From 62ee7eb00143dbe631d0522abfb5b0dfd7143ddd Mon Sep 17 00:00:00 2001 From: CI Date: Tue, 20 Aug 2024 21:20:44 +0000 Subject: [PATCH] Build branch qualimap with version qualimap (75e5f79) Build pipeline: viash-hub.biobox.qualimap-2ndms Source commit: https://github.com/viash-hub/biobox/commit/75e5f792a43356af870bc580059461ba8810c0ec Source message: Update CHANGELOG.md --- CHANGELOG.md | 8 +- .../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 +- target/executable/qualimap/.config.vsh.yaml | 2 +- target/executable/qualimap/qualimap | 4 +- .../salmon/salmon_index/.config.vsh.yaml | 2 +- .../salmon/salmon_index/salmon_index | 4 +- .../salmon/salmon_quant/.config.vsh.yaml | 2 +- .../salmon/salmon_quant/salmon_quant | 4 +- .../samtools_collate/.config.vsh.yaml | 2 +- .../samtools_collate/samtools_collate | 4 +- .../samtools/samtools_faidx/.config.vsh.yaml | 2 +- .../samtools/samtools_faidx/samtools_faidx | 4 +- .../samtools/samtools_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 +- 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 +- 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 +- target/nextflow/qualimap/.config.vsh.yaml | 2 +- target/nextflow/qualimap/main.nf | 2 +- .../salmon/salmon_index/.config.vsh.yaml | 2 +- target/nextflow/salmon/salmon_index/main.nf | 2 +- .../salmon/salmon_quant/.config.vsh.yaml | 2 +- target/nextflow/salmon/salmon_quant/main.nf | 2 +- .../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_fasta/nextflow_schema.json | 348 ++++++++++++++++++ .../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 +- 178 files changed, 570 insertions(+), 226 deletions(-) create mode 100644 target/nextflow/samtools/samtools_fasta/nextflow_schema.json diff --git a/CHANGELOG.md b/CHANGELOG.md index 2d36e453..2f4c0c71 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -31,17 +31,13 @@ - `bedtools/bedtools_sort`: Sorts a feature file (bed/gff/vcf) by chromosome and other criteria (PR #98). - `bedtools/bedtools_bamtofastq`: Convert BAM alignments to FASTQ files (PR #101). - `bedtools/bedtools_bedtobam`: Converts genomic feature records (bed/gff/vcf) to BAM format (PR #111). + +* `qualimap/qualimap_rnaseq`: RNA-seq QC analysis using qualimap (PR #74). ## MINOR CHANGES * `busco` components: update BUSCO to `5.7.1` (PR #72). -## NEW FEATURES - -* `qualimap/qualimap_rnaseq`: RNA-seq QC analysis using qualimap (PR #74). - -# biobox 0.1.0 - * Update CI to reusable workflow in `viash-io/viash-actions` (PR #86). * Update several components in order to avoid duplicate code when using `unset` on boolean arguments (PR #133). diff --git a/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml b/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml index 35daadd9..e5b09643 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 0fdb9e6b..4daef4ab 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="2024-08-20T12:16:46Z" +LABEL org.opencontainers.image.created="2024-08-20T21:04:18Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="fed809e057c4349db71e25046c388aaa6542bc45" +LABEL org.opencontainers.image.revision="75e5f792a43356af870bc580059461ba8810c0ec" 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 643171f2..ef9a1de2 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 5ba05e7a..90307329 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="2024-08-20T12:16:46Z" +LABEL org.opencontainers.image.created="2024-08-20T21:04:18Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="fed809e057c4349db71e25046c388aaa6542bc45" +LABEL org.opencontainers.image.revision="75e5f792a43356af870bc580059461ba8810c0ec" 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 bc6fa6c3..3f58871b 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 ed67a063..d9a84863 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="2024-08-20T12:16:47Z" +LABEL org.opencontainers.image.created="2024-08-20T21:04:19Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="fed809e057c4349db71e25046c388aaa6542bc45" +LABEL org.opencontainers.image.revision="75e5f792a43356af870bc580059461ba8810c0ec" 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 38aa5d43..b29f49aa 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 44c997a3..0c1b227b 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="2024-08-20T12:16:46Z" +LABEL org.opencontainers.image.created="2024-08-20T21:04:18Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="fed809e057c4349db71e25046c388aaa6542bc45" +LABEL org.opencontainers.image.revision="75e5f792a43356af870bc580059461ba8810c0ec" 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 a5d01064..452edab0 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 a07a4c02..22da1825 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="2024-08-20T12:16:45Z" +LABEL org.opencontainers.image.created="2024-08-20T21:04:17Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="fed809e057c4349db71e25046c388aaa6542bc45" +LABEL org.opencontainers.image.revision="75e5f792a43356af870bc580059461ba8810c0ec" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER diff --git a/target/executable/arriba/.config.vsh.yaml b/target/executable/arriba/.config.vsh.yaml index 868786d6..5f47514e 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 b08dcf04..5160c52e 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="2024-08-20T12:16:48Z" +LABEL org.opencontainers.image.created="2024-08-20T21:04:20Z" LABEL org.opencontainers.image.source="https://github.com/suhrig/arriba" -LABEL org.opencontainers.image.revision="fed809e057c4349db71e25046c388aaa6542bc45" +LABEL org.opencontainers.image.revision="75e5f792a43356af870bc580059461ba8810c0ec" 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 09b55faa..aa175917 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 59bc7343..d58c29b3 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="2024-08-20T12:16:47Z" +LABEL org.opencontainers.image.created="2024-08-20T21:04:20Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox" -LABEL org.opencontainers.image.revision="fed809e057c4349db71e25046c388aaa6542bc45" +LABEL org.opencontainers.image.revision="75e5f792a43356af870bc580059461ba8810c0ec" 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 cd78a146..038e1f52 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 6bbaf82a..95cf49d3 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="2024-08-20T12:16:50Z" +LABEL org.opencontainers.image.created="2024-08-20T21:04:22Z" LABEL org.opencontainers.image.source="https://bitbucket.org/CRSwDev/cwl/src/master/v2.2.1/Extra_Utilities/" -LABEL org.opencontainers.image.revision="fed809e057c4349db71e25046c388aaa6542bc45" +LABEL org.opencontainers.image.revision="75e5f792a43356af870bc580059461ba8810c0ec" 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 96112142..b6bb2856 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 350ebcb2..3bf720d5 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="2024-08-20T12:16:37Z" +LABEL org.opencontainers.image.created="2024-08-20T21:04:08Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="fed809e057c4349db71e25046c388aaa6542bc45" +LABEL org.opencontainers.image.revision="75e5f792a43356af870bc580059461ba8810c0ec" 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 54032e81..63d15ffd 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 bee5d7f8..3b806467 100755 --- a/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam +++ b/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam @@ -495,9 +495,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bedtobam" -LABEL org.opencontainers.image.created="2024-08-20T12:16:37Z" +LABEL org.opencontainers.image.created="2024-08-20T21:04:08Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="fed809e057c4349db71e25046c388aaa6542bc45" +LABEL org.opencontainers.image.revision="75e5f792a43356af870bc580059461ba8810c0ec" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER diff --git a/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml b/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml index 6594056c..c3b8a3bd 100644 --- a/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml @@ -232,7 +232,7 @@ build_info: output: "target/executable/bedtools/bedtools_getfasta" executable: "target/executable/bedtools/bedtools_getfasta/bedtools_getfasta" viash_version: "0.9.0-RC6" - git_commit: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta b/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta index 8b478caf..56c49a31 100755 --- a/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta +++ b/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta @@ -525,9 +525,9 @@ RUN echo "bedtools: \"$(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="2024-08-20T12:16:36Z" +LABEL org.opencontainers.image.created="2024-08-20T21:04:07Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="fed809e057c4349db71e25046c388aaa6542bc45" +LABEL org.opencontainers.image.revision="75e5f792a43356af870bc580059461ba8810c0ec" 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 7866a4c3..82140776 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 408a93a2..384b70a1 100755 --- a/target/executable/bedtools/bedtools_intersect/bedtools_intersect +++ b/target/executable/bedtools/bedtools_intersect/bedtools_intersect @@ -632,9 +632,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_intersect" -LABEL org.opencontainers.image.created="2024-08-20T12:16:36Z" +LABEL org.opencontainers.image.created="2024-08-20T21:04:07Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="fed809e057c4349db71e25046c388aaa6542bc45" +LABEL org.opencontainers.image.revision="75e5f792a43356af870bc580059461ba8810c0ec" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER diff --git a/target/executable/bedtools/bedtools_sort/.config.vsh.yaml b/target/executable/bedtools/bedtools_sort/.config.vsh.yaml index dff7afc2..b19fa5d9 100644 --- a/target/executable/bedtools/bedtools_sort/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_sort/.config.vsh.yaml @@ -222,7 +222,7 @@ build_info: output: "target/executable/bedtools/bedtools_sort" executable: "target/executable/bedtools/bedtools_sort/bedtools_sort" viash_version: "0.9.0-RC6" - git_commit: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/bedtools/bedtools_sort/bedtools_sort b/target/executable/bedtools/bedtools_sort/bedtools_sort index 515e35f0..bdcfe736 100755 --- a/target/executable/bedtools/bedtools_sort/bedtools_sort +++ b/target/executable/bedtools/bedtools_sort/bedtools_sort @@ -508,9 +508,9 @@ RUN echo "bedtools: \"$(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="2024-08-20T12:16:37Z" +LABEL org.opencontainers.image.created="2024-08-20T21:04:08Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="fed809e057c4349db71e25046c388aaa6542bc45" +LABEL org.opencontainers.image.revision="75e5f792a43356af870bc580059461ba8810c0ec" 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 da7957b3..491b93ae 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 4e3d4163..7d92f864 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="2024-08-20T12:16:44Z" +LABEL org.opencontainers.image.created="2024-08-20T21:04:16Z" LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco" -LABEL org.opencontainers.image.revision="fed809e057c4349db71e25046c388aaa6542bc45" +LABEL org.opencontainers.image.revision="75e5f792a43356af870bc580059461ba8810c0ec" 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 4e2830f6..05597250 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 81ac1558..83eca5f4 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="2024-08-20T12:16:45Z" +LABEL org.opencontainers.image.created="2024-08-20T21:04:17Z" LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco" -LABEL org.opencontainers.image.revision="fed809e057c4349db71e25046c388aaa6542bc45" +LABEL org.opencontainers.image.revision="75e5f792a43356af870bc580059461ba8810c0ec" 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 b44f039c..78a94818 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 aaa43a3d..f6a405d0 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="2024-08-20T12:16:45Z" +LABEL org.opencontainers.image.created="2024-08-20T21:04:17Z" LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco" -LABEL org.opencontainers.image.revision="fed809e057c4349db71e25046c388aaa6542bc45" +LABEL org.opencontainers.image.revision="75e5f792a43356af870bc580059461ba8810c0ec" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER diff --git a/target/executable/cutadapt/.config.vsh.yaml b/target/executable/cutadapt/.config.vsh.yaml index a77946c6..bdcc3595 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 6b556691..3f7f3c62 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="2024-08-20T12:16:49Z" +LABEL org.opencontainers.image.created="2024-08-20T21:04:21Z" LABEL org.opencontainers.image.source="https://github.com/marcelm/cutadapt" -LABEL org.opencontainers.image.revision="fed809e057c4349db71e25046c388aaa6542bc45" +LABEL org.opencontainers.image.revision="75e5f792a43356af870bc580059461ba8810c0ec" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER diff --git a/target/executable/falco/.config.vsh.yaml b/target/executable/falco/.config.vsh.yaml index c3033d76..8a1f39ad 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 4bd6a93d..c89aaf3c 100755 --- a/target/executable/falco/falco +++ b/target/executable/falco/falco @@ -588,9 +588,9 @@ RUN echo "falco: \"$(falco -v | sed -n 's/^falco //p')\"" > /var/software_versio LABEL org.opencontainers.image.authors="Toni Verbeiren" LABEL org.opencontainers.image.description="Companion container for running component falco" -LABEL org.opencontainers.image.created="2024-08-20T12:16:50Z" +LABEL org.opencontainers.image.created="2024-08-20T21:04:22Z" LABEL org.opencontainers.image.source="https://github.com/smithlabcode/falco" -LABEL org.opencontainers.image.revision="fed809e057c4349db71e25046c388aaa6542bc45" +LABEL org.opencontainers.image.revision="75e5f792a43356af870bc580059461ba8810c0ec" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER diff --git a/target/executable/fastp/.config.vsh.yaml b/target/executable/fastp/.config.vsh.yaml index a9baa45a..20661e06 100644 --- a/target/executable/fastp/.config.vsh.yaml +++ b/target/executable/fastp/.config.vsh.yaml @@ -1083,7 +1083,7 @@ build_info: output: "target/executable/fastp" executable: "target/executable/fastp/fastp" viash_version: "0.9.0-RC6" - git_commit: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/fastp/fastp b/target/executable/fastp/fastp index 27a794c4..fe8b8e26 100755 --- a/target/executable/fastp/fastp +++ b/target/executable/fastp/fastp @@ -1027,9 +1027,9 @@ RUN fastp --version 2>&1 | sed 's# #: "#;s#$#"#' > /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="2024-08-20T12:16:47Z" +LABEL org.opencontainers.image.created="2024-08-20T21:04:19Z" LABEL org.opencontainers.image.source="https://github.com/OpenGene/fastp" -LABEL org.opencontainers.image.revision="fed809e057c4349db71e25046c388aaa6542bc45" +LABEL org.opencontainers.image.revision="75e5f792a43356af870bc580059461ba8810c0ec" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER diff --git a/target/executable/featurecounts/.config.vsh.yaml b/target/executable/featurecounts/.config.vsh.yaml index 31b859fb..e07e22b6 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 4bc26b45..f8be14e5 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="2024-08-20T12:16:43Z" +LABEL org.opencontainers.image.created="2024-08-20T21:04:15Z" LABEL org.opencontainers.image.source="https://github.com/ShiLab-Bioinformatics/subread" -LABEL org.opencontainers.image.revision="fed809e057c4349db71e25046c388aaa6542bc45" +LABEL org.opencontainers.image.revision="75e5f792a43356af870bc580059461ba8810c0ec" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER diff --git a/target/executable/gffread/.config.vsh.yaml b/target/executable/gffread/.config.vsh.yaml index 0d78ea69..ba549dd8 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 2dbec026..e5030e4e 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="2024-08-20T12:16:35Z" +LABEL org.opencontainers.image.created="2024-08-20T21:04:06Z" LABEL org.opencontainers.image.source="https://github.com/gpertea/gffread" -LABEL org.opencontainers.image.revision="fed809e057c4349db71e25046c388aaa6542bc45" +LABEL org.opencontainers.image.revision="75e5f792a43356af870bc580059461ba8810c0ec" 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 410dc2cf..a69c7b5d 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 4e55b0ca..f9a0da21 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="2024-08-20T12:16:43Z" +LABEL org.opencontainers.image.created="2024-08-20T21:04:14Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox" -LABEL org.opencontainers.image.revision="fed809e057c4349db71e25046c388aaa6542bc45" +LABEL org.opencontainers.image.revision="75e5f792a43356af870bc580059461ba8810c0ec" 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 471ca050..a3ea6eea 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 2a716d57..4793b01c 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="2024-08-20T12:16:42Z" +LABEL org.opencontainers.image.created="2024-08-20T21:04:14Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox" -LABEL org.opencontainers.image.revision="fed809e057c4349db71e25046c388aaa6542bc45" +LABEL org.opencontainers.image.revision="75e5f792a43356af870bc580059461ba8810c0ec" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER diff --git a/target/executable/multiqc/.config.vsh.yaml b/target/executable/multiqc/.config.vsh.yaml index a7108d6f..f8d5c207 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 f69c8941..af0a1926 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="2024-08-20T12:16:49Z" +LABEL org.opencontainers.image.created="2024-08-20T21:04:22Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox" -LABEL org.opencontainers.image.revision="fed809e057c4349db71e25046c388aaa6542bc45" +LABEL org.opencontainers.image.revision="75e5f792a43356af870bc580059461ba8810c0ec" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER diff --git a/target/executable/pear/.config.vsh.yaml b/target/executable/pear/.config.vsh.yaml index 49f43e00..5ed96d55 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 6d268f7f..f52998d6 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="2024-08-20T12:16:37Z" +LABEL org.opencontainers.image.created="2024-08-20T21:04:09Z" LABEL org.opencontainers.image.source="https://github.com/tseemann/PEAR" -LABEL org.opencontainers.image.revision="fed809e057c4349db71e25046c388aaa6542bc45" +LABEL org.opencontainers.image.revision="75e5f792a43356af870bc580059461ba8810c0ec" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER diff --git a/target/executable/qualimap/.config.vsh.yaml b/target/executable/qualimap/.config.vsh.yaml index 1bf04c8a..108eee01 100644 --- a/target/executable/qualimap/.config.vsh.yaml +++ b/target/executable/qualimap/.config.vsh.yaml @@ -281,7 +281,7 @@ build_info: output: "target/executable/qualimap" executable: "target/executable/qualimap/qualimap" viash_version: "0.9.0-RC6" - git_commit: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/qualimap/qualimap b/target/executable/qualimap/qualimap index ca8f9f70..76314bd9 100755 --- a/target/executable/qualimap/qualimap +++ b/target/executable/qualimap/qualimap @@ -541,9 +541,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component qualimap" -LABEL org.opencontainers.image.created="2024-08-20T12:16:41Z" +LABEL org.opencontainers.image.created="2024-08-20T21:04:13Z" LABEL org.opencontainers.image.source="https://bitbucket.org/kokonech/qualimap/commits/branch/master" -LABEL org.opencontainers.image.revision="fed809e057c4349db71e25046c388aaa6542bc45" +LABEL org.opencontainers.image.revision="75e5f792a43356af870bc580059461ba8810c0ec" LABEL org.opencontainers.image.version="qualimap" VIASHDOCKER diff --git a/target/executable/salmon/salmon_index/.config.vsh.yaml b/target/executable/salmon/salmon_index/.config.vsh.yaml index be56d4c3..60c9b3b5 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 d114d1b5..89b69d58 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="2024-08-20T12:16:48Z" +LABEL org.opencontainers.image.created="2024-08-20T21:04:20Z" LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon" -LABEL org.opencontainers.image.revision="fed809e057c4349db71e25046c388aaa6542bc45" +LABEL org.opencontainers.image.revision="75e5f792a43356af870bc580059461ba8810c0ec" 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 e80645c0..4d6bc9ee 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 d0c2218f..18f46cec 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="2024-08-20T12:16:48Z" +LABEL org.opencontainers.image.created="2024-08-20T21:04:21Z" LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon" -LABEL org.opencontainers.image.revision="fed809e057c4349db71e25046c388aaa6542bc45" +LABEL org.opencontainers.image.revision="75e5f792a43356af870bc580059461ba8810c0ec" 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 550369f9..157b7885 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 6f336464..975c309b 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="2024-08-20T12:16:40Z" +LABEL org.opencontainers.image.created="2024-08-20T21:04:11Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="fed809e057c4349db71e25046c388aaa6542bc45" +LABEL org.opencontainers.image.revision="75e5f792a43356af870bc580059461ba8810c0ec" 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 993629c9..ea4a74e4 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 524e8967..a8b154d9 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="2024-08-20T12:16:39Z" +LABEL org.opencontainers.image.created="2024-08-20T21:04:11Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="fed809e057c4349db71e25046c388aaa6542bc45" +LABEL org.opencontainers.image.revision="75e5f792a43356af870bc580059461ba8810c0ec" 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 177a4e91..69033ee9 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 647cfcd9..06f6d8a8 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="2024-08-20T12:16:40Z" +LABEL org.opencontainers.image.created="2024-08-20T21:04:12Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="fed809e057c4349db71e25046c388aaa6542bc45" +LABEL org.opencontainers.image.revision="75e5f792a43356af870bc580059461ba8810c0ec" 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 d242f2f2..288c153f 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 6bfb3e72..8df86957 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="2024-08-20T12:16:39Z" +LABEL org.opencontainers.image.created="2024-08-20T21:04:11Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="fed809e057c4349db71e25046c388aaa6542bc45" +LABEL org.opencontainers.image.revision="75e5f792a43356af870bc580059461ba8810c0ec" 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 b22b65f0..9fc3cbcf 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 965f63cb..ef9d2db3 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="2024-08-20T12:16:39Z" +LABEL org.opencontainers.image.created="2024-08-20T21:04:10Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="fed809e057c4349db71e25046c388aaa6542bc45" +LABEL org.opencontainers.image.revision="75e5f792a43356af870bc580059461ba8810c0ec" 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 56151069..0c0ae0f0 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 46ceeaa6..b7f96e19 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="2024-08-20T12:16:38Z" +LABEL org.opencontainers.image.created="2024-08-20T21:04:09Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="fed809e057c4349db71e25046c388aaa6542bc45" +LABEL org.opencontainers.image.revision="75e5f792a43356af870bc580059461ba8810c0ec" 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 0434b9a1..ec475a4a 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 23d03e83..cef0684d 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="2024-08-20T12:16:38Z" +LABEL org.opencontainers.image.created="2024-08-20T21:04:09Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="fed809e057c4349db71e25046c388aaa6542bc45" +LABEL org.opencontainers.image.revision="75e5f792a43356af870bc580059461ba8810c0ec" 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 8f940148..77e50640 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 2694b500..c3e80956 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="2024-08-20T12:16:40Z" +LABEL org.opencontainers.image.created="2024-08-20T21:04:12Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="fed809e057c4349db71e25046c388aaa6542bc45" +LABEL org.opencontainers.image.revision="75e5f792a43356af870bc580059461ba8810c0ec" 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 a9818c71..1f308d5a 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 3e78d7bf..1337165f 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="2024-08-20T12:16:41Z" +LABEL org.opencontainers.image.created="2024-08-20T21:04:12Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="fed809e057c4349db71e25046c388aaa6542bc45" +LABEL org.opencontainers.image.revision="75e5f792a43356af870bc580059461ba8810c0ec" 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 f19c1789..ad6e497d 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 5c20bf06..af4afccd 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="2024-08-20T12:16:38Z" +LABEL org.opencontainers.image.created="2024-08-20T21:04:10Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="fed809e057c4349db71e25046c388aaa6542bc45" +LABEL org.opencontainers.image.revision="75e5f792a43356af870bc580059461ba8810c0ec" 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 49cd093b..936d8885 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 dda7e967..3e2d58c4 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="2024-08-20T12:16:51Z" +LABEL org.opencontainers.image.created="2024-08-20T21:04:23Z" LABEL org.opencontainers.image.source="https://github.com/lh3/seqtk/tree/v1.4" -LABEL org.opencontainers.image.revision="fed809e057c4349db71e25046c388aaa6542bc45" +LABEL org.opencontainers.image.revision="75e5f792a43356af870bc580059461ba8810c0ec" 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 06c28052..2a4ae59a 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 3795e59c..5a461111 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="2024-08-20T12:16:50Z" +LABEL org.opencontainers.image.created="2024-08-20T21:04:23Z" LABEL org.opencontainers.image.source="https://github.com/lh3/seqtk/tree/v1.4" -LABEL org.opencontainers.image.revision="fed809e057c4349db71e25046c388aaa6542bc45" +LABEL org.opencontainers.image.revision="75e5f792a43356af870bc580059461ba8810c0ec" 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 f9cf6e03..90fbfa55 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 35eea501..09667edd 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="2024-08-20T12:16:44Z" +LABEL org.opencontainers.image.created="2024-08-20T21:04:16Z" LABEL org.opencontainers.image.source="https://github.com/alexdobin/STAR" -LABEL org.opencontainers.image.revision="fed809e057c4349db71e25046c388aaa6542bc45" +LABEL org.opencontainers.image.revision="75e5f792a43356af870bc580059461ba8810c0ec" 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 e429a861..782772e5 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 cb06ca04..f0751fc8 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="2024-08-20T12:16:43Z" +LABEL org.opencontainers.image.created="2024-08-20T21:04:15Z" LABEL org.opencontainers.image.source="https://github.com/alexdobin/STAR" -LABEL org.opencontainers.image.revision="fed809e057c4349db71e25046c388aaa6542bc45" +LABEL org.opencontainers.image.revision="75e5f792a43356af870bc580059461ba8810c0ec" 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 6c10240f..ebfb138c 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 02a07643..1c31d77c 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="2024-08-20T12:16:42Z" +LABEL org.opencontainers.image.created="2024-08-20T21:04:14Z" LABEL org.opencontainers.image.source="https://github.com/CGATOxford/UMI-tools" -LABEL org.opencontainers.image.revision="fed809e057c4349db71e25046c388aaa6542bc45" +LABEL org.opencontainers.image.revision="75e5f792a43356af870bc580059461ba8810c0ec" 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 d6bae713..0725a996 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 23bd2c62..ab02c21e 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="2024-08-20T12:16:41Z" +LABEL org.opencontainers.image.created="2024-08-20T21:04:13Z" LABEL org.opencontainers.image.source="https://github.com/CGATOxford/UMI-tools" -LABEL org.opencontainers.image.revision="fed809e057c4349db71e25046c388aaa6542bc45" +LABEL org.opencontainers.image.revision="75e5f792a43356af870bc580059461ba8810c0ec" 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 46434df2..4f1c6279 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 20faeca1..195eb2e3 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" : "fed809e057c4349db71e25046c388aaa6542bc45", + "git_commit" : "75e5f792a43356af870bc580059461ba8810c0ec", "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 646cb0fe..43200b97 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 2c0e7277..b0ecd0e0 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" : "fed809e057c4349db71e25046c388aaa6542bc45", + "git_commit" : "75e5f792a43356af870bc580059461ba8810c0ec", "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 49040513..8ae010a6 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 65ed3f1e..c273bae2 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" : "fed809e057c4349db71e25046c388aaa6542bc45", + "git_commit" : "75e5f792a43356af870bc580059461ba8810c0ec", "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 a1d98971..da0264b4 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 d6a9e44e..97354629 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" : "fed809e057c4349db71e25046c388aaa6542bc45", + "git_commit" : "75e5f792a43356af870bc580059461ba8810c0ec", "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 2778c184..fb602df4 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 71508b88..34a26cd2 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" : "fed809e057c4349db71e25046c388aaa6542bc45", + "git_commit" : "75e5f792a43356af870bc580059461ba8810c0ec", "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 bc54d198..490219de 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 b61daae9..3538bf57 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" : "fed809e057c4349db71e25046c388aaa6542bc45", + "git_commit" : "75e5f792a43356af870bc580059461ba8810c0ec", "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 c8074b0a..274bd573 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 5f454c0b..fa854614 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" : "fed809e057c4349db71e25046c388aaa6542bc45", + "git_commit" : "75e5f792a43356af870bc580059461ba8810c0ec", "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 8bfa86b9..57255886 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 f0319224..28ef3a39 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" : "fed809e057c4349db71e25046c388aaa6542bc45", + "git_commit" : "75e5f792a43356af870bc580059461ba8810c0ec", "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 a94da18c..7f673d59 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 8f8831f0..601c9694 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" : "fed809e057c4349db71e25046c388aaa6542bc45", + "git_commit" : "75e5f792a43356af870bc580059461ba8810c0ec", "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 57e4b7ad..15dcfbe3 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 fd445461..0296df8e 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" : "fed809e057c4349db71e25046c388aaa6542bc45", + "git_commit" : "75e5f792a43356af870bc580059461ba8810c0ec", "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 29655324..566b22c7 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 46465485..c635b056 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" : "fed809e057c4349db71e25046c388aaa6542bc45", + "git_commit" : "75e5f792a43356af870bc580059461ba8810c0ec", "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 1fab6799..02775863 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 ef16e7ac..91144933 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" : "fed809e057c4349db71e25046c388aaa6542bc45", + "git_commit" : "75e5f792a43356af870bc580059461ba8810c0ec", "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 a121e004..9c5faff8 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 7f9e9ab1..7463131e 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" : "fed809e057c4349db71e25046c388aaa6542bc45", + "git_commit" : "75e5f792a43356af870bc580059461ba8810c0ec", "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 eac7b831..0ce64c19 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 c609f37f..6619c982 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" : "fed809e057c4349db71e25046c388aaa6542bc45", + "git_commit" : "75e5f792a43356af870bc580059461ba8810c0ec", "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 303fbaf0..17b9f27d 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 0d648928..d3eb4560 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" : "fed809e057c4349db71e25046c388aaa6542bc45", + "git_commit" : "75e5f792a43356af870bc580059461ba8810c0ec", "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 5099efa7..94550589 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 4203766a..7faf157b 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" : "fed809e057c4349db71e25046c388aaa6542bc45", + "git_commit" : "75e5f792a43356af870bc580059461ba8810c0ec", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/cutadapt/.config.vsh.yaml b/target/nextflow/cutadapt/.config.vsh.yaml index 5fd80e2f..81cc5ff1 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 57593e42..995168c6 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" : "fed809e057c4349db71e25046c388aaa6542bc45", + "git_commit" : "75e5f792a43356af870bc580059461ba8810c0ec", "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 f0a48766..9d8db87c 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 9fea92a7..8b75e1de 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" : "fed809e057c4349db71e25046c388aaa6542bc45", + "git_commit" : "75e5f792a43356af870bc580059461ba8810c0ec", "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 e5d1e5d7..c9f15652 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 8d2cbd03..7a39cafd 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" : "fed809e057c4349db71e25046c388aaa6542bc45", + "git_commit" : "75e5f792a43356af870bc580059461ba8810c0ec", "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 c73fca77..bb4104ff 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 ff4a158c..d9feb124 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" : "fed809e057c4349db71e25046c388aaa6542bc45", + "git_commit" : "75e5f792a43356af870bc580059461ba8810c0ec", "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 0737fe99..f613e3b4 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 54dae1d8..ab3c4c3e 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" : "fed809e057c4349db71e25046c388aaa6542bc45", + "git_commit" : "75e5f792a43356af870bc580059461ba8810c0ec", "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 1b13c2f4..549a2d71 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 0961c8f8..a1d14bab 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" : "fed809e057c4349db71e25046c388aaa6542bc45", + "git_commit" : "75e5f792a43356af870bc580059461ba8810c0ec", "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 e32c1513..be506ddb 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 86b77d54..118d0464 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" : "fed809e057c4349db71e25046c388aaa6542bc45", + "git_commit" : "75e5f792a43356af870bc580059461ba8810c0ec", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/multiqc/.config.vsh.yaml b/target/nextflow/multiqc/.config.vsh.yaml index 88440e9a..03a727d3 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 6e93563a..da3bae28 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" : "fed809e057c4349db71e25046c388aaa6542bc45", + "git_commit" : "75e5f792a43356af870bc580059461ba8810c0ec", "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 db3568dc..42e1603a 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 8a28403d..55ff79ab 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" : "fed809e057c4349db71e25046c388aaa6542bc45", + "git_commit" : "75e5f792a43356af870bc580059461ba8810c0ec", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/qualimap/.config.vsh.yaml b/target/nextflow/qualimap/.config.vsh.yaml index 85a56920..08082963 100644 --- a/target/nextflow/qualimap/.config.vsh.yaml +++ b/target/nextflow/qualimap/.config.vsh.yaml @@ -281,7 +281,7 @@ build_info: output: "target/nextflow/qualimap" executable: "target/nextflow/qualimap/main.nf" viash_version: "0.9.0-RC6" - git_commit: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/qualimap/main.nf b/target/nextflow/qualimap/main.nf index d288ecd7..7f22b684 100644 --- a/target/nextflow/qualimap/main.nf +++ b/target/nextflow/qualimap/main.nf @@ -3124,7 +3124,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/qualimap", "viash_version" : "0.9.0-RC6", - "git_commit" : "fed809e057c4349db71e25046c388aaa6542bc45", + "git_commit" : "75e5f792a43356af870bc580059461ba8810c0ec", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/salmon/salmon_index/.config.vsh.yaml b/target/nextflow/salmon/salmon_index/.config.vsh.yaml index 2e379837..460b7f65 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 9e819c28..a6b621bd 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" : "fed809e057c4349db71e25046c388aaa6542bc45", + "git_commit" : "75e5f792a43356af870bc580059461ba8810c0ec", "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 5e29f66b..0c66d51d 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 b3e7e420..49bca0cb 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" : "fed809e057c4349db71e25046c388aaa6542bc45", + "git_commit" : "75e5f792a43356af870bc580059461ba8810c0ec", "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 5728424c..81b5dd16 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 75833a5d..fa606c89 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" : "fed809e057c4349db71e25046c388aaa6542bc45", + "git_commit" : "75e5f792a43356af870bc580059461ba8810c0ec", "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 7f247017..a4c072a3 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 94171c85..b2c17eb5 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" : "fed809e057c4349db71e25046c388aaa6542bc45", + "git_commit" : "75e5f792a43356af870bc580059461ba8810c0ec", "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 e91a8378..7ea276df 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 e69b3b6b..d3daf2cf 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" : "fed809e057c4349db71e25046c388aaa6542bc45", + "git_commit" : "75e5f792a43356af870bc580059461ba8810c0ec", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/samtools/samtools_fasta/nextflow_schema.json b/target/nextflow/samtools/samtools_fasta/nextflow_schema.json new file mode 100644 index 00000000..730fe87a --- /dev/null +++ b/target/nextflow/samtools/samtools_fasta/nextflow_schema.json @@ -0,0 +1,348 @@ +{ +"$schema": "http://json-schema.org/draft-07/schema", +"title": "samtools_fasta", +"description": "Converts a SAM, BAM or CRAM to FASTA format.", +"type": "object", +"definitions": { + + + + "inputs" : { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + + + "input": { + "type": + "string", + "description": "Type: `file`, required. input SAM/BAM/CRAM file", + "help_text": "Type: `file`, required. input SAM/BAM/CRAM file" + + } + + +} +}, + + + "outputs" : { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + + + "output": { + "type": + "string", + "description": "Type: `file`, required, default: `$id.$key.output.output`. output FASTA file", + "help_text": "Type: `file`, required, default: `$id.$key.output.output`. output FASTA file" + , + "default": "$id.$key.output.output" + } + + +} +}, + + + "options" : { + "title": "Options", + "type": "object", + "description": "No description", + "properties": { + + + "no_suffix": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. By default, either \u0027/1\u0027 or \u0027/2\u0027 is added to the end of read names where the corresponding \nREAD1 or READ2 FLAG bit is set", + "help_text": "Type: `boolean_true`, default: `false`. By default, either \u0027/1\u0027 or \u0027/2\u0027 is added to the end of read names where the corresponding \nREAD1 or READ2 FLAG bit is set. Using -n causes read names to be left as they are.\n" + , + "default": "False" + } + + + , + "suffix": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Always add either \u0027/1\u0027 or \u0027/2\u0027 to the end of read names even when put into different files", + "help_text": "Type: `boolean_true`, default: `false`. Always add either \u0027/1\u0027 or \u0027/2\u0027 to the end of read names even when put into different files.\n" + , + "default": "False" + } + + + , + "use_oq": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Use quality values from OQ tags in preference to standard quality string if available", + "help_text": "Type: `boolean_true`, default: `false`. Use quality values from OQ tags in preference to standard quality string if available.\n" + , + "default": "False" + } + + + , + "singleton": { + "type": + "string", + "description": "Type: `file`. write singleton reads to FILE", + "help_text": "Type: `file`. write singleton reads to FILE." + + } + + + , + "copy_tags": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Copy RG, BC and QT tags to the FASTA header line, if they exist", + "help_text": "Type: `boolean_true`, default: `false`. Copy RG, BC and QT tags to the FASTA header line, if they exist.\n" + , + "default": "False" + } + + + , + "copy_tags_list": { + "type": + "string", + "description": "Type: `string`. Specify a comma-separated list of tags to copy to the FASTA header line, if they exist", + "help_text": "Type: `string`. Specify a comma-separated list of tags to copy to the FASTA header line, if they exist. \nTAGLIST can be blank or `*` to indicate all tags should be copied to the output. If using `*`, \nbe careful to quote it to avoid unwanted shell expansion.\n" + + } + + + , + "read1": { + "type": + "string", + "description": "Type: `file`, default: `$id.$key.read1.read1`. Write reads with the READ1 FLAG set (and READ2 not set) to FILE instead of outputting them", + "help_text": "Type: `file`, default: `$id.$key.read1.read1`. Write reads with the READ1 FLAG set (and READ2 not set) to FILE instead of outputting them. \nIf the -s option is used, only paired reads will be written to this file.\n" + , + "default": "$id.$key.read1.read1" + } + + + , + "read2": { + "type": + "string", + "description": "Type: `file`, default: `$id.$key.read2.read2`. Write reads with the READ2 FLAG set (and READ1 not set) to FILE instead of outputting them", + "help_text": "Type: `file`, default: `$id.$key.read2.read2`. Write reads with the READ2 FLAG set (and READ1 not set) to FILE instead of outputting them. \nIf the -s option is used, only paired reads will be written to this file.\n" + , + "default": "$id.$key.read2.read2" + } + + + , + "output_reads": { + "type": + "string", + "description": "Type: `file`, default: `$id.$key.output_reads.output_reads`. Write reads with either READ1 FLAG or READ2 flag set to FILE instead of outputting them to stdout", + "help_text": "Type: `file`, default: `$id.$key.output_reads.output_reads`. Write reads with either READ1 FLAG or READ2 flag set to FILE instead of outputting them to stdout. \nThis is equivalent to -1 FILE -2 FILE.\n" + , + "default": "$id.$key.output_reads.output_reads" + } + + + , + "output_reads_both": { + "type": + "string", + "description": "Type: `file`, default: `$id.$key.output_reads_both.output_reads_both`. Write reads where the READ1 and READ2 FLAG bits set are either both set or both unset to FILE \ninstead of outputting them", + "help_text": "Type: `file`, default: `$id.$key.output_reads_both.output_reads_both`. Write reads where the READ1 and READ2 FLAG bits set are either both set or both unset to FILE \ninstead of outputting them.\n" + , + "default": "$id.$key.output_reads_both.output_reads_both" + } + + + , + "filter_flags": { + "type": + "integer", + "description": "Type: `integer`, example: `0`. Only output alignments with all bits set in INT present in the FLAG field", + "help_text": "Type: `integer`, example: `0`. Only output alignments with all bits set in INT present in the FLAG field. INT can be specified \nin hex by beginning with \u00270x\u0027 (i.e. /^0x[0-9A-F]+/) or in octal by beginning with \u00270\u0027 \n(i.e. /^0[0-7]+/). Default: `0`.\n" + + } + + + , + "excl_flags": { + "type": + "string", + "description": "Type: `string`, example: `0x900`. Do not output alignments with any bits set in INT present in the FLAG field", + "help_text": "Type: `string`, example: `0x900`. Do not output alignments with any bits set in INT present in the FLAG field. INT can be specified \nin hex by beginning with \u00270x\u0027 (i.e. /^0x[0-9A-F]+/) or in octal by beginning with \u00270\u0027\n(i.e. /^0[0-7]+/). This defaults to 0x900 representing filtering of secondary and \nsupplementary alignments. Default: `0x900`.\n" + + } + + + , + "incl_flags": { + "type": + "string", + "description": "Type: `string`, example: `0`. Only output alignments with any bits set in INT present in the FLAG field", + "help_text": "Type: `string`, example: `0`. Only output alignments with any bits set in INT present in the FLAG field. INT can be specified \nin hex by beginning with \u00270x\u0027 (i.e. /^0x[0-9A-F]+/), in octal by beginning with \u00270\u0027\n(i.e. /^0[0-7]+/), as a decimal number not beginning with \u00270\u0027 or as a comma-separated list of \nflag names. Default: `0`.\n" + + } + + + , + "excl_flags_all": { + "type": + "integer", + "description": "Type: `integer`, example: `0`. Only EXCLUDE reads with all of the bits set in INT present in the FLAG field", + "help_text": "Type: `integer`, example: `0`. Only EXCLUDE reads with all of the bits set in INT present in the FLAG field. INT can be specified \nin hex by beginning with \u00270x\u0027 (i.e. /^0x[0-9A-F]+/) or in octal by beginning with \u00270\u0027 (i.e. /^0[0-7]+/).\nDefault: `0`.\n" + + } + + + , + "aux_tag": { + "type": + "string", + "description": "Type: `string`. Only output alignments containing an auxiliary tag matching both TAG and VAL", + "help_text": "Type: `string`. Only output alignments containing an auxiliary tag matching both TAG and VAL. If VAL is omitted \nthen any value is accepted. The tag types supported are i, f, Z, A and H. \"B\" arrays are not \nsupported. This is comparable to the method used in samtools view --tag. The option may be specified \nmultiple times and is equivalent to using the --aux_tag_file option.\n" + + } + + + , + "aux_tag_file": { + "type": + "string", + "description": "Type: `string`. Only output alignments containing an auxiliary tag matching TAG and having a value listed in FILE", + "help_text": "Type: `string`. Only output alignments containing an auxiliary tag matching TAG and having a value listed in FILE. \nThe format of the file is one line per value. This is equivalent to specifying --aux_tag multiple times.\n" + + } + + + , + "casava": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. add Illumina Casava 1", + "help_text": "Type: `boolean_true`, default: `false`. add Illumina Casava 1.8 format entry to header (eg 1:N:0:ATCACG)" + , + "default": "False" + } + + + , + "compression": { + "type": + "integer", + "description": "Type: `integer`, example: `0`. set compression level when writing gz or bgzf fasta files", + "help_text": "Type: `integer`, example: `0`. set compression level when writing gz or bgzf fasta files." + + } + + + , + "index1": { + "type": + "string", + "description": "Type: `file`. write first index reads to FILE", + "help_text": "Type: `file`. write first index reads to FILE." + + } + + + , + "index2": { + "type": + "string", + "description": "Type: `file`. write second index reads to FILE", + "help_text": "Type: `file`. write second index reads to FILE." + + } + + + , + "barcode_tag": { + "type": + "string", + "description": "Type: `string`, example: `BC`. Auxiliary tag to find index reads in", + "help_text": "Type: `string`, example: `BC`. Auxiliary tag to find index reads in. Default: `BC`.\n" + + } + + + , + "quality_tag": { + "type": + "string", + "description": "Type: `string`, example: `QT`. Auxiliary tag to find index quality in", + "help_text": "Type: `string`, example: `QT`. Auxiliary tag to find index quality in. Default: `QT`.\n" + + } + + + , + "index_format": { + "type": + "string", + "description": "Type: `string`. string to describe how to parse the barcode and quality tags", + "help_text": "Type: `string`. string to describe how to parse the barcode and quality tags. For example:\n* `i14i8`: the first 14 characters are index 1, the next 8 characters are index 2.\n* `n8i14`: ignore the first 8 characters, and use the next 14 characters for index 1.\nIf the tag contains a separator, then the numeric part can be replaced with`*` to mean \n\u0027read until the separator or end of tag\u0027, for example: `n*i*`.\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/options" + }, + + { + "$ref": "#/definitions/nextflow input-output arguments" + } +] +} diff --git a/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml b/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml index c5ac0aae..b2c1eeff 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 0f86e4b4..a0c532d7 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" : "fed809e057c4349db71e25046c388aaa6542bc45", + "git_commit" : "75e5f792a43356af870bc580059461ba8810c0ec", "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 e5915037..b0b29672 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 bfd4e660..c4b6afeb 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" : "fed809e057c4349db71e25046c388aaa6542bc45", + "git_commit" : "75e5f792a43356af870bc580059461ba8810c0ec", "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 f37b1b4f..3faf4777 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 55229744..4a93f443 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" : "fed809e057c4349db71e25046c388aaa6542bc45", + "git_commit" : "75e5f792a43356af870bc580059461ba8810c0ec", "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 62c14dea..67089b70 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 65b5c1f6..cf5cb851 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" : "fed809e057c4349db71e25046c388aaa6542bc45", + "git_commit" : "75e5f792a43356af870bc580059461ba8810c0ec", "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 c61943ee..decec57e 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 d717e977..2158a923 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" : "fed809e057c4349db71e25046c388aaa6542bc45", + "git_commit" : "75e5f792a43356af870bc580059461ba8810c0ec", "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 0de09d4d..702ecebf 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 4f156a36..8bbd7639 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" : "fed809e057c4349db71e25046c388aaa6542bc45", + "git_commit" : "75e5f792a43356af870bc580059461ba8810c0ec", "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 f9cc3dd0..5333ef4b 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 a5cd1f17..a1698c4b 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" : "fed809e057c4349db71e25046c388aaa6542bc45", + "git_commit" : "75e5f792a43356af870bc580059461ba8810c0ec", "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 3105963c..9b14f731 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 23095c25..6498bc90 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" : "fed809e057c4349db71e25046c388aaa6542bc45", + "git_commit" : "75e5f792a43356af870bc580059461ba8810c0ec", "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 c56a8bcd..808fd86f 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 fab6e7cf..7fe1bfe1 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" : "fed809e057c4349db71e25046c388aaa6542bc45", + "git_commit" : "75e5f792a43356af870bc580059461ba8810c0ec", "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 6469d8f2..e46f62f7 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 480dd7e6..e7065611 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" : "fed809e057c4349db71e25046c388aaa6542bc45", + "git_commit" : "75e5f792a43356af870bc580059461ba8810c0ec", "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 85bbd9b9..3c6048e3 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 19789353..2499b678 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" : "fed809e057c4349db71e25046c388aaa6542bc45", + "git_commit" : "75e5f792a43356af870bc580059461ba8810c0ec", "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 494a5c93..065f4dbb 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 c7594921..5044ab2f 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" : "fed809e057c4349db71e25046c388aaa6542bc45", + "git_commit" : "75e5f792a43356af870bc580059461ba8810c0ec", "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 67cd3750..d7dd4151 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: "fed809e057c4349db71e25046c388aaa6542bc45" + git_commit: "75e5f792a43356af870bc580059461ba8810c0ec" 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 38bfde6f..859669c9 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" : "fed809e057c4349db71e25046c388aaa6542bc45", + "git_commit" : "75e5f792a43356af870bc580059461ba8810c0ec", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : {