" LABEL org.opencontainers.image.source="https://github.com/alexdobin/STAR" -LABEL org.opencontainers.image.revision="d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" +LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER 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 324b21dd..b187d9c4 100644 --- a/target/executable/umi_tools/umi_tools_dedup/.config.vsh.yaml +++ b/target/executable/umi_tools/umi_tools_dedup/.config.vsh.yaml @@ -611,7 +611,7 @@ build_info: output: "target/executable/umi_tools/umi_tools_dedup" executable: "target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" 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 d3221208..6fdcf490 100755 --- a/target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup +++ b/target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup @@ -769,9 +769,9 @@ RUN umi_tools -v | sed 's/ version//g' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component umi_tools umi_tools_dedup" -LABEL org.opencontainers.image.created="2024-08-20T21:04:57Z" +LABEL org.opencontainers.image.created="2024-08-21T07:00:53Z" LABEL org.opencontainers.image.source="https://github.com/CGATOxford/UMI-tools" -LABEL org.opencontainers.image.revision="d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" +LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER diff --git a/target/executable/umi_tools/umi_tools_extract/.config.vsh.yaml b/target/executable/umi_tools/umi_tools_extract/.config.vsh.yaml index 92bc5e73..002b4103 100644 --- a/target/executable/umi_tools/umi_tools_extract/.config.vsh.yaml +++ b/target/executable/umi_tools/umi_tools_extract/.config.vsh.yaml @@ -449,7 +449,7 @@ build_info: output: "target/executable/umi_tools/umi_tools_extract" executable: "target/executable/umi_tools/umi_tools_extract/umi_tools_extract" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" 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 da80980c..360cd4bf 100755 --- a/target/executable/umi_tools/umi_tools_extract/umi_tools_extract +++ b/target/executable/umi_tools/umi_tools_extract/umi_tools_extract @@ -636,9 +636,9 @@ ENTRYPOINT [] RUN umi_tools -v | sed 's/ version//g' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component umi_tools umi_tools_extract" -LABEL org.opencontainers.image.created="2024-08-20T21:04:57Z" +LABEL org.opencontainers.image.created="2024-08-21T07:00:52Z" LABEL org.opencontainers.image.source="https://github.com/CGATOxford/UMI-tools" -LABEL org.opencontainers.image.revision="d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" +LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER diff --git a/target/nextflow/agat/agat_convert_bed2gff/.config.vsh.yaml b/target/nextflow/agat/agat_convert_bed2gff/.config.vsh.yaml index af7f58d2..9f6d207e 100644 --- a/target/nextflow/agat/agat_convert_bed2gff/.config.vsh.yaml +++ b/target/nextflow/agat/agat_convert_bed2gff/.config.vsh.yaml @@ -235,7 +235,7 @@ build_info: output: "target/nextflow/agat/agat_convert_bed2gff" executable: "target/nextflow/agat/agat_convert_bed2gff/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/agat/agat_convert_bed2gff/main.nf b/target/nextflow/agat/agat_convert_bed2gff/main.nf index 6be54ff1..dbf1d52c 100644 --- a/target/nextflow/agat/agat_convert_bed2gff/main.nf +++ b/target/nextflow/agat/agat_convert_bed2gff/main.nf @@ -3066,7 +3066,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/agat_convert_bed2gff", "viash_version" : "0.9.0-RC6", - "git_commit" : "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e", + "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/agat/agat_convert_embl2gff/.config.vsh.yaml b/target/nextflow/agat/agat_convert_embl2gff/.config.vsh.yaml index 596b6a48..172b7977 100644 --- a/target/nextflow/agat/agat_convert_embl2gff/.config.vsh.yaml +++ b/target/nextflow/agat/agat_convert_embl2gff/.config.vsh.yaml @@ -225,7 +225,7 @@ build_info: output: "target/nextflow/agat/agat_convert_embl2gff" executable: "target/nextflow/agat/agat_convert_embl2gff/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/agat/agat_convert_embl2gff/main.nf b/target/nextflow/agat/agat_convert_embl2gff/main.nf index f3fede9e..d8a0b66f 100644 --- a/target/nextflow/agat/agat_convert_embl2gff/main.nf +++ b/target/nextflow/agat/agat_convert_embl2gff/main.nf @@ -3059,7 +3059,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/agat_convert_embl2gff", "viash_version" : "0.9.0-RC6", - "git_commit" : "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e", + "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { 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 696e33be..3a393136 100644 --- a/target/nextflow/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml +++ b/target/nextflow/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml @@ -228,7 +228,7 @@ build_info: output: "target/nextflow/agat/agat_convert_sp_gff2gtf" executable: "target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf b/target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf index 4873ad06..0a4484c3 100644 --- a/target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf +++ b/target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf @@ -3042,7 +3042,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/agat_convert_sp_gff2gtf", "viash_version" : "0.9.0-RC6", - "git_commit" : "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e", + "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { 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 8bdcce58..ffaa82df 100644 --- a/target/nextflow/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml +++ b/target/nextflow/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml @@ -188,7 +188,7 @@ build_info: output: "target/nextflow/agat/agat_convert_sp_gff2tsv" executable: "target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf b/target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf index 583fb45e..92e07291 100644 --- a/target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf +++ b/target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf @@ -3020,7 +3020,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/agat_convert_sp_gff2tsv", "viash_version" : "0.9.0-RC6", - "git_commit" : "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e", + "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { 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 31e99f8c..76f64f38 100644 --- a/target/nextflow/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml +++ b/target/nextflow/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml @@ -195,7 +195,7 @@ build_info: output: "target/nextflow/agat/agat_convert_sp_gxf2gxf" executable: "target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf b/target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf index e961f977..b65d81d7 100644 --- a/target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf +++ b/target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf @@ -3020,7 +3020,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/agat_convert_sp_gxf2gxf", "viash_version" : "0.9.0-RC6", - "git_commit" : "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e", + "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/arriba/.config.vsh.yaml b/target/nextflow/arriba/.config.vsh.yaml index d16f15f4..53bf7152 100644 --- a/target/nextflow/arriba/.config.vsh.yaml +++ b/target/nextflow/arriba/.config.vsh.yaml @@ -706,7 +706,7 @@ build_info: output: "target/nextflow/arriba" executable: "target/nextflow/arriba/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/arriba/main.nf b/target/nextflow/arriba/main.nf index 85cfd2c3..17f7854c 100644 --- a/target/nextflow/arriba/main.nf +++ b/target/nextflow/arriba/main.nf @@ -3566,7 +3566,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/arriba", "viash_version" : "0.9.0-RC6", - "git_commit" : "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e", + "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/bcl_convert/.config.vsh.yaml b/target/nextflow/bcl_convert/.config.vsh.yaml index 7781a7e6..05c3a5bc 100644 --- a/target/nextflow/bcl_convert/.config.vsh.yaml +++ b/target/nextflow/bcl_convert/.config.vsh.yaml @@ -418,7 +418,7 @@ build_info: output: "target/nextflow/bcl_convert" executable: "target/nextflow/bcl_convert/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/bcl_convert/main.nf b/target/nextflow/bcl_convert/main.nf index 281c9079..216ba5ed 100644 --- a/target/nextflow/bcl_convert/main.nf +++ b/target/nextflow/bcl_convert/main.nf @@ -3303,7 +3303,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bcl_convert", "viash_version" : "0.9.0-RC6", - "git_commit" : "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e", + "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { 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 c2e436f0..bf772f6e 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 @@ -270,7 +270,7 @@ build_info: output: "target/nextflow/bd_rhapsody/bd_rhapsody_make_reference" executable: "target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" 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 bd2a8a82..0dcf2f37 100644 --- a/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf +++ b/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf @@ -3116,7 +3116,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bd_rhapsody/bd_rhapsody_make_reference", "viash_version" : "0.9.0-RC6", - "git_commit" : "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e", + "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/bedtools/bedtools_bamtofastq/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_bamtofastq/.config.vsh.yaml index e991cd5f..0960986c 100644 --- a/target/nextflow/bedtools/bedtools_bamtofastq/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_bamtofastq/.config.vsh.yaml @@ -187,7 +187,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_bamtofastq" executable: "target/nextflow/bedtools/bedtools_bamtofastq/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/bedtools/bedtools_bamtofastq/main.nf b/target/nextflow/bedtools/bedtools_bamtofastq/main.nf index 9d75ac2b..05cec1e0 100644 --- a/target/nextflow/bedtools/bedtools_bamtofastq/main.nf +++ b/target/nextflow/bedtools/bedtools_bamtofastq/main.nf @@ -3024,7 +3024,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_bamtofastq", "viash_version" : "0.9.0-RC6", - "git_commit" : "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e", + "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/bedtools/bedtools_bedtobam/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_bedtobam/.config.vsh.yaml index 2017821f..e199a7f4 100644 --- a/target/nextflow/bedtools/bedtools_bedtobam/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_bedtobam/.config.vsh.yaml @@ -214,7 +214,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_bedtobam" executable: "target/nextflow/bedtools/bedtools_bedtobam/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/bedtools/bedtools_bedtobam/main.nf b/target/nextflow/bedtools/bedtools_bedtobam/main.nf index f6fcb462..7e6a2864 100644 --- a/target/nextflow/bedtools/bedtools_bedtobam/main.nf +++ b/target/nextflow/bedtools/bedtools_bedtobam/main.nf @@ -3057,7 +3057,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_bedtobam", "viash_version" : "0.9.0-RC6", - "git_commit" : "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e", + "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml index f6f98f85..7a11efed 100644 --- a/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml @@ -232,7 +232,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_getfasta" executable: "target/nextflow/bedtools/bedtools_getfasta/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/bedtools/bedtools_getfasta/main.nf b/target/nextflow/bedtools/bedtools_getfasta/main.nf index 44f5d684..f36fcb88 100644 --- a/target/nextflow/bedtools/bedtools_getfasta/main.nf +++ b/target/nextflow/bedtools/bedtools_getfasta/main.nf @@ -3060,7 +3060,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_getfasta", "viash_version" : "0.9.0-RC6", - "git_commit" : "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e", + "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/bedtools/bedtools_intersect/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_intersect/.config.vsh.yaml index f0c936bd..adeb5d3a 100644 --- a/target/nextflow/bedtools/bedtools_intersect/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_intersect/.config.vsh.yaml @@ -410,7 +410,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_intersect" executable: "target/nextflow/bedtools/bedtools_intersect/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/bedtools/bedtools_intersect/main.nf b/target/nextflow/bedtools/bedtools_intersect/main.nf index 128b24cd..97854d68 100644 --- a/target/nextflow/bedtools/bedtools_intersect/main.nf +++ b/target/nextflow/bedtools/bedtools_intersect/main.nf @@ -3256,7 +3256,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_intersect", "viash_version" : "0.9.0-RC6", - "git_commit" : "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e", + "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/bedtools/bedtools_sort/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_sort/.config.vsh.yaml index 9c57d8f9..29a88ee8 100644 --- a/target/nextflow/bedtools/bedtools_sort/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_sort/.config.vsh.yaml @@ -222,7 +222,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_sort" executable: "target/nextflow/bedtools/bedtools_sort/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/bedtools/bedtools_sort/main.nf b/target/nextflow/bedtools/bedtools_sort/main.nf index 6b1a1b25..0914d594 100644 --- a/target/nextflow/bedtools/bedtools_sort/main.nf +++ b/target/nextflow/bedtools/bedtools_sort/main.nf @@ -3066,7 +3066,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_sort", "viash_version" : "0.9.0-RC6", - "git_commit" : "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e", + "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml b/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml index d781cff8..9cb32945 100644 --- a/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml +++ b/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml @@ -158,7 +158,7 @@ build_info: output: "target/nextflow/busco/busco_download_datasets" executable: "target/nextflow/busco/busco_download_datasets/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/busco/busco_download_datasets/main.nf b/target/nextflow/busco/busco_download_datasets/main.nf index 826ffb8d..1407b5c6 100644 --- a/target/nextflow/busco/busco_download_datasets/main.nf +++ b/target/nextflow/busco/busco_download_datasets/main.nf @@ -2985,7 +2985,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/busco/busco_download_datasets", "viash_version" : "0.9.0-RC6", - "git_commit" : "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e", + "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml b/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml index 9d2c55b8..907af319 100644 --- a/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml +++ b/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml @@ -145,7 +145,7 @@ build_info: output: "target/nextflow/busco/busco_list_datasets" executable: "target/nextflow/busco/busco_list_datasets/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/busco/busco_list_datasets/main.nf b/target/nextflow/busco/busco_list_datasets/main.nf index 4cf56aed..d407efa6 100644 --- a/target/nextflow/busco/busco_list_datasets/main.nf +++ b/target/nextflow/busco/busco_list_datasets/main.nf @@ -2971,7 +2971,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/busco/busco_list_datasets", "viash_version" : "0.9.0-RC6", - "git_commit" : "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e", + "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/busco/busco_run/.config.vsh.yaml b/target/nextflow/busco/busco_run/.config.vsh.yaml index 9b89ad2d..7af42796 100644 --- a/target/nextflow/busco/busco_run/.config.vsh.yaml +++ b/target/nextflow/busco/busco_run/.config.vsh.yaml @@ -423,7 +423,7 @@ build_info: output: "target/nextflow/busco/busco_run" executable: "target/nextflow/busco/busco_run/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/busco/busco_run/main.nf b/target/nextflow/busco/busco_run/main.nf index d6e59496..0680494a 100644 --- a/target/nextflow/busco/busco_run/main.nf +++ b/target/nextflow/busco/busco_run/main.nf @@ -3283,7 +3283,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/busco/busco_run", "viash_version" : "0.9.0-RC6", - "git_commit" : "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e", + "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/busco/busco_run/nextflow_schema.json b/target/nextflow/busco/busco_run/nextflow_schema.json deleted file mode 100644 index 64390d89..00000000 --- a/target/nextflow/busco/busco_run/nextflow_schema.json +++ /dev/null @@ -1,471 +0,0 @@ -{ -"$schema": "http://json-schema.org/draft-07/schema", -"title": "busco_run", -"description": "Assessment of genome assembly and annotation completeness with single copy orthologs", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "input": { - "type": - "string", - "description": "Type: `file`, required, example: `file.fasta`. Input sequence file in FASTA format", - "help_text": "Type: `file`, required, example: `file.fasta`. Input sequence file in FASTA format. Can be an assembled genome or transcriptome (DNA), or protein sequences from an annotated gene set. Also possible to use a path to a directory containing multiple input files.\n" - - } - - - , - "mode": { - "type": - "string", - "description": "Type: `string`, required, example: `proteins`, choices: ``genome`, `geno`, `transcriptome`, `tran`, `proteins`, `prot``. Specify which BUSCO analysis mode to run", - "help_text": "Type: `string`, required, example: `proteins`, choices: ``genome`, `geno`, `transcriptome`, `tran`, `proteins`, `prot``. Specify which BUSCO analysis mode to run. There are three valid modes:\n - geno or genome, for genome assemblies (DNA)\n - tran or transcriptome, for transcriptome assemblies (DNA)\n - prot or proteins, for annotated gene sets (protein)\n", - "enum": ["genome", "geno", "transcriptome", "tran", "proteins", "prot"] - - - } - - - , - "lineage_dataset": { - "type": - "string", - "description": "Type: `string`, example: `stramenopiles_odb10`. Specify a BUSCO lineage dataset that is most closely related to the assembly or gene set being assessed", - "help_text": "Type: `string`, example: `stramenopiles_odb10`. Specify a BUSCO lineage dataset that is most closely related to the assembly or gene set being assessed. \nThe full list of available datasets can be viewed [here](https://busco-data.ezlab.org/v5/data/lineages/) or by running the busco/busco_list_datasets component.\nWhen unsure, the \"--auto_lineage\" flag can be set to automatically find the optimal lineage path.\nBUSCO will automatically download the requested dataset if it is not already present in the download folder. \nYou can optionally provide a path to a local dataset instead of a name, e.g. path/to/dataset.\nDatasets can be downloaded using the busco/busco_download_dataset component.\n" - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "short_summary_json": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.short_summary_json.json`, example: `short_summary.json`. Output file for short summary in JSON format", - "help_text": "Type: `file`, default: `$id.$key.short_summary_json.json`, example: `short_summary.json`. Output file for short summary in JSON format.\n" - , - "default": "$id.$key.short_summary_json.json" - } - - - , - "short_summary_txt": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.short_summary_txt.txt`, example: `short_summary.txt`. Output file for short summary in TXT format", - "help_text": "Type: `file`, default: `$id.$key.short_summary_txt.txt`, example: `short_summary.txt`. Output file for short summary in TXT format.\n" - , - "default": "$id.$key.short_summary_txt.txt" - } - - - , - "full_table": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.full_table.tsv`, example: `full_table.tsv`. Full table output in TSV format", - "help_text": "Type: `file`, default: `$id.$key.full_table.tsv`, example: `full_table.tsv`. Full table output in TSV format.\n" - , - "default": "$id.$key.full_table.tsv" - } - - - , - "missing_busco_list": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.missing_busco_list.tsv`, example: `missing_busco_list.tsv`. Missing list output in TSV format", - "help_text": "Type: `file`, default: `$id.$key.missing_busco_list.tsv`, example: `missing_busco_list.tsv`. Missing list output in TSV format.\n" - , - "default": "$id.$key.missing_busco_list.tsv" - } - - - , - "output_dir": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.output_dir.output_dir`, example: `output_dir/`. The full output directory, if so desired", - "help_text": "Type: `file`, default: `$id.$key.output_dir.output_dir`, example: `output_dir/`. The full output directory, if so desired.\n" - , - "default": "$id.$key.output_dir.output_dir" - } - - -} -}, - - - "resource and run settings" : { - "title": "Resource and Run Settings", - "type": "object", - "description": "No description", - "properties": { - - - "force": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Force rewriting of existing files", - "help_text": "Type: `boolean_true`, default: `false`. Force rewriting of existing files. Must be used when output files with the provided name already exist.\n" - , - "default": "False" - } - - - , - "quiet": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Disable the info logs, displays only errors", - "help_text": "Type: `boolean_true`, default: `false`. Disable the info logs, displays only errors.\n" - , - "default": "False" - } - - - , - "restart": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Continue a run that had already partially completed", - "help_text": "Type: `boolean_true`, default: `false`. Continue a run that had already partially completed. Restarting skips calls to tools that have completed but performs all pre- and post-processing steps.\n" - , - "default": "False" - } - - - , - "tar": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Compress some subdirectories with many files to save space", - "help_text": "Type: `boolean_true`, default: `false`. Compress some subdirectories with many files to save space.\n" - , - "default": "False" - } - - -} -}, - - - "lineage dataset settings" : { - "title": "Lineage Dataset Settings", - "type": "object", - "description": "No description", - "properties": { - - - "auto_lineage": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Run auto-lineage pipelilne to automatically determine BUSCO lineage dataset that is most closely related to the assembly or gene set being assessed", - "help_text": "Type: `boolean_true`, default: `false`. Run auto-lineage pipelilne to automatically determine BUSCO lineage dataset that is most closely related to the assembly or gene set being assessed.\n" - , - "default": "False" - } - - - , - "auto_lineage_euk": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Run auto-placement just on eukaryota tree to find optimal lineage path", - "help_text": "Type: `boolean_true`, default: `false`. Run auto-placement just on eukaryota tree to find optimal lineage path.\n" - , - "default": "False" - } - - - , - "auto_lineage_prok": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Run auto_lineage just on prokaryota trees to find optimum lineage path", - "help_text": "Type: `boolean_true`, default: `false`. Run auto_lineage just on prokaryota trees to find optimum lineage path.\n" - , - "default": "False" - } - - - , - "datasets_version": { - "type": - "string", - "description": "Type: `string`, example: `odb10`. Specify the version of BUSCO datasets\n", - "help_text": "Type: `string`, example: `odb10`. Specify the version of BUSCO datasets\n" - - } - - -} -}, - - - "augustus settings" : { - "title": "Augustus Settings", - "type": "object", - "description": "No description", - "properties": { - - - "augustus": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Use augustus gene predictor for eukaryote runs", - "help_text": "Type: `boolean_true`, default: `false`. Use augustus gene predictor for eukaryote runs.\n" - , - "default": "False" - } - - - , - "augustus_parameters": { - "type": - "string", - "description": "Type: `string`, example: `--PARAM1=VALUE1,--PARAM2=VALUE2`. Additional parameters to be passed to Augustus (see Augustus documentation: https://github", - "help_text": "Type: `string`, example: `--PARAM1=VALUE1,--PARAM2=VALUE2`. Additional parameters to be passed to Augustus (see Augustus documentation: https://github.com/Gaius-Augustus/Augustus/blob/master/docs/RUNNING-AUGUSTUS.md).\nParameters should be contained within a single string, without whitespace and seperated by commas.\n" - - } - - - , - "augustus_species": { - "type": - "string", - "description": "Type: `string`. Specify the augustus species\n", - "help_text": "Type: `string`. Specify the augustus species\n" - - } - - - , - "long": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Optimize Augustus self-training mode", - "help_text": "Type: `boolean_true`, default: `false`. Optimize Augustus self-training mode. This adds considerably to the run time, but can improve results for some non-model organisms.\n" - , - "default": "False" - } - - -} -}, - - - "bbtools settings" : { - "title": "BBTools Settings", - "type": "object", - "description": "No description", - "properties": { - - - "contig_break": { - "type": - "integer", - "description": "Type: `integer`. Number of contiguous Ns to signify a break between contigs in BBTools analysis", - "help_text": "Type: `integer`. Number of contiguous Ns to signify a break between contigs in BBTools analysis.\n" - - } - - - , - "limit": { - "type": - "integer", - "description": "Type: `integer`. Number of candidate regions (contig or transcript) from the BLAST output to consider per BUSCO", - "help_text": "Type: `integer`. Number of candidate regions (contig or transcript) from the BLAST output to consider per BUSCO.\nThis option is only effective in pipelines using BLAST, i.e. the genome pipeline (see --augustus) or the prokaryota transcriptome pipeline.\n" - - } - - - , - "scaffold_composition": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Writes ACGTN content per scaffold to a file scaffold_composition", - "help_text": "Type: `boolean_true`, default: `false`. Writes ACGTN content per scaffold to a file scaffold_composition.txt.\n" - , - "default": "False" - } - - -} -}, - - - "blast settings" : { - "title": "BLAST Settings", - "type": "object", - "description": "No description", - "properties": { - - - "e_value": { - "type": - "number", - "description": "Type: `double`. E-value cutoff for BLAST searches", - "help_text": "Type: `double`. E-value cutoff for BLAST searches.\n" - - } - - -} -}, - - - "protein gene prediction settings" : { - "title": "Protein Gene Prediction settings", - "type": "object", - "description": "No description", - "properties": { - - - "miniprot": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Use Miniprot gene predictor", - "help_text": "Type: `boolean_true`, default: `false`. Use Miniprot gene predictor.\n" - , - "default": "False" - } - - -} -}, - - - "metaeuk settings" : { - "title": "MetaEuk Settings", - "type": "object", - "description": "No description", - "properties": { - - - "metaeuk": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Use Metaeuk gene predictor", - "help_text": "Type: `boolean_true`, default: `false`. Use Metaeuk gene predictor.\n" - , - "default": "False" - } - - - , - "metaeuk_parameters": { - "type": - "string", - "description": "Type: `string`, example: `--max-overlap=15,--min-exon-aa=15`. Pass additional arguments to Metaeuk for the first run (see Metaeuk documentation https://github", - "help_text": "Type: `string`, example: `--max-overlap=15,--min-exon-aa=15`. Pass additional arguments to Metaeuk for the first run (see Metaeuk documentation https://github.com/soedinglab/metaeuk).\nAll parameters should be contained within a single string with no white space, with each parameter separated by a comma.\n" - - } - - - , - "metaeuk_rerun_parameters": { - "type": - "string", - "description": "Type: `string`, example: `--max-overlap=15,--min-exon-aa=15`. Pass additional arguments to Metaeuk for the second run (see Metaeuk documentation https://github", - "help_text": "Type: `string`, example: `--max-overlap=15,--min-exon-aa=15`. Pass additional arguments to Metaeuk for the second run (see Metaeuk documentation https://github.com/soedinglab/metaeuk).\nAll parameters should be contained within a single string with no white space, with each parameter separated by a comma.\n" - - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" - }, - - { - "$ref": "#/definitions/outputs" - }, - - { - "$ref": "#/definitions/resource and run settings" - }, - - { - "$ref": "#/definitions/lineage dataset settings" - }, - - { - "$ref": "#/definitions/augustus settings" - }, - - { - "$ref": "#/definitions/bbtools settings" - }, - - { - "$ref": "#/definitions/blast settings" - }, - - { - "$ref": "#/definitions/protein gene prediction settings" - }, - - { - "$ref": "#/definitions/metaeuk settings" - }, - - { - "$ref": "#/definitions/nextflow input-output arguments" - } -] -} diff --git a/target/nextflow/cutadapt/.config.vsh.yaml b/target/nextflow/cutadapt/.config.vsh.yaml index 5720766c..7e526f2d 100644 --- a/target/nextflow/cutadapt/.config.vsh.yaml +++ b/target/nextflow/cutadapt/.config.vsh.yaml @@ -740,7 +740,7 @@ build_info: output: "target/nextflow/cutadapt" executable: "target/nextflow/cutadapt/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/cutadapt/main.nf b/target/nextflow/cutadapt/main.nf index 596d06ea..e037c66e 100644 --- a/target/nextflow/cutadapt/main.nf +++ b/target/nextflow/cutadapt/main.nf @@ -3593,7 +3593,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/cutadapt", "viash_version" : "0.9.0-RC6", - "git_commit" : "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e", + "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/falco/.config.vsh.yaml b/target/nextflow/falco/.config.vsh.yaml index 9fcca91b..249d747c 100644 --- a/target/nextflow/falco/.config.vsh.yaml +++ b/target/nextflow/falco/.config.vsh.yaml @@ -317,7 +317,7 @@ build_info: output: "target/nextflow/falco" executable: "target/nextflow/falco/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/falco/main.nf b/target/nextflow/falco/main.nf index 279be84c..7a41eb91 100644 --- a/target/nextflow/falco/main.nf +++ b/target/nextflow/falco/main.nf @@ -3144,7 +3144,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/falco", "viash_version" : "0.9.0-RC6", - "git_commit" : "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e", + "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/fastp/.config.vsh.yaml b/target/nextflow/fastp/.config.vsh.yaml index 2b51fc5d..a6343f34 100644 --- a/target/nextflow/fastp/.config.vsh.yaml +++ b/target/nextflow/fastp/.config.vsh.yaml @@ -1083,7 +1083,7 @@ build_info: output: "target/nextflow/fastp" executable: "target/nextflow/fastp/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/fastp/main.nf b/target/nextflow/fastp/main.nf index 65b1fbde..213b89d8 100644 --- a/target/nextflow/fastp/main.nf +++ b/target/nextflow/fastp/main.nf @@ -3997,7 +3997,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/fastp", "viash_version" : "0.9.0-RC6", - "git_commit" : "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e", + "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/featurecounts/.config.vsh.yaml b/target/nextflow/featurecounts/.config.vsh.yaml index 94cf136e..b6b8aff1 100644 --- a/target/nextflow/featurecounts/.config.vsh.yaml +++ b/target/nextflow/featurecounts/.config.vsh.yaml @@ -645,7 +645,7 @@ build_info: output: "target/nextflow/featurecounts" executable: "target/nextflow/featurecounts/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/featurecounts/main.nf b/target/nextflow/featurecounts/main.nf index 488cc02e..fa4ea6b8 100644 --- a/target/nextflow/featurecounts/main.nf +++ b/target/nextflow/featurecounts/main.nf @@ -3523,7 +3523,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/featurecounts", "viash_version" : "0.9.0-RC6", - "git_commit" : "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e", + "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/gffread/.config.vsh.yaml b/target/nextflow/gffread/.config.vsh.yaml index c8187142..6ec65249 100644 --- a/target/nextflow/gffread/.config.vsh.yaml +++ b/target/nextflow/gffread/.config.vsh.yaml @@ -685,7 +685,7 @@ build_info: output: "target/nextflow/gffread" executable: "target/nextflow/gffread/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/gffread/main.nf b/target/nextflow/gffread/main.nf index 84c082fa..b2b9c0f2 100644 --- a/target/nextflow/gffread/main.nf +++ b/target/nextflow/gffread/main.nf @@ -3580,7 +3580,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/gffread", "viash_version" : "0.9.0-RC6", - "git_commit" : "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e", + "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml b/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml index 68e1097d..07d76b28 100644 --- a/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml +++ b/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml @@ -507,7 +507,7 @@ build_info: output: "target/nextflow/lofreq/lofreq_call" executable: "target/nextflow/lofreq/lofreq_call/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/lofreq/lofreq_call/main.nf b/target/nextflow/lofreq/lofreq_call/main.nf index adec0e2a..476a775d 100644 --- a/target/nextflow/lofreq/lofreq_call/main.nf +++ b/target/nextflow/lofreq/lofreq_call/main.nf @@ -3388,7 +3388,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/lofreq/lofreq_call", "viash_version" : "0.9.0-RC6", - "git_commit" : "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e", + "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml b/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml index ff948e0b..afdc6819 100644 --- a/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml +++ b/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml @@ -215,7 +215,7 @@ build_info: output: "target/nextflow/lofreq/lofreq_indelqual" executable: "target/nextflow/lofreq/lofreq_indelqual/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/lofreq/lofreq_indelqual/main.nf b/target/nextflow/lofreq/lofreq_indelqual/main.nf index 40682c3c..22fae3cc 100644 --- a/target/nextflow/lofreq/lofreq_indelqual/main.nf +++ b/target/nextflow/lofreq/lofreq_indelqual/main.nf @@ -3051,7 +3051,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/lofreq/lofreq_indelqual", "viash_version" : "0.9.0-RC6", - "git_commit" : "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e", + "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/lofreq/lofreq_indelqual/nextflow_schema.json b/target/nextflow/lofreq/lofreq_indelqual/nextflow_schema.json deleted file mode 100644 index fc09ea50..00000000 --- a/target/nextflow/lofreq/lofreq_indelqual/nextflow_schema.json +++ /dev/null @@ -1,151 +0,0 @@ -{ -"$schema": "http://json-schema.org/draft-07/schema", -"title": "lofreq_indelqual", -"description": "Insert indel qualities into BAM file (required for indel predictions).\n\nThe preferred way of inserting indel qualities should be via GATK\u0027s BQSR (\u003e=2) If that\u0027s not possible, use this subcommand.\nThe command has two modes: \u0027uniform\u0027 and \u0027dindel\u0027:\n- \u0027uniform\u0027 will assign a given value uniformly, whereas\n- \u0027dindel\u0027 will insert indel qualities based on Dindel (PMID 20980555).\nBoth will overwrite any existing values.\nDo not realign your BAM file afterwards!\n", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "input": { - "type": - "string", - "description": "Type: `file`, required, example: `normal.bam`. Input BAM file", - "help_text": "Type: `file`, required, example: `normal.bam`. Input BAM file.\n" - - } - - - , - "ref": { - "type": - "string", - "description": "Type: `file`, example: `reference.fasta`. Reference sequence used for mapping (Only required for --dindel)", - "help_text": "Type: `file`, example: `reference.fasta`. Reference sequence used for mapping (Only required for --dindel).\n" - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "out": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.out.bam`, example: `output.bam`. Output BAM file", - "help_text": "Type: `file`, required, default: `$id.$key.out.bam`, example: `output.bam`. Output BAM file.\n" - , - "default": "$id.$key.out.bam" - } - - -} -}, - - - "arguments" : { - "title": "Arguments", - "type": "object", - "description": "No description", - "properties": { - - - "uniform": { - "type": - "string", - "description": "Type: `string`, example: `50,50`. Add this indel quality uniformly to all bases", - "help_text": "Type: `string`, example: `50,50`. Add this indel quality uniformly to all bases. Use two comma separated values to specify insertion and deletion quality separately. (clashes with --dindel).\n" - - } - - - , - "dindel": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Add Dindel\u0027s indel qualities (Illumina specific) (clashes with -u; needs --ref)", - "help_text": "Type: `boolean_true`, default: `false`. Add Dindel\u0027s indel qualities (Illumina specific) (clashes with -u; needs --ref).\n" - , - "default": "False" - } - - - , - "verbose": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Be verbose", - "help_text": "Type: `boolean_true`, default: `false`. Be verbose.\n" - , - "default": "False" - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" - }, - - { - "$ref": "#/definitions/outputs" - }, - - { - "$ref": "#/definitions/arguments" - }, - - { - "$ref": "#/definitions/nextflow input-output arguments" - } -] -} diff --git a/target/nextflow/multiqc/.config.vsh.yaml b/target/nextflow/multiqc/.config.vsh.yaml index 8a75bc2d..982b9e76 100644 --- a/target/nextflow/multiqc/.config.vsh.yaml +++ b/target/nextflow/multiqc/.config.vsh.yaml @@ -456,7 +456,7 @@ build_info: output: "target/nextflow/multiqc" executable: "target/nextflow/multiqc/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/multiqc/main.nf b/target/nextflow/multiqc/main.nf index 612220a4..3014c2c6 100644 --- a/target/nextflow/multiqc/main.nf +++ b/target/nextflow/multiqc/main.nf @@ -3340,7 +3340,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/multiqc", "viash_version" : "0.9.0-RC6", - "git_commit" : "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e", + "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/pear/.config.vsh.yaml b/target/nextflow/pear/.config.vsh.yaml index 06eea9ae..ca6e4455 100644 --- a/target/nextflow/pear/.config.vsh.yaml +++ b/target/nextflow/pear/.config.vsh.yaml @@ -398,7 +398,7 @@ build_info: output: "target/nextflow/pear" executable: "target/nextflow/pear/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/pear/main.nf b/target/nextflow/pear/main.nf index c6c769b4..3c47d2bd 100644 --- a/target/nextflow/pear/main.nf +++ b/target/nextflow/pear/main.nf @@ -3233,7 +3233,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/pear", "viash_version" : "0.9.0-RC6", - "git_commit" : "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e", + "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/qualimap/.config.vsh.yaml b/target/nextflow/qualimap/qualimap_rnaseq/.config.vsh.yaml similarity index 91% rename from target/nextflow/qualimap/.config.vsh.yaml rename to target/nextflow/qualimap/qualimap_rnaseq/.config.vsh.yaml index bfe73661..bff4c40c 100644 --- a/target/nextflow/qualimap/.config.vsh.yaml +++ b/target/nextflow/qualimap/qualimap_rnaseq/.config.vsh.yaml @@ -1,4 +1,5 @@ -name: "qualimap" +name: "qualimap_rnaseq" +namespace: "qualimap" version: "qualimap" authors: - name: "Dorien Roosen" @@ -244,32 +245,14 @@ runners: engines: - type: "docker" id: "docker" - image: "ubuntu:22.04" + image: "quay.io/biocontainers/qualimap:2.3--hdfd78af_0" target_registry: "images.viash-hub.com" target_tag: "qualimap" namespace_separator: "/" setup: - - type: "apt" - packages: - - "r-base" - - "unzip" - - "wget" - - "openjdk-8-jdk" - - "libxml2-dev" - - "libcurl4-openssl-dev" - interactive: false - type: "docker" run: - - "wget https://bitbucket.org/kokonech/qualimap/downloads/qualimap_v2.3.zip &&\ - \ \\\nunzip qualimap_v2.3.zip && \\\ncp -a qualimap_v2.3/. usr/bin && \\\nunset\ - \ DISPLAY && \\\nmkdir -p tmp && \\\nexport _JAVA_OPTIONS=-Djava.io.tmpdir=./tmp\ - \ && \\\necho \"qualimap: v2.3\" > /var/software_versions.txt\n" - - type: "r" - cran: - - "optparse" - bioc: - - "NOISeqr" - bioc_force_install: false + - "echo QualiMap: $(qualimap 2>&1 | grep QualiMap | sed 's/^.*QualiMap//')\n" entrypoint: [] cmd: null - type: "native" @@ -278,10 +261,10 @@ build_info: config: "src/qualimap/qualimap_rnaseq/config.vsh.yaml" runner: "nextflow" engine: "docker|native" - output: "target/nextflow/qualimap" - executable: "target/nextflow/qualimap/main.nf" + output: "target/nextflow/qualimap/qualimap_rnaseq" + executable: "target/nextflow/qualimap/qualimap_rnaseq/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/qualimap/main.nf b/target/nextflow/qualimap/qualimap_rnaseq/main.nf similarity index 99% rename from target/nextflow/qualimap/main.nf rename to target/nextflow/qualimap/qualimap_rnaseq/main.nf index 43aa34e3..fd132076 100644 --- a/target/nextflow/qualimap/main.nf +++ b/target/nextflow/qualimap/qualimap_rnaseq/main.nf @@ -1,4 +1,4 @@ -// qualimap qualimap +// qualimap_rnaseq qualimap // // This wrapper script is auto-generated by viash 0.9.0-RC6 and is thus a // derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from @@ -2781,7 +2781,8 @@ nextflow.enable.dsl=2 meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ - "name" : "qualimap", + "name" : "qualimap_rnaseq", + "namespace" : "qualimap", "version" : "qualimap", "authors" : [ { @@ -3078,38 +3079,16 @@ meta = [ { "type" : "docker", "id" : "docker", - "image" : "ubuntu:22.04", + "image" : "quay.io/biocontainers/qualimap:2.3--hdfd78af_0", "target_registry" : "images.viash-hub.com", "target_tag" : "qualimap", "namespace_separator" : "/", "setup" : [ - { - "type" : "apt", - "packages" : [ - "r-base", - "unzip", - "wget", - "openjdk-8-jdk", - "libxml2-dev", - "libcurl4-openssl-dev" - ], - "interactive" : false - }, { "type" : "docker", "run" : [ - "wget https://bitbucket.org/kokonech/qualimap/downloads/qualimap_v2.3.zip && \\\\\nunzip qualimap_v2.3.zip && \\\\\ncp -a qualimap_v2.3/. usr/bin && \\\\\nunset DISPLAY && \\\\\nmkdir -p tmp && \\\\\nexport _JAVA_OPTIONS=-Djava.io.tmpdir=./tmp && \\\\\necho \\"qualimap: v2.3\\" > /var/software_versions.txt\n" + "echo QualiMap: $(qualimap 2>&1 | grep QualiMap | sed 's/^.*QualiMap//')\n" ] - }, - { - "type" : "r", - "cran" : [ - "optparse" - ], - "bioc" : [ - "NOISeqr" - ], - "bioc_force_install" : false } ] }, @@ -3122,9 +3101,9 @@ meta = [ "config" : "/workdir/root/repo/src/qualimap/qualimap_rnaseq/config.vsh.yaml", "runner" : "nextflow", "engine" : "docker|native", - "output" : "target/nextflow/qualimap", + "output" : "target/nextflow/qualimap/qualimap_rnaseq", "viash_version" : "0.9.0-RC6", - "git_commit" : "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e", + "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -3603,7 +3582,7 @@ meta["defaults"] = [ directives: readJsonBlob('''{ "container" : { "registry" : "images.viash-hub.com", - "image" : "vsh/biobox/qualimap", + "image" : "vsh/biobox/qualimap/qualimap_rnaseq", "tag" : "qualimap" }, "tag" : "$id" diff --git a/target/nextflow/qualimap/nextflow.config b/target/nextflow/qualimap/qualimap_rnaseq/nextflow.config similarity index 99% rename from target/nextflow/qualimap/nextflow.config rename to target/nextflow/qualimap/qualimap_rnaseq/nextflow.config index 3d07fc6b..e3085afe 100644 --- a/target/nextflow/qualimap/nextflow.config +++ b/target/nextflow/qualimap/qualimap_rnaseq/nextflow.config @@ -1,5 +1,5 @@ manifest { - name = 'qualimap' + name = 'qualimap/qualimap_rnaseq' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' version = 'qualimap' diff --git a/target/nextflow/qualimap/nextflow_schema.json b/target/nextflow/qualimap/qualimap_rnaseq/nextflow_schema.json similarity index 99% rename from target/nextflow/qualimap/nextflow_schema.json rename to target/nextflow/qualimap/qualimap_rnaseq/nextflow_schema.json index 2c7afc31..aaf2e054 100644 --- a/target/nextflow/qualimap/nextflow_schema.json +++ b/target/nextflow/qualimap/qualimap_rnaseq/nextflow_schema.json @@ -1,6 +1,6 @@ { "$schema": "http://json-schema.org/draft-07/schema", -"title": "qualimap", +"title": "qualimap_rnaseq", "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\u2019-3\u2019 bias computation.\n", "type": "object", "definitions": { diff --git a/target/nextflow/salmon/salmon_index/.config.vsh.yaml b/target/nextflow/salmon/salmon_index/.config.vsh.yaml index 2f9b9a3d..1b451807 100644 --- a/target/nextflow/salmon/salmon_index/.config.vsh.yaml +++ b/target/nextflow/salmon/salmon_index/.config.vsh.yaml @@ -277,7 +277,7 @@ build_info: output: "target/nextflow/salmon/salmon_index" executable: "target/nextflow/salmon/salmon_index/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/salmon/salmon_index/main.nf b/target/nextflow/salmon/salmon_index/main.nf index 3f4ccffb..11164449 100644 --- a/target/nextflow/salmon/salmon_index/main.nf +++ b/target/nextflow/salmon/salmon_index/main.nf @@ -3103,7 +3103,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/salmon/salmon_index", "viash_version" : "0.9.0-RC6", - "git_commit" : "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e", + "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/salmon/salmon_quant/.config.vsh.yaml b/target/nextflow/salmon/salmon_quant/.config.vsh.yaml index e5c1d818..38979ae3 100644 --- a/target/nextflow/salmon/salmon_quant/.config.vsh.yaml +++ b/target/nextflow/salmon/salmon_quant/.config.vsh.yaml @@ -1173,7 +1173,7 @@ build_info: output: "target/nextflow/salmon/salmon_quant" executable: "target/nextflow/salmon/salmon_quant/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/salmon/salmon_quant/main.nf b/target/nextflow/salmon/salmon_quant/main.nf index 3eacfa8c..7d0de287 100644 --- a/target/nextflow/salmon/salmon_quant/main.nf +++ b/target/nextflow/salmon/salmon_quant/main.nf @@ -3938,7 +3938,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/salmon/salmon_quant", "viash_version" : "0.9.0-RC6", - "git_commit" : "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e", + "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/samtools/samtools_collate/.config.vsh.yaml b/target/nextflow/samtools/samtools_collate/.config.vsh.yaml index 1ff4d307..e0563f7d 100644 --- a/target/nextflow/samtools/samtools_collate/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_collate/.config.vsh.yaml @@ -264,7 +264,7 @@ build_info: output: "target/nextflow/samtools/samtools_collate" executable: "target/nextflow/samtools/samtools_collate/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/samtools/samtools_collate/main.nf b/target/nextflow/samtools/samtools_collate/main.nf index 10f43299..827fadae 100644 --- a/target/nextflow/samtools/samtools_collate/main.nf +++ b/target/nextflow/samtools/samtools_collate/main.nf @@ -3114,7 +3114,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_collate", "viash_version" : "0.9.0-RC6", - "git_commit" : "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e", + "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml b/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml index 2eb22415..e4b0062d 100644 --- a/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml @@ -243,7 +243,7 @@ build_info: output: "target/nextflow/samtools/samtools_faidx" executable: "target/nextflow/samtools/samtools_faidx/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/samtools/samtools_faidx/main.nf b/target/nextflow/samtools/samtools_faidx/main.nf index a42a3257..61b1e2a3 100644 --- a/target/nextflow/samtools/samtools_faidx/main.nf +++ b/target/nextflow/samtools/samtools_faidx/main.nf @@ -3086,7 +3086,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_faidx", "viash_version" : "0.9.0-RC6", - "git_commit" : "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e", + "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/samtools/samtools_fasta/.config.vsh.yaml b/target/nextflow/samtools/samtools_fasta/.config.vsh.yaml index 0e2dd1fc..28bc252a 100644 --- a/target/nextflow/samtools/samtools_fasta/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_fasta/.config.vsh.yaml @@ -433,7 +433,7 @@ build_info: output: "target/nextflow/samtools/samtools_fasta" executable: "target/nextflow/samtools/samtools_fasta/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/samtools/samtools_fasta/main.nf b/target/nextflow/samtools/samtools_fasta/main.nf index 761c69c4..9a92aae7 100644 --- a/target/nextflow/samtools/samtools_fasta/main.nf +++ b/target/nextflow/samtools/samtools_fasta/main.nf @@ -3278,7 +3278,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_fasta", "viash_version" : "0.9.0-RC6", - "git_commit" : "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e", + "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml b/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml index 76c09189..e68b3220 100644 --- a/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml @@ -433,7 +433,7 @@ build_info: output: "target/nextflow/samtools/samtools_fastq" executable: "target/nextflow/samtools/samtools_fastq/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/samtools/samtools_fastq/main.nf b/target/nextflow/samtools/samtools_fastq/main.nf index 2f7ea61c..b1e85156 100644 --- a/target/nextflow/samtools/samtools_fastq/main.nf +++ b/target/nextflow/samtools/samtools_fastq/main.nf @@ -3278,7 +3278,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_fastq", "viash_version" : "0.9.0-RC6", - "git_commit" : "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e", + "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml b/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml index 300456f9..b4d17f34 100644 --- a/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml @@ -173,7 +173,7 @@ build_info: output: "target/nextflow/samtools/samtools_flagstat" executable: "target/nextflow/samtools/samtools_flagstat/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/samtools/samtools_flagstat/main.nf b/target/nextflow/samtools/samtools_flagstat/main.nf index 5ac2a34c..c332943d 100644 --- a/target/nextflow/samtools/samtools_flagstat/main.nf +++ b/target/nextflow/samtools/samtools_flagstat/main.nf @@ -3002,7 +3002,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_flagstat", "viash_version" : "0.9.0-RC6", - "git_commit" : "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e", + "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml b/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml index 2b49e823..90ea03bb 100644 --- a/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml @@ -183,7 +183,7 @@ build_info: output: "target/nextflow/samtools/samtools_idxstats" executable: "target/nextflow/samtools/samtools_idxstats/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/samtools/samtools_idxstats/main.nf b/target/nextflow/samtools/samtools_idxstats/main.nf index 454e65e3..6b828d53 100644 --- a/target/nextflow/samtools/samtools_idxstats/main.nf +++ b/target/nextflow/samtools/samtools_idxstats/main.nf @@ -3014,7 +3014,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_idxstats", "viash_version" : "0.9.0-RC6", - "git_commit" : "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e", + "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/samtools/samtools_index/.config.vsh.yaml b/target/nextflow/samtools/samtools_index/.config.vsh.yaml index 79574a03..0c67a6b0 100644 --- a/target/nextflow/samtools/samtools_index/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_index/.config.vsh.yaml @@ -189,7 +189,7 @@ build_info: output: "target/nextflow/samtools/samtools_index" executable: "target/nextflow/samtools/samtools_index/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/samtools/samtools_index/main.nf b/target/nextflow/samtools/samtools_index/main.nf index 14b671fa..abc08324 100644 --- a/target/nextflow/samtools/samtools_index/main.nf +++ b/target/nextflow/samtools/samtools_index/main.nf @@ -3027,7 +3027,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_index", "viash_version" : "0.9.0-RC6", - "git_commit" : "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e", + "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/samtools/samtools_sort/.config.vsh.yaml b/target/nextflow/samtools/samtools_sort/.config.vsh.yaml index e5e58c78..8a7b8834 100644 --- a/target/nextflow/samtools/samtools_sort/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_sort/.config.vsh.yaml @@ -332,7 +332,7 @@ build_info: output: "target/nextflow/samtools/samtools_sort" executable: "target/nextflow/samtools/samtools_sort/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/samtools/samtools_sort/main.nf b/target/nextflow/samtools/samtools_sort/main.nf index 7659fede..991bbc26 100644 --- a/target/nextflow/samtools/samtools_sort/main.nf +++ b/target/nextflow/samtools/samtools_sort/main.nf @@ -3199,7 +3199,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_sort", "viash_version" : "0.9.0-RC6", - "git_commit" : "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e", + "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/samtools/samtools_stats/.config.vsh.yaml b/target/nextflow/samtools/samtools_stats/.config.vsh.yaml index 868fe861..1ee0c9c3 100644 --- a/target/nextflow/samtools/samtools_stats/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_stats/.config.vsh.yaml @@ -401,7 +401,7 @@ build_info: output: "target/nextflow/samtools/samtools_stats" executable: "target/nextflow/samtools/samtools_stats/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/samtools/samtools_stats/main.nf b/target/nextflow/samtools/samtools_stats/main.nf index 771107f2..83749a85 100644 --- a/target/nextflow/samtools/samtools_stats/main.nf +++ b/target/nextflow/samtools/samtools_stats/main.nf @@ -3269,7 +3269,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_stats", "viash_version" : "0.9.0-RC6", - "git_commit" : "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e", + "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/samtools/samtools_view/.config.vsh.yaml b/target/nextflow/samtools/samtools_view/.config.vsh.yaml index 97764ddb..6fd652fb 100644 --- a/target/nextflow/samtools/samtools_view/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_view/.config.vsh.yaml @@ -665,7 +665,7 @@ build_info: output: "target/nextflow/samtools/samtools_view" executable: "target/nextflow/samtools/samtools_view/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/samtools/samtools_view/main.nf b/target/nextflow/samtools/samtools_view/main.nf index 19beb21b..52ef1e75 100644 --- a/target/nextflow/samtools/samtools_view/main.nf +++ b/target/nextflow/samtools/samtools_view/main.nf @@ -3450,7 +3450,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_view", "viash_version" : "0.9.0-RC6", - "git_commit" : "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e", + "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/seqtk/seqtk_sample/.config.vsh.yaml b/target/nextflow/seqtk/seqtk_sample/.config.vsh.yaml index 149ee141..d8eb835a 100644 --- a/target/nextflow/seqtk/seqtk_sample/.config.vsh.yaml +++ b/target/nextflow/seqtk/seqtk_sample/.config.vsh.yaml @@ -173,7 +173,7 @@ build_info: output: "target/nextflow/seqtk/seqtk_sample" executable: "target/nextflow/seqtk/seqtk_sample/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/seqtk/seqtk_sample/main.nf b/target/nextflow/seqtk/seqtk_sample/main.nf index 652527c2..7f8dd131 100644 --- a/target/nextflow/seqtk/seqtk_sample/main.nf +++ b/target/nextflow/seqtk/seqtk_sample/main.nf @@ -3004,7 +3004,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/seqtk/seqtk_sample", "viash_version" : "0.9.0-RC6", - "git_commit" : "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e", + "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/seqtk/seqtk_subseq/.config.vsh.yaml b/target/nextflow/seqtk/seqtk_subseq/.config.vsh.yaml index 34125352..10afff7b 100644 --- a/target/nextflow/seqtk/seqtk_subseq/.config.vsh.yaml +++ b/target/nextflow/seqtk/seqtk_subseq/.config.vsh.yaml @@ -196,7 +196,7 @@ build_info: output: "target/nextflow/seqtk/seqtk_subseq" executable: "target/nextflow/seqtk/seqtk_subseq/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/seqtk/seqtk_subseq/main.nf b/target/nextflow/seqtk/seqtk_subseq/main.nf index 3bcd350d..30176bf6 100644 --- a/target/nextflow/seqtk/seqtk_subseq/main.nf +++ b/target/nextflow/seqtk/seqtk_subseq/main.nf @@ -3034,7 +3034,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/seqtk/seqtk_subseq", "viash_version" : "0.9.0-RC6", - "git_commit" : "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e", + "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/star/star_align_reads/.config.vsh.yaml b/target/nextflow/star/star_align_reads/.config.vsh.yaml index a348b04c..77f86191 100644 --- a/target/nextflow/star/star_align_reads/.config.vsh.yaml +++ b/target/nextflow/star/star_align_reads/.config.vsh.yaml @@ -2663,7 +2663,7 @@ build_info: output: "target/nextflow/star/star_align_reads" executable: "target/nextflow/star/star_align_reads/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/star/star_align_reads/main.nf b/target/nextflow/star/star_align_reads/main.nf index dc2844b6..1886f2bc 100644 --- a/target/nextflow/star/star_align_reads/main.nf +++ b/target/nextflow/star/star_align_reads/main.nf @@ -5917,7 +5917,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/star/star_align_reads", "viash_version" : "0.9.0-RC6", - "git_commit" : "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e", + "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/star/star_genome_generate/.config.vsh.yaml b/target/nextflow/star/star_genome_generate/.config.vsh.yaml index 686f5f9e..4324d0d1 100644 --- a/target/nextflow/star/star_genome_generate/.config.vsh.yaml +++ b/target/nextflow/star/star_genome_generate/.config.vsh.yaml @@ -333,7 +333,7 @@ build_info: output: "target/nextflow/star/star_genome_generate" executable: "target/nextflow/star/star_genome_generate/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/star/star_genome_generate/main.nf b/target/nextflow/star/star_genome_generate/main.nf index 8ce75b95..2b364228 100644 --- a/target/nextflow/star/star_genome_generate/main.nf +++ b/target/nextflow/star/star_genome_generate/main.nf @@ -3169,7 +3169,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/star/star_genome_generate", "viash_version" : "0.9.0-RC6", - "git_commit" : "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e", + "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { 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 ba9d6592..90ac782a 100644 --- a/target/nextflow/umi_tools/umi_tools_dedup/.config.vsh.yaml +++ b/target/nextflow/umi_tools/umi_tools_dedup/.config.vsh.yaml @@ -611,7 +611,7 @@ build_info: output: "target/nextflow/umi_tools/umi_tools_dedup" executable: "target/nextflow/umi_tools/umi_tools_dedup/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/umi_tools/umi_tools_dedup/main.nf b/target/nextflow/umi_tools/umi_tools_dedup/main.nf index b09df550..f0d33bd6 100644 --- a/target/nextflow/umi_tools/umi_tools_dedup/main.nf +++ b/target/nextflow/umi_tools/umi_tools_dedup/main.nf @@ -3461,7 +3461,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/umi_tools/umi_tools_dedup", "viash_version" : "0.9.0-RC6", - "git_commit" : "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e", + "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { 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 9dab261a..2cd0f1f7 100644 --- a/target/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml +++ b/target/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml @@ -449,7 +449,7 @@ build_info: output: "target/nextflow/umi_tools/umi_tools_extract" executable: "target/nextflow/umi_tools/umi_tools_extract/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e" + git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/umi_tools/umi_tools_extract/main.nf b/target/nextflow/umi_tools/umi_tools_extract/main.nf index 20d47517..38413b45 100644 --- a/target/nextflow/umi_tools/umi_tools_extract/main.nf +++ b/target/nextflow/umi_tools/umi_tools_extract/main.nf @@ -3290,7 +3290,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/umi_tools/umi_tools_extract", "viash_version" : "0.9.0-RC6", - "git_commit" : "d476dee6bdcf7ee5444385acbfa0d1d3ae06557e", + "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : {