From 9747a7a8d91aa96936cdbf65bfca0297b436368e Mon Sep 17 00:00:00 2001 From: CI Date: Mon, 24 Jun 2024 09:29:59 +0000 Subject: [PATCH] Build branch main with version main (3481750) Build pipeline: viash-hub.biobox.main-2mtst Source commit: https://github.com/viash-hub/biobox/commit/3481750f6e2d77defa28423d832ff251da3a1f9e Source message: Output alignments to the transcriptome (#56) * Output alignments to the transcriptome * Change argument name --- src/star/star_align_reads/config.vsh.yaml | 6 + src/star/star_align_reads/script.py | 3 +- src/star/star_align_reads/test.sh | 3 + target/executable/arriba/.config.vsh.yaml | 2 +- target/executable/arriba/arriba | 4 +- .../executable/bcl_convert/.config.vsh.yaml | 2 +- target/executable/bcl_convert/bcl_convert | 4 +- .../bedtools_getfasta/.config.vsh.yaml | 2 +- .../bedtools_getfasta/bedtools_getfasta | 4 +- .../busco_download_datasets/.config.vsh.yaml | 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 +- .../salmon/salmon_index/.config.vsh.yaml | 2 +- .../salmon/salmon_index/salmon_index | 4 +- .../salmon/salmon_quant/.config.vsh.yaml | 2 +- .../salmon/salmon_quant/salmon_quant | 4 +- .../samtools_collate/.config.vsh.yaml | 2 +- .../samtools_collate/samtools_collate | 4 +- .../samtools/samtools_faidx/.config.vsh.yaml | 2 +- .../samtools/samtools_faidx/samtools_faidx | 4 +- .../samtools/samtools_fastq/.config.vsh.yaml | 2 +- .../samtools/samtools_fastq/samtools_fastq | 4 +- .../samtools_flagstat/.config.vsh.yaml | 2 +- .../samtools_flagstat/samtools_flagstat | 4 +- .../samtools_idxstats/.config.vsh.yaml | 2 +- .../samtools_idxstats/samtools_idxstats | 4 +- .../samtools/samtools_index/.config.vsh.yaml | 2 +- .../samtools/samtools_index/samtools_index | 4 +- .../samtools/samtools_sort/.config.vsh.yaml | 2 +- .../samtools/samtools_sort/samtools_sort | 4 +- .../samtools/samtools_stats/.config.vsh.yaml | 2 +- .../samtools/samtools_stats/samtools_stats | 4 +- .../samtools/samtools_view/.config.vsh.yaml | 2 +- .../samtools/samtools_view/samtools_view | 4 +- .../star/star_align_reads/.config.vsh.yaml | 15 +- .../star/star_align_reads/star_align_reads | 43 +++++- .../star_genome_generate/.config.vsh.yaml | 2 +- .../star_genome_generate/star_genome_generate | 4 +- target/nextflow/arriba/.config.vsh.yaml | 2 +- target/nextflow/arriba/main.nf | 2 +- target/nextflow/bcl_convert/.config.vsh.yaml | 2 +- target/nextflow/bcl_convert/main.nf | 2 +- .../bedtools_getfasta/.config.vsh.yaml | 2 +- .../bedtools/bedtools_getfasta/main.nf | 2 +- .../busco_download_datasets/.config.vsh.yaml | 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 +- .../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_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_index/nextflow_schema.json | 141 ------------------ .../samtools/samtools_sort/.config.vsh.yaml | 2 +- .../nextflow/samtools/samtools_sort/main.nf | 2 +- .../samtools/samtools_stats/.config.vsh.yaml | 2 +- .../nextflow/samtools/samtools_stats/main.nf | 2 +- .../samtools/samtools_view/.config.vsh.yaml | 2 +- .../nextflow/samtools/samtools_view/main.nf | 2 +- .../star/star_align_reads/.config.vsh.yaml | 15 +- target/nextflow/star/star_align_reads/main.nf | 22 ++- .../star_align_reads/nextflow_schema.json | 11 ++ .../star_genome_generate/.config.vsh.yaml | 2 +- .../star/star_genome_generate/main.nf | 2 +- 117 files changed, 243 insertions(+), 286 deletions(-) delete mode 100644 target/nextflow/samtools/samtools_index/nextflow_schema.json diff --git a/src/star/star_align_reads/config.vsh.yaml b/src/star/star_align_reads/config.vsh.yaml index 8fdd5256..eab65b35 100644 --- a/src/star/star_align_reads/config.vsh.yaml +++ b/src/star/star_align_reads/config.vsh.yaml @@ -72,6 +72,12 @@ argument_groups: description: The output file containing the splice junctions. direction: output example: splice_junctions.tsv + - type: file + name: --reads_aligned_to_transcriptome + required: false + description: The output file containing the alignments to transcriptome in BAM formats. This file is generated when --quantMode is set to TranscriptomeSAM. + direction: output + example: transcriptome_aligned.bam # other arguments are defined in a separate file __merge__: argument_groups.yaml resources: diff --git a/src/star/star_align_reads/script.py b/src/star/star_align_reads/script.py index 2bde8798..f3d64a57 100644 --- a/src/star/star_align_reads/script.py +++ b/src/star/star_align_reads/script.py @@ -58,7 +58,8 @@ expected_outputs = { "log": "Log.final.out", "splice_junctions": "SJ.out.tab", "unmapped": "Unmapped.out.mate1", - "unmapped_r2": "Unmapped.out.mate2" + "unmapped_r2": "Unmapped.out.mate2", + "reads_aligned_to_transcriptome": "Aligned.toTranscriptome.out.bam" } output_paths = {name: par[name] for name in expected_outputs.keys()} for name in expected_outputs.keys(): diff --git a/src/star/star_align_reads/test.sh b/src/star/star_align_reads/test.sh index 374b9014..a15ea599 100644 --- a/src/star/star_align_reads/test.sh +++ b/src/star/star_align_reads/test.sh @@ -98,6 +98,7 @@ echo "> Run star_align_reads on SE" --reads_per_gene "reads_per_gene.tsv" \ --outSJtype Standard \ --splice_junctions "splice_junctions.tsv" \ + --reads_aligned_to_transcriptome "transcriptome_aligned.bam" \ ${meta_cpus:+---cpus $meta_cpus} # TODO: Test data doesn't contain any chimeric reads yet @@ -111,6 +112,7 @@ assert_file_exists "reads_per_gene.tsv" # assert_file_exists "chimeric_junctions.tsv" assert_file_exists "splice_junctions.tsv" assert_file_exists "unmapped.sam" +assert_file_exists "transcriptome_aligned.bam" echo ">> Check if output contents are not empty" assert_file_not_empty "output.sam" @@ -119,6 +121,7 @@ assert_file_not_empty "reads_per_gene.tsv" # assert_file_not_empty "chimeric_junctions.tsv" # assert_file_not_empty "splice_junctions.tsv" # TODO: test data doesn't contain any splice junctions yet assert_file_not_empty "unmapped.sam" +assert_file_not_empty "transcriptome_aligned.bam" echo ">> Check if output contents are correct" assert_file_contains "log.txt" "Number of input reads \\| 2" diff --git a/target/executable/arriba/.config.vsh.yaml b/target/executable/arriba/.config.vsh.yaml index e9b0f1ec..4fdd680d 100644 --- a/target/executable/arriba/.config.vsh.yaml +++ b/target/executable/arriba/.config.vsh.yaml @@ -688,7 +688,7 @@ build_info: output: "target/executable/arriba" executable: "target/executable/arriba/arriba" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" 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 4c1e7521..11d352e0 100755 --- a/target/executable/arriba/arriba +++ b/target/executable/arriba/arriba @@ -749,9 +749,9 @@ ENTRYPOINT [] RUN arriba -h | grep 'Version:' 2>&1 | sed 's/Version:\s\(.*\)/arriba: "\1"/' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component arriba" -LABEL org.opencontainers.image.created="2024-06-24T08:36:43Z" +LABEL org.opencontainers.image.created="2024-06-24T09:14:58Z" LABEL org.opencontainers.image.source="https://github.com/suhrig/arriba" -LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198" +LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bcl_convert/.config.vsh.yaml b/target/executable/bcl_convert/.config.vsh.yaml index 5ca4f853..7dd5ecc2 100644 --- a/target/executable/bcl_convert/.config.vsh.yaml +++ b/target/executable/bcl_convert/.config.vsh.yaml @@ -386,7 +386,7 @@ build_info: output: "target/executable/bcl_convert" executable: "target/executable/bcl_convert/bcl_convert" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" 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 d96bae66..911710ad 100755 --- a/target/executable/bcl_convert/bcl_convert +++ b/target/executable/bcl_convert/bcl_convert @@ -593,9 +593,9 @@ rm /tmp/bcl-convert.rpm RUN echo "bcl-convert: \"$(bcl-convert -V 2>&1 >/dev/null | sed -n '/Version/ s/^bcl-convert\ Version //p')\"" > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component bcl_convert" -LABEL org.opencontainers.image.created="2024-06-24T08:36:37Z" +LABEL org.opencontainers.image.created="2024-06-24T09:14:52Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox" -LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198" +LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml b/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml index d36016e5..2f7f6add 100644 --- a/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml @@ -217,7 +217,7 @@ build_info: output: "target/executable/bedtools/bedtools_getfasta" executable: "target/executable/bedtools/bedtools_getfasta/bedtools_getfasta" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta b/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta index 09ced562..6667c1fd 100755 --- a/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta +++ b/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta @@ -521,9 +521,9 @@ RUN apt-get update && \ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_getfasta" -LABEL org.opencontainers.image.created="2024-06-24T08:36:44Z" +LABEL org.opencontainers.image.created="2024-06-24T09:14:59Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198" +LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/busco/busco_download_datasets/.config.vsh.yaml b/target/executable/busco/busco_download_datasets/.config.vsh.yaml index 9e903bf8..e8006c3a 100644 --- a/target/executable/busco/busco_download_datasets/.config.vsh.yaml +++ b/target/executable/busco/busco_download_datasets/.config.vsh.yaml @@ -144,7 +144,7 @@ build_info: output: "target/executable/busco/busco_download_datasets" executable: "target/executable/busco/busco_download_datasets/busco_download_datasets" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" 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 6fc6d579..ebac43aa 100755 --- a/target/executable/busco/busco_download_datasets/busco_download_datasets +++ b/target/executable/busco/busco_download_datasets/busco_download_datasets @@ -470,9 +470,9 @@ ENTRYPOINT [] RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component busco busco_download_datasets" -LABEL org.opencontainers.image.created="2024-06-24T08:36:44Z" +LABEL org.opencontainers.image.created="2024-06-24T09:14:59Z" LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco" -LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198" +LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/busco/busco_list_datasets/.config.vsh.yaml b/target/executable/busco/busco_list_datasets/.config.vsh.yaml index 816eba36..2a82a186 100644 --- a/target/executable/busco/busco_list_datasets/.config.vsh.yaml +++ b/target/executable/busco/busco_list_datasets/.config.vsh.yaml @@ -131,7 +131,7 @@ build_info: output: "target/executable/busco/busco_list_datasets" executable: "target/executable/busco/busco_list_datasets/busco_list_datasets" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" 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 638824a9..c739f9dc 100755 --- a/target/executable/busco/busco_list_datasets/busco_list_datasets +++ b/target/executable/busco/busco_list_datasets/busco_list_datasets @@ -460,9 +460,9 @@ ENTRYPOINT [] RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component busco busco_list_datasets" -LABEL org.opencontainers.image.created="2024-06-24T08:36:43Z" +LABEL org.opencontainers.image.created="2024-06-24T09:14:59Z" LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco" -LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198" +LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/busco/busco_run/.config.vsh.yaml b/target/executable/busco/busco_run/.config.vsh.yaml index fc6e63d6..2d4c0d7a 100644 --- a/target/executable/busco/busco_run/.config.vsh.yaml +++ b/target/executable/busco/busco_run/.config.vsh.yaml @@ -404,7 +404,7 @@ build_info: output: "target/executable/busco/busco_run" executable: "target/executable/busco/busco_run/busco_run" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" 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 ac4172a2..2b9447af 100755 --- a/target/executable/busco/busco_run/busco_run +++ b/target/executable/busco/busco_run/busco_run @@ -623,9 +623,9 @@ ENTRYPOINT [] RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component busco busco_run" -LABEL org.opencontainers.image.created="2024-06-24T08:36:43Z" +LABEL org.opencontainers.image.created="2024-06-24T09:14:59Z" LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco" -LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198" +LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/cutadapt/.config.vsh.yaml b/target/executable/cutadapt/.config.vsh.yaml index dff8adbe..b55876dc 100644 --- a/target/executable/cutadapt/.config.vsh.yaml +++ b/target/executable/cutadapt/.config.vsh.yaml @@ -707,7 +707,7 @@ build_info: output: "target/executable/cutadapt" executable: "target/executable/cutadapt/cutadapt" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" 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 0d2822b4..566babb8 100755 --- a/target/executable/cutadapt/cutadapt +++ b/target/executable/cutadapt/cutadapt @@ -810,9 +810,9 @@ RUN pip install --upgrade pip && \ RUN cutadapt --version | sed 's/\(.*\)/cutadapt: "\1"/' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component cutadapt" -LABEL org.opencontainers.image.created="2024-06-24T08:36:37Z" +LABEL org.opencontainers.image.created="2024-06-24T09:14:52Z" LABEL org.opencontainers.image.source="https://github.com/marcelm/cutadapt" -LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198" +LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/falco/.config.vsh.yaml b/target/executable/falco/.config.vsh.yaml index c27d4bdd..fa3d6d7f 100644 --- a/target/executable/falco/.config.vsh.yaml +++ b/target/executable/falco/.config.vsh.yaml @@ -304,7 +304,7 @@ build_info: output: "target/executable/falco" executable: "target/executable/falco/falco" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" 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 7b0c1af7..13bf0fe6 100755 --- a/target/executable/falco/falco +++ b/target/executable/falco/falco @@ -584,9 +584,9 @@ make install RUN echo "falco: \"$(falco -v | sed -n 's/^falco //p')\"" > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component falco" -LABEL org.opencontainers.image.created="2024-06-24T08:36:47Z" +LABEL org.opencontainers.image.created="2024-06-24T09:15:02Z" LABEL org.opencontainers.image.source="https://github.com/smithlabcode/falco" -LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198" +LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/fastp/.config.vsh.yaml b/target/executable/fastp/.config.vsh.yaml index def2d877..46a30f27 100644 --- a/target/executable/fastp/.config.vsh.yaml +++ b/target/executable/fastp/.config.vsh.yaml @@ -1065,7 +1065,7 @@ build_info: output: "target/executable/fastp" executable: "target/executable/fastp/fastp" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/fastp/fastp b/target/executable/fastp/fastp index 3405dc37..4b531639 100755 --- a/target/executable/fastp/fastp +++ b/target/executable/fastp/fastp @@ -1023,9 +1023,9 @@ ENTRYPOINT [] RUN fastp --version 2>&1 | sed 's# #: "#;s#$#"#' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component fastp" -LABEL org.opencontainers.image.created="2024-06-24T08:36:44Z" +LABEL org.opencontainers.image.created="2024-06-24T09:15:00Z" LABEL org.opencontainers.image.source="https://github.com/OpenGene/fastp" -LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198" +LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/featurecounts/.config.vsh.yaml b/target/executable/featurecounts/.config.vsh.yaml index 7042eabe..04a73b41 100644 --- a/target/executable/featurecounts/.config.vsh.yaml +++ b/target/executable/featurecounts/.config.vsh.yaml @@ -631,7 +631,7 @@ build_info: output: "target/executable/featurecounts" executable: "target/executable/featurecounts/featurecounts" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" 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 49f6e3d8..124b2a8f 100755 --- a/target/executable/featurecounts/featurecounts +++ b/target/executable/featurecounts/featurecounts @@ -749,9 +749,9 @@ ENTRYPOINT [] RUN featureCounts -v 2>&1 | sed 's/featureCounts v\([0-9.]*\)/featureCounts: \1/' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component featurecounts" -LABEL org.opencontainers.image.created="2024-06-24T08:36:36Z" +LABEL org.opencontainers.image.created="2024-06-24T09:14:51Z" LABEL org.opencontainers.image.source="https://github.com/ShiLab-Bioinformatics/subread" -LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198" +LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/gffread/.config.vsh.yaml b/target/executable/gffread/.config.vsh.yaml index 26ef7d49..c39eba12 100644 --- a/target/executable/gffread/.config.vsh.yaml +++ b/target/executable/gffread/.config.vsh.yaml @@ -671,7 +671,7 @@ build_info: output: "target/executable/gffread" executable: "target/executable/gffread/gffread" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" 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 c659368e..a00b1a24 100755 --- a/target/executable/gffread/gffread +++ b/target/executable/gffread/gffread @@ -802,9 +802,9 @@ ENTRYPOINT [] RUN echo "gffread: \"$(gffread --version 2>&1)\"" > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component gffread" -LABEL org.opencontainers.image.created="2024-06-24T08:36:41Z" +LABEL org.opencontainers.image.created="2024-06-24T09:14:57Z" LABEL org.opencontainers.image.source="https://github.com/gpertea/gffread" -LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198" +LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/lofreq/lofreq_call/.config.vsh.yaml b/target/executable/lofreq/lofreq_call/.config.vsh.yaml index f0933ee4..8d592615 100644 --- a/target/executable/lofreq/lofreq_call/.config.vsh.yaml +++ b/target/executable/lofreq/lofreq_call/.config.vsh.yaml @@ -489,7 +489,7 @@ build_info: output: "target/executable/lofreq/lofreq_call" executable: "target/executable/lofreq/lofreq_call/lofreq_call" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/lofreq/lofreq_call/lofreq_call b/target/executable/lofreq/lofreq_call/lofreq_call index 3364f9b7..b162e1c9 100755 --- a/target/executable/lofreq/lofreq_call/lofreq_call +++ b/target/executable/lofreq/lofreq_call/lofreq_call @@ -651,9 +651,9 @@ RUN version=$(lofreq version | grep 'version' | sed 's/version: //') && \ echo "lofreq: $version" > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component lofreq lofreq_call" -LABEL org.opencontainers.image.created="2024-06-24T08:36:46Z" +LABEL org.opencontainers.image.created="2024-06-24T09:15:02Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox" -LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198" +LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml b/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml index ff268c44..2bda6e01 100644 --- a/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml +++ b/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml @@ -197,7 +197,7 @@ build_info: output: "target/executable/lofreq/lofreq_indelqual" executable: "target/executable/lofreq/lofreq_indelqual/lofreq_indelqual" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual b/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual index ea48dc2d..a5aa39f4 100755 --- a/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual +++ b/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual @@ -496,9 +496,9 @@ RUN version=$(lofreq version | grep 'version' | sed 's/version: //') && \ echo "lofreq: $version" > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component lofreq lofreq_indelqual" -LABEL org.opencontainers.image.created="2024-06-24T08:36:46Z" +LABEL org.opencontainers.image.created="2024-06-24T09:15:02Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox" -LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198" +LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/multiqc/.config.vsh.yaml b/target/executable/multiqc/.config.vsh.yaml index 847d7d67..fd7c778d 100644 --- a/target/executable/multiqc/.config.vsh.yaml +++ b/target/executable/multiqc/.config.vsh.yaml @@ -438,7 +438,7 @@ build_info: output: "target/executable/multiqc" executable: "target/executable/multiqc/multiqc" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" 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 f2859389..d86c52b2 100755 --- a/target/executable/multiqc/multiqc +++ b/target/executable/multiqc/multiqc @@ -632,9 +632,9 @@ ENTRYPOINT [] RUN multiqc --version | sed 's/multiqc, version\s\(.*\)/multiqc: "\1"/' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component multiqc" -LABEL org.opencontainers.image.created="2024-06-24T08:36:38Z" +LABEL org.opencontainers.image.created="2024-06-24T09:14:53Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox" -LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198" +LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/pear/.config.vsh.yaml b/target/executable/pear/.config.vsh.yaml index 6387d96b..0cfdac97 100644 --- a/target/executable/pear/.config.vsh.yaml +++ b/target/executable/pear/.config.vsh.yaml @@ -380,7 +380,7 @@ build_info: output: "target/executable/pear" executable: "target/executable/pear/pear" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" 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 b031dc00..978a7c6a 100755 --- a/target/executable/pear/pear +++ b/target/executable/pear/pear @@ -592,9 +592,9 @@ RUN version=$(pear -h | grep 'PEAR v' | sed 's/PEAR v//' | sed 's/ .*//') && \ echo "pear: $version" > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component pear" -LABEL org.opencontainers.image.created="2024-06-24T08:36:41Z" +LABEL org.opencontainers.image.created="2024-06-24T09:14:56Z" LABEL org.opencontainers.image.source="https://github.com/tseemann/PEAR" -LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198" +LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/salmon/salmon_index/.config.vsh.yaml b/target/executable/salmon/salmon_index/.config.vsh.yaml index 131fc613..8555d6c4 100644 --- a/target/executable/salmon/salmon_index/.config.vsh.yaml +++ b/target/executable/salmon/salmon_index/.config.vsh.yaml @@ -263,7 +263,7 @@ build_info: output: "target/executable/salmon/salmon_index" executable: "target/executable/salmon/salmon_index/salmon_index" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" 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 ef87e13f..bcf63ee6 100755 --- a/target/executable/salmon/salmon_index/salmon_index +++ b/target/executable/salmon/salmon_index/salmon_index @@ -541,9 +541,9 @@ ENTRYPOINT [] RUN salmon index -v 2>&1 | sed 's/salmon \([0-9.]*\)/salmon: \1/' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component salmon salmon_index" -LABEL org.opencontainers.image.created="2024-06-24T08:36:42Z" +LABEL org.opencontainers.image.created="2024-06-24T09:14:58Z" LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon" -LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198" +LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/salmon/salmon_quant/.config.vsh.yaml b/target/executable/salmon/salmon_quant/.config.vsh.yaml index 885dac66..5b7bc97d 100644 --- a/target/executable/salmon/salmon_quant/.config.vsh.yaml +++ b/target/executable/salmon/salmon_quant/.config.vsh.yaml @@ -1159,7 +1159,7 @@ build_info: output: "target/executable/salmon/salmon_quant" executable: "target/executable/salmon/salmon_quant/salmon_quant" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" 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 b13a56cc..2e237ed8 100755 --- a/target/executable/salmon/salmon_quant/salmon_quant +++ b/target/executable/salmon/salmon_quant/salmon_quant @@ -1163,9 +1163,9 @@ ENTRYPOINT [] RUN salmon index -v 2>&1 | sed 's/salmon \([0-9.]*\)/salmon: \1/' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component salmon salmon_quant" -LABEL org.opencontainers.image.created="2024-06-24T08:36:42Z" +LABEL org.opencontainers.image.created="2024-06-24T09:14:57Z" LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon" -LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198" +LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/samtools/samtools_collate/.config.vsh.yaml b/target/executable/samtools/samtools_collate/.config.vsh.yaml index 84b9b48f..b9b45c2b 100644 --- a/target/executable/samtools/samtools_collate/.config.vsh.yaml +++ b/target/executable/samtools/samtools_collate/.config.vsh.yaml @@ -250,7 +250,7 @@ build_info: output: "target/executable/samtools/samtools_collate" executable: "target/executable/samtools/samtools_collate/samtools_collate" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" 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 b116c8ca..61fc0f0c 100755 --- a/target/executable/samtools/samtools_collate/samtools_collate +++ b/target/executable/samtools/samtools_collate/samtools_collate @@ -514,9 +514,9 @@ RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_collate" -LABEL org.opencontainers.image.created="2024-06-24T08:36:40Z" +LABEL org.opencontainers.image.created="2024-06-24T09:14:56Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198" +LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/samtools/samtools_faidx/.config.vsh.yaml b/target/executable/samtools/samtools_faidx/.config.vsh.yaml index 9c03e06a..b9c88846 100644 --- a/target/executable/samtools/samtools_faidx/.config.vsh.yaml +++ b/target/executable/samtools/samtools_faidx/.config.vsh.yaml @@ -229,7 +229,7 @@ build_info: output: "target/executable/samtools/samtools_faidx" executable: "target/executable/samtools/samtools_faidx/samtools_faidx" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" 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 8ed78227..963162ba 100755 --- a/target/executable/samtools/samtools_faidx/samtools_faidx +++ b/target/executable/samtools/samtools_faidx/samtools_faidx @@ -507,9 +507,9 @@ RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_faidx" -LABEL org.opencontainers.image.created="2024-06-24T08:36:38Z" +LABEL org.opencontainers.image.created="2024-06-24T09:14:54Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198" +LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/samtools/samtools_fastq/.config.vsh.yaml b/target/executable/samtools/samtools_fastq/.config.vsh.yaml index 9dc8ec0a..63276fdd 100644 --- a/target/executable/samtools/samtools_fastq/.config.vsh.yaml +++ b/target/executable/samtools/samtools_fastq/.config.vsh.yaml @@ -417,7 +417,7 @@ build_info: output: "target/executable/samtools/samtools_fastq" executable: "target/executable/samtools/samtools_fastq/samtools_fastq" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" 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 ef47ef18..7a6492f5 100755 --- a/target/executable/samtools/samtools_fastq/samtools_fastq +++ b/target/executable/samtools/samtools_fastq/samtools_fastq @@ -620,9 +620,9 @@ RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_fastq" -LABEL org.opencontainers.image.created="2024-06-24T08:36:41Z" +LABEL org.opencontainers.image.created="2024-06-24T09:14:56Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198" +LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/samtools/samtools_flagstat/.config.vsh.yaml b/target/executable/samtools/samtools_flagstat/.config.vsh.yaml index 1972c8e7..66642787 100644 --- a/target/executable/samtools/samtools_flagstat/.config.vsh.yaml +++ b/target/executable/samtools/samtools_flagstat/.config.vsh.yaml @@ -159,7 +159,7 @@ build_info: output: "target/executable/samtools/samtools_flagstat" executable: "target/executable/samtools/samtools_flagstat/samtools_flagstat" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" 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 3a1d0331..7ea0bae5 100755 --- a/target/executable/samtools/samtools_flagstat/samtools_flagstat +++ b/target/executable/samtools/samtools_flagstat/samtools_flagstat @@ -469,9 +469,9 @@ RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_flagstat" -LABEL org.opencontainers.image.created="2024-06-24T08:36:40Z" +LABEL org.opencontainers.image.created="2024-06-24T09:14:55Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198" +LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/samtools/samtools_idxstats/.config.vsh.yaml b/target/executable/samtools/samtools_idxstats/.config.vsh.yaml index f12dbeb1..1f77ac92 100644 --- a/target/executable/samtools/samtools_idxstats/.config.vsh.yaml +++ b/target/executable/samtools/samtools_idxstats/.config.vsh.yaml @@ -169,7 +169,7 @@ build_info: output: "target/executable/samtools/samtools_idxstats" executable: "target/executable/samtools/samtools_idxstats/samtools_idxstats" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" 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 8a670f6c..f3be7d2d 100755 --- a/target/executable/samtools/samtools_idxstats/samtools_idxstats +++ b/target/executable/samtools/samtools_idxstats/samtools_idxstats @@ -473,9 +473,9 @@ RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_idxstats" -LABEL org.opencontainers.image.created="2024-06-24T08:36:39Z" +LABEL org.opencontainers.image.created="2024-06-24T09:14:54Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198" +LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/samtools/samtools_index/.config.vsh.yaml b/target/executable/samtools/samtools_index/.config.vsh.yaml index ce6d9daa..3f8f7a79 100644 --- a/target/executable/samtools/samtools_index/.config.vsh.yaml +++ b/target/executable/samtools/samtools_index/.config.vsh.yaml @@ -175,7 +175,7 @@ build_info: output: "target/executable/samtools/samtools_index" executable: "target/executable/samtools/samtools_index/samtools_index" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" 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 a12d81c9..8ff940a1 100755 --- a/target/executable/samtools/samtools_index/samtools_index +++ b/target/executable/samtools/samtools_index/samtools_index @@ -480,9 +480,9 @@ RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_index" -LABEL org.opencontainers.image.created="2024-06-24T08:36:40Z" +LABEL org.opencontainers.image.created="2024-06-24T09:14:55Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198" +LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/samtools/samtools_sort/.config.vsh.yaml b/target/executable/samtools/samtools_sort/.config.vsh.yaml index 3cb18e42..7b7de649 100644 --- a/target/executable/samtools/samtools_sort/.config.vsh.yaml +++ b/target/executable/samtools/samtools_sort/.config.vsh.yaml @@ -318,7 +318,7 @@ build_info: output: "target/executable/samtools/samtools_sort" executable: "target/executable/samtools/samtools_sort/samtools_sort" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" 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 c967b262..44eb31aa 100755 --- a/target/executable/samtools/samtools_sort/samtools_sort +++ b/target/executable/samtools/samtools_sort/samtools_sort @@ -551,9 +551,9 @@ RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_sort" -LABEL org.opencontainers.image.created="2024-06-24T08:36:39Z" +LABEL org.opencontainers.image.created="2024-06-24T09:14:54Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198" +LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/samtools/samtools_stats/.config.vsh.yaml b/target/executable/samtools/samtools_stats/.config.vsh.yaml index e562edf2..fac92db4 100644 --- a/target/executable/samtools/samtools_stats/.config.vsh.yaml +++ b/target/executable/samtools/samtools_stats/.config.vsh.yaml @@ -380,7 +380,7 @@ build_info: output: "target/executable/samtools/samtools_stats" executable: "target/executable/samtools/samtools_stats/samtools_stats" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" 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 60e5f05f..69a8e075 100755 --- a/target/executable/samtools/samtools_stats/samtools_stats +++ b/target/executable/samtools/samtools_stats/samtools_stats @@ -568,9 +568,9 @@ RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_stats" -LABEL org.opencontainers.image.created="2024-06-24T08:36:39Z" +LABEL org.opencontainers.image.created="2024-06-24T09:14:55Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198" +LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/samtools/samtools_view/.config.vsh.yaml b/target/executable/samtools/samtools_view/.config.vsh.yaml index 3873e2aa..2033b48d 100644 --- a/target/executable/samtools/samtools_view/.config.vsh.yaml +++ b/target/executable/samtools/samtools_view/.config.vsh.yaml @@ -651,7 +651,7 @@ build_info: output: "target/executable/samtools/samtools_view" executable: "target/executable/samtools/samtools_view/samtools_view" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" 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 a0169701..0121f65f 100755 --- a/target/executable/samtools/samtools_view/samtools_view +++ b/target/executable/samtools/samtools_view/samtools_view @@ -820,9 +820,9 @@ RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_view" -LABEL org.opencontainers.image.created="2024-06-24T08:36:38Z" +LABEL org.opencontainers.image.created="2024-06-24T09:14:53Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198" +LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/star/star_align_reads/.config.vsh.yaml b/target/executable/star/star_align_reads/.config.vsh.yaml index 4fa8fad7..5fb5f4be 100644 --- a/target/executable/star/star_align_reads/.config.vsh.yaml +++ b/target/executable/star/star_align_reads/.config.vsh.yaml @@ -1966,6 +1966,19 @@ argument_groups: direction: "output" multiple: false multiple_sep: ";" + - type: "file" + name: "--reads_aligned_to_transcriptome" + description: "The output file containing the alignments to transcriptome in BAM\ + \ formats. This file is generated when --quantMode is set to TranscriptomeSAM." + info: null + example: + - "transcriptome_aligned.bam" + must_exist: true + create_parent: true + required: false + direction: "output" + multiple: false + multiple_sep: ";" resources: - type: "python_script" path: "script.py" @@ -2095,7 +2108,7 @@ build_info: output: "target/executable/star/star_align_reads" executable: "target/executable/star/star_align_reads/star_align_reads" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" 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 c385a9e7..843c6cc4 100755 --- a/target/executable/star/star_align_reads/star_align_reads +++ b/target/executable/star/star_align_reads/star_align_reads @@ -1360,6 +1360,13 @@ function ViashHelp { echo " type: file, output, file must exist" echo " example: splice_junctions.tsv" echo " The output file containing the splice junctions." + echo "" + echo " --reads_aligned_to_transcriptome" + echo " type: file, output, file must exist" + echo " example: transcriptome_aligned.bam" + echo " The output file containing the alignments to transcriptome in BAM" + echo " formats. This file is generated when --quantMode is set to" + echo " TranscriptomeSAM." } # initialise variables @@ -1658,9 +1665,9 @@ RUN apt-get update && \ RUN STAR --version | sed 's#\(.*\)#star: "\1"#' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component star star_align_reads" -LABEL org.opencontainers.image.created="2024-06-24T08:36:45Z" +LABEL org.opencontainers.image.created="2024-06-24T09:15:00Z" LABEL org.opencontainers.image.source="https://github.com/alexdobin/STAR" -LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198" +LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -3821,6 +3828,17 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_SPLICE_JUNCTIONS=$(ViashRemoveFlags "$1") shift 1 ;; + --reads_aligned_to_transcriptome) + [ -n "$VIASH_PAR_READS_ALIGNED_TO_TRANSCRIPTOME" ] && ViashError Bad arguments for option \'--reads_aligned_to_transcriptome\': \'$VIASH_PAR_READS_ALIGNED_TO_TRANSCRIPTOME\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_READS_ALIGNED_TO_TRANSCRIPTOME="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --reads_aligned_to_transcriptome. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --reads_aligned_to_transcriptome=*) + [ -n "$VIASH_PAR_READS_ALIGNED_TO_TRANSCRIPTOME" ] && ViashError Bad arguments for option \'--reads_aligned_to_transcriptome=*\': \'$VIASH_PAR_READS_ALIGNED_TO_TRANSCRIPTOME\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_READS_ALIGNED_TO_TRANSCRIPTOME=$(ViashRemoveFlags "$1") + shift 1 + ;; ---engine) VIASH_ENGINE_ID="$2" shift 2 @@ -4814,6 +4832,9 @@ fi if [ ! -z "$VIASH_PAR_SPLICE_JUNCTIONS" ] && [ ! -d "$(dirname "$VIASH_PAR_SPLICE_JUNCTIONS")" ]; then mkdir -p "$(dirname "$VIASH_PAR_SPLICE_JUNCTIONS")" fi +if [ ! -z "$VIASH_PAR_READS_ALIGNED_TO_TRANSCRIPTOME" ] && [ ! -d "$(dirname "$VIASH_PAR_READS_ALIGNED_TO_TRANSCRIPTOME")" ]; then + mkdir -p "$(dirname "$VIASH_PAR_READS_ALIGNED_TO_TRANSCRIPTOME")" +fi if [ "$VIASH_ENGINE_ID" == "native" ] ; then if [ "$VIASH_MODE" == "run" ]; then @@ -4907,6 +4928,11 @@ if [ ! -z "$VIASH_PAR_SPLICE_JUNCTIONS" ]; then VIASH_PAR_SPLICE_JUNCTIONS=$(ViashDockerAutodetectMount "$VIASH_PAR_SPLICE_JUNCTIONS") VIASH_CHOWN_VARS+=( "$VIASH_PAR_SPLICE_JUNCTIONS" ) fi +if [ ! -z "$VIASH_PAR_READS_ALIGNED_TO_TRANSCRIPTOME" ]; then + VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_READS_ALIGNED_TO_TRANSCRIPTOME")" ) + VIASH_PAR_READS_ALIGNED_TO_TRANSCRIPTOME=$(ViashDockerAutodetectMount "$VIASH_PAR_READS_ALIGNED_TO_TRANSCRIPTOME") + VIASH_CHOWN_VARS+=( "$VIASH_PAR_READS_ALIGNED_TO_TRANSCRIPTOME" ) +fi if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_RESOURCES_DIR")" ) VIASH_META_RESOURCES_DIR=$(ViashDockerAutodetectMount "$VIASH_META_RESOURCES_DIR") @@ -5146,7 +5172,8 @@ par = { 'unmapped_r2': $( if [ ! -z ${VIASH_PAR_UNMAPPED_R2+x} ]; then echo "r'${VIASH_PAR_UNMAPPED_R2//\'/\'\"\'\"r\'}'"; else echo None; fi ), 'chimeric_junctions': $( if [ ! -z ${VIASH_PAR_CHIMERIC_JUNCTIONS+x} ]; then echo "r'${VIASH_PAR_CHIMERIC_JUNCTIONS//\'/\'\"\'\"r\'}'"; else echo None; fi ), 'log': $( if [ ! -z ${VIASH_PAR_LOG+x} ]; then echo "r'${VIASH_PAR_LOG//\'/\'\"\'\"r\'}'"; else echo None; fi ), - 'splice_junctions': $( if [ ! -z ${VIASH_PAR_SPLICE_JUNCTIONS+x} ]; then echo "r'${VIASH_PAR_SPLICE_JUNCTIONS//\'/\'\"\'\"r\'}'"; else echo None; fi ) + 'splice_junctions': $( if [ ! -z ${VIASH_PAR_SPLICE_JUNCTIONS+x} ]; then echo "r'${VIASH_PAR_SPLICE_JUNCTIONS//\'/\'\"\'\"r\'}'"; else echo None; fi ), + 'reads_aligned_to_transcriptome': $( if [ ! -z ${VIASH_PAR_READS_ALIGNED_TO_TRANSCRIPTOME+x} ]; then echo "r'${VIASH_PAR_READS_ALIGNED_TO_TRANSCRIPTOME//\'/\'\"\'\"r\'}'"; else echo None; fi ) } meta = { 'name': $( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "r'${VIASH_META_NAME//\'/\'\"\'\"r\'}'"; else echo None; fi ), @@ -5210,7 +5237,8 @@ expected_outputs = { "log": "Log.final.out", "splice_junctions": "SJ.out.tab", "unmapped": "Unmapped.out.mate1", - "unmapped_r2": "Unmapped.out.mate2" + "unmapped_r2": "Unmapped.out.mate2", + "reads_aligned_to_transcriptome": "Aligned.toTranscriptome.out.bam" } output_paths = {name: par[name] for name in expected_outputs.keys()} for name in expected_outputs.keys(): @@ -5338,6 +5366,9 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then if [ ! -z "$VIASH_PAR_SPLICE_JUNCTIONS" ]; then VIASH_PAR_SPLICE_JUNCTIONS=$(ViashDockerStripAutomount "$VIASH_PAR_SPLICE_JUNCTIONS") fi + if [ ! -z "$VIASH_PAR_READS_ALIGNED_TO_TRANSCRIPTOME" ]; then + VIASH_PAR_READS_ALIGNED_TO_TRANSCRIPTOME=$(ViashDockerStripAutomount "$VIASH_PAR_READS_ALIGNED_TO_TRANSCRIPTOME") + fi if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then VIASH_META_RESOURCES_DIR=$(ViashDockerStripAutomount "$VIASH_META_RESOURCES_DIR") fi @@ -5382,6 +5413,10 @@ if [ ! -z "$VIASH_PAR_SPLICE_JUNCTIONS" ] && [ ! -e "$VIASH_PAR_SPLICE_JUNCTIONS ViashError "Output file '$VIASH_PAR_SPLICE_JUNCTIONS' does not exist." exit 1 fi +if [ ! -z "$VIASH_PAR_READS_ALIGNED_TO_TRANSCRIPTOME" ] && [ ! -e "$VIASH_PAR_READS_ALIGNED_TO_TRANSCRIPTOME" ]; then + ViashError "Output file '$VIASH_PAR_READS_ALIGNED_TO_TRANSCRIPTOME' does not exist." + exit 1 +fi exit 0 diff --git a/target/executable/star/star_genome_generate/.config.vsh.yaml b/target/executable/star/star_genome_generate/.config.vsh.yaml index 10558d7e..d1ae513b 100644 --- a/target/executable/star/star_genome_generate/.config.vsh.yaml +++ b/target/executable/star/star_genome_generate/.config.vsh.yaml @@ -319,7 +319,7 @@ build_info: output: "target/executable/star/star_genome_generate" executable: "target/executable/star/star_genome_generate/star_genome_generate" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" 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 61865f20..c6bfa3e7 100755 --- a/target/executable/star/star_genome_generate/star_genome_generate +++ b/target/executable/star/star_genome_generate/star_genome_generate @@ -572,9 +572,9 @@ RUN apt-get update && \ RUN STAR --version | sed 's#\(.*\)#star: "\1"#' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component star star_genome_generate" -LABEL org.opencontainers.image.created="2024-06-24T08:36:46Z" +LABEL org.opencontainers.image.created="2024-06-24T09:15:01Z" LABEL org.opencontainers.image.source="https://github.com/alexdobin/STAR" -LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198" +LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/nextflow/arriba/.config.vsh.yaml b/target/nextflow/arriba/.config.vsh.yaml index ce15f276..97b468c0 100644 --- a/target/nextflow/arriba/.config.vsh.yaml +++ b/target/nextflow/arriba/.config.vsh.yaml @@ -688,7 +688,7 @@ build_info: output: "target/nextflow/arriba" executable: "target/nextflow/arriba/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" 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 2a6088b4..be8f5c6e 100644 --- a/target/nextflow/arriba/main.nf +++ b/target/nextflow/arriba/main.nf @@ -3534,7 +3534,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/arriba", "viash_version" : "0.9.0-RC6", - "git_commit" : "d0c648fb7eefe067f5b5b3d402a204354bb37198", + "git_commit" : "3481750f6e2d77defa28423d832ff251da3a1f9e", "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 a410028c..5936b9b8 100644 --- a/target/nextflow/bcl_convert/.config.vsh.yaml +++ b/target/nextflow/bcl_convert/.config.vsh.yaml @@ -386,7 +386,7 @@ build_info: output: "target/nextflow/bcl_convert" executable: "target/nextflow/bcl_convert/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" 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 cdc631da..ec4377d8 100644 --- a/target/nextflow/bcl_convert/main.nf +++ b/target/nextflow/bcl_convert/main.nf @@ -3249,7 +3249,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bcl_convert", "viash_version" : "0.9.0-RC6", - "git_commit" : "d0c648fb7eefe067f5b5b3d402a204354bb37198", + "git_commit" : "3481750f6e2d77defa28423d832ff251da3a1f9e", "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 56c803f0..0e583172 100644 --- a/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml @@ -217,7 +217,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_getfasta" executable: "target/nextflow/bedtools/bedtools_getfasta/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" 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 e0952c6e..d972783d 100644 --- a/target/nextflow/bedtools/bedtools_getfasta/main.nf +++ b/target/nextflow/bedtools/bedtools_getfasta/main.nf @@ -3033,7 +3033,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_getfasta", "viash_version" : "0.9.0-RC6", - "git_commit" : "d0c648fb7eefe067f5b5b3d402a204354bb37198", + "git_commit" : "3481750f6e2d77defa28423d832ff251da3a1f9e", "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 5558e1dc..0a9aa054 100644 --- a/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml +++ b/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml @@ -144,7 +144,7 @@ build_info: output: "target/nextflow/busco/busco_download_datasets" executable: "target/nextflow/busco/busco_download_datasets/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" 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 aa27b1c9..5726619b 100644 --- a/target/nextflow/busco/busco_download_datasets/main.nf +++ b/target/nextflow/busco/busco_download_datasets/main.nf @@ -2959,7 +2959,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/busco/busco_download_datasets", "viash_version" : "0.9.0-RC6", - "git_commit" : "d0c648fb7eefe067f5b5b3d402a204354bb37198", + "git_commit" : "3481750f6e2d77defa28423d832ff251da3a1f9e", "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 e3131512..b5fefa61 100644 --- a/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml +++ b/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml @@ -131,7 +131,7 @@ build_info: output: "target/nextflow/busco/busco_list_datasets" executable: "target/nextflow/busco/busco_list_datasets/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" 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 4857d947..e3e3f350 100644 --- a/target/nextflow/busco/busco_list_datasets/main.nf +++ b/target/nextflow/busco/busco_list_datasets/main.nf @@ -2945,7 +2945,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/busco/busco_list_datasets", "viash_version" : "0.9.0-RC6", - "git_commit" : "d0c648fb7eefe067f5b5b3d402a204354bb37198", + "git_commit" : "3481750f6e2d77defa28423d832ff251da3a1f9e", "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 cee05b75..441c9a38 100644 --- a/target/nextflow/busco/busco_run/.config.vsh.yaml +++ b/target/nextflow/busco/busco_run/.config.vsh.yaml @@ -404,7 +404,7 @@ build_info: output: "target/nextflow/busco/busco_run" executable: "target/nextflow/busco/busco_run/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" 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 4ce390b1..73c16369 100644 --- a/target/nextflow/busco/busco_run/main.nf +++ b/target/nextflow/busco/busco_run/main.nf @@ -3251,7 +3251,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/busco/busco_run", "viash_version" : "0.9.0-RC6", - "git_commit" : "d0c648fb7eefe067f5b5b3d402a204354bb37198", + "git_commit" : "3481750f6e2d77defa28423d832ff251da3a1f9e", "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 0656b87b..0b8634f9 100644 --- a/target/nextflow/cutadapt/.config.vsh.yaml +++ b/target/nextflow/cutadapt/.config.vsh.yaml @@ -707,7 +707,7 @@ build_info: output: "target/nextflow/cutadapt" executable: "target/nextflow/cutadapt/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" 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 e96ec886..eff30786 100644 --- a/target/nextflow/cutadapt/main.nf +++ b/target/nextflow/cutadapt/main.nf @@ -3549,7 +3549,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/cutadapt", "viash_version" : "0.9.0-RC6", - "git_commit" : "d0c648fb7eefe067f5b5b3d402a204354bb37198", + "git_commit" : "3481750f6e2d77defa28423d832ff251da3a1f9e", "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 5bab198b..0777613d 100644 --- a/target/nextflow/falco/.config.vsh.yaml +++ b/target/nextflow/falco/.config.vsh.yaml @@ -304,7 +304,7 @@ build_info: output: "target/nextflow/falco" executable: "target/nextflow/falco/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" 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 6ca5a5a4..dce282fb 100644 --- a/target/nextflow/falco/main.nf +++ b/target/nextflow/falco/main.nf @@ -3119,7 +3119,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/falco", "viash_version" : "0.9.0-RC6", - "git_commit" : "d0c648fb7eefe067f5b5b3d402a204354bb37198", + "git_commit" : "3481750f6e2d77defa28423d832ff251da3a1f9e", "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 bee26ba8..8db64381 100644 --- a/target/nextflow/fastp/.config.vsh.yaml +++ b/target/nextflow/fastp/.config.vsh.yaml @@ -1065,7 +1065,7 @@ build_info: output: "target/nextflow/fastp" executable: "target/nextflow/fastp/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" 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 503263af..cb77e9d6 100644 --- a/target/nextflow/fastp/main.nf +++ b/target/nextflow/fastp/main.nf @@ -3965,7 +3965,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/fastp", "viash_version" : "0.9.0-RC6", - "git_commit" : "d0c648fb7eefe067f5b5b3d402a204354bb37198", + "git_commit" : "3481750f6e2d77defa28423d832ff251da3a1f9e", "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 b8ac7d6f..9d2f2523 100644 --- a/target/nextflow/featurecounts/.config.vsh.yaml +++ b/target/nextflow/featurecounts/.config.vsh.yaml @@ -631,7 +631,7 @@ build_info: output: "target/nextflow/featurecounts" executable: "target/nextflow/featurecounts/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" 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 01a22bfc..d7c778db 100644 --- a/target/nextflow/featurecounts/main.nf +++ b/target/nextflow/featurecounts/main.nf @@ -3497,7 +3497,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/featurecounts", "viash_version" : "0.9.0-RC6", - "git_commit" : "d0c648fb7eefe067f5b5b3d402a204354bb37198", + "git_commit" : "3481750f6e2d77defa28423d832ff251da3a1f9e", "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 f7e6cc4f..026b7522 100644 --- a/target/nextflow/gffread/.config.vsh.yaml +++ b/target/nextflow/gffread/.config.vsh.yaml @@ -671,7 +671,7 @@ build_info: output: "target/nextflow/gffread" executable: "target/nextflow/gffread/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" 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 a2a270ec..d9a89ade 100644 --- a/target/nextflow/gffread/main.nf +++ b/target/nextflow/gffread/main.nf @@ -3554,7 +3554,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/gffread", "viash_version" : "0.9.0-RC6", - "git_commit" : "d0c648fb7eefe067f5b5b3d402a204354bb37198", + "git_commit" : "3481750f6e2d77defa28423d832ff251da3a1f9e", "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 c39253ee..c80b2908 100644 --- a/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml +++ b/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml @@ -489,7 +489,7 @@ build_info: output: "target/nextflow/lofreq/lofreq_call" executable: "target/nextflow/lofreq/lofreq_call/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" 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 aad0ddd7..d2ccaaf4 100644 --- a/target/nextflow/lofreq/lofreq_call/main.nf +++ b/target/nextflow/lofreq/lofreq_call/main.nf @@ -3356,7 +3356,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/lofreq/lofreq_call", "viash_version" : "0.9.0-RC6", - "git_commit" : "d0c648fb7eefe067f5b5b3d402a204354bb37198", + "git_commit" : "3481750f6e2d77defa28423d832ff251da3a1f9e", "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 551cb9c4..93c44618 100644 --- a/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml +++ b/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml @@ -197,7 +197,7 @@ build_info: output: "target/nextflow/lofreq/lofreq_indelqual" executable: "target/nextflow/lofreq/lofreq_indelqual/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" 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 bc790eca..edca61bc 100644 --- a/target/nextflow/lofreq/lofreq_indelqual/main.nf +++ b/target/nextflow/lofreq/lofreq_indelqual/main.nf @@ -3019,7 +3019,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/lofreq/lofreq_indelqual", "viash_version" : "0.9.0-RC6", - "git_commit" : "d0c648fb7eefe067f5b5b3d402a204354bb37198", + "git_commit" : "3481750f6e2d77defa28423d832ff251da3a1f9e", "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 96cb9c7c..b1a6cd5e 100644 --- a/target/nextflow/multiqc/.config.vsh.yaml +++ b/target/nextflow/multiqc/.config.vsh.yaml @@ -438,7 +438,7 @@ build_info: output: "target/nextflow/multiqc" executable: "target/nextflow/multiqc/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" 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 a323a79b..b0d9c142 100644 --- a/target/nextflow/multiqc/main.nf +++ b/target/nextflow/multiqc/main.nf @@ -3310,7 +3310,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/multiqc", "viash_version" : "0.9.0-RC6", - "git_commit" : "d0c648fb7eefe067f5b5b3d402a204354bb37198", + "git_commit" : "3481750f6e2d77defa28423d832ff251da3a1f9e", "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 57af6ce6..dafb3b5a 100644 --- a/target/nextflow/pear/.config.vsh.yaml +++ b/target/nextflow/pear/.config.vsh.yaml @@ -380,7 +380,7 @@ build_info: output: "target/nextflow/pear" executable: "target/nextflow/pear/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" 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 eb614385..353ecbb5 100644 --- a/target/nextflow/pear/main.nf +++ b/target/nextflow/pear/main.nf @@ -3201,7 +3201,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/pear", "viash_version" : "0.9.0-RC6", - "git_commit" : "d0c648fb7eefe067f5b5b3d402a204354bb37198", + "git_commit" : "3481750f6e2d77defa28423d832ff251da3a1f9e", "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 e91ccd89..d3afc428 100644 --- a/target/nextflow/salmon/salmon_index/.config.vsh.yaml +++ b/target/nextflow/salmon/salmon_index/.config.vsh.yaml @@ -263,7 +263,7 @@ build_info: output: "target/nextflow/salmon/salmon_index" executable: "target/nextflow/salmon/salmon_index/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" 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 d75113e7..2d4857cc 100644 --- a/target/nextflow/salmon/salmon_index/main.nf +++ b/target/nextflow/salmon/salmon_index/main.nf @@ -3077,7 +3077,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/salmon/salmon_index", "viash_version" : "0.9.0-RC6", - "git_commit" : "d0c648fb7eefe067f5b5b3d402a204354bb37198", + "git_commit" : "3481750f6e2d77defa28423d832ff251da3a1f9e", "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 39a27b49..7e537801 100644 --- a/target/nextflow/salmon/salmon_quant/.config.vsh.yaml +++ b/target/nextflow/salmon/salmon_quant/.config.vsh.yaml @@ -1159,7 +1159,7 @@ build_info: output: "target/nextflow/salmon/salmon_quant" executable: "target/nextflow/salmon/salmon_quant/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" 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 e678eae2..d611f2a4 100644 --- a/target/nextflow/salmon/salmon_quant/main.nf +++ b/target/nextflow/salmon/salmon_quant/main.nf @@ -3912,7 +3912,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/salmon/salmon_quant", "viash_version" : "0.9.0-RC6", - "git_commit" : "d0c648fb7eefe067f5b5b3d402a204354bb37198", + "git_commit" : "3481750f6e2d77defa28423d832ff251da3a1f9e", "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 e411d54b..f8c5017f 100644 --- a/target/nextflow/samtools/samtools_collate/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_collate/.config.vsh.yaml @@ -250,7 +250,7 @@ build_info: output: "target/nextflow/samtools/samtools_collate" executable: "target/nextflow/samtools/samtools_collate/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" 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 c0357eca..d158d5be 100644 --- a/target/nextflow/samtools/samtools_collate/main.nf +++ b/target/nextflow/samtools/samtools_collate/main.nf @@ -3088,7 +3088,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_collate", "viash_version" : "0.9.0-RC6", - "git_commit" : "d0c648fb7eefe067f5b5b3d402a204354bb37198", + "git_commit" : "3481750f6e2d77defa28423d832ff251da3a1f9e", "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 c1d56b6c..252dcc58 100644 --- a/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml @@ -229,7 +229,7 @@ build_info: output: "target/nextflow/samtools/samtools_faidx" executable: "target/nextflow/samtools/samtools_faidx/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" 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 841a3afb..51faf4c8 100644 --- a/target/nextflow/samtools/samtools_faidx/main.nf +++ b/target/nextflow/samtools/samtools_faidx/main.nf @@ -3060,7 +3060,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_faidx", "viash_version" : "0.9.0-RC6", - "git_commit" : "d0c648fb7eefe067f5b5b3d402a204354bb37198", + "git_commit" : "3481750f6e2d77defa28423d832ff251da3a1f9e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml b/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml index 7338fd1f..dc986107 100644 --- a/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml @@ -417,7 +417,7 @@ build_info: output: "target/nextflow/samtools/samtools_fastq" executable: "target/nextflow/samtools/samtools_fastq/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" 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 488020e2..e345d0b8 100644 --- a/target/nextflow/samtools/samtools_fastq/main.nf +++ b/target/nextflow/samtools/samtools_fastq/main.nf @@ -3252,7 +3252,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_fastq", "viash_version" : "0.9.0-RC6", - "git_commit" : "d0c648fb7eefe067f5b5b3d402a204354bb37198", + "git_commit" : "3481750f6e2d77defa28423d832ff251da3a1f9e", "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 971641d8..2947eb8a 100644 --- a/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml @@ -159,7 +159,7 @@ build_info: output: "target/nextflow/samtools/samtools_flagstat" executable: "target/nextflow/samtools/samtools_flagstat/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" 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 7eb25fa5..7c21b14b 100644 --- a/target/nextflow/samtools/samtools_flagstat/main.nf +++ b/target/nextflow/samtools/samtools_flagstat/main.nf @@ -2976,7 +2976,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_flagstat", "viash_version" : "0.9.0-RC6", - "git_commit" : "d0c648fb7eefe067f5b5b3d402a204354bb37198", + "git_commit" : "3481750f6e2d77defa28423d832ff251da3a1f9e", "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 2b778a7c..d98a75c2 100644 --- a/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml @@ -169,7 +169,7 @@ build_info: output: "target/nextflow/samtools/samtools_idxstats" executable: "target/nextflow/samtools/samtools_idxstats/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" 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 6256d859..579acf0d 100644 --- a/target/nextflow/samtools/samtools_idxstats/main.nf +++ b/target/nextflow/samtools/samtools_idxstats/main.nf @@ -2988,7 +2988,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_idxstats", "viash_version" : "0.9.0-RC6", - "git_commit" : "d0c648fb7eefe067f5b5b3d402a204354bb37198", + "git_commit" : "3481750f6e2d77defa28423d832ff251da3a1f9e", "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 1eabb436..3732822e 100644 --- a/target/nextflow/samtools/samtools_index/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_index/.config.vsh.yaml @@ -175,7 +175,7 @@ build_info: output: "target/nextflow/samtools/samtools_index" executable: "target/nextflow/samtools/samtools_index/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" 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 5917fdee..34753dc3 100644 --- a/target/nextflow/samtools/samtools_index/main.nf +++ b/target/nextflow/samtools/samtools_index/main.nf @@ -3001,7 +3001,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_index", "viash_version" : "0.9.0-RC6", - "git_commit" : "d0c648fb7eefe067f5b5b3d402a204354bb37198", + "git_commit" : "3481750f6e2d77defa28423d832ff251da3a1f9e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/samtools/samtools_index/nextflow_schema.json b/target/nextflow/samtools/samtools_index/nextflow_schema.json deleted file mode 100644 index 38b24926..00000000 --- a/target/nextflow/samtools/samtools_index/nextflow_schema.json +++ /dev/null @@ -1,141 +0,0 @@ -{ -"$schema": "http://json-schema.org/draft-07/schema", -"title": "samtools_index", -"description": "Index SAM/BAM/CRAM files.", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "input": { - "type": - "string", - "description": "Type: `file`, required. Input file name", - "help_text": "Type: `file`, required. Input file name" - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "output": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.output.bai`, example: `out.bam.bai`. Output file name", - "help_text": "Type: `file`, required, default: `$id.$key.output.bai`, example: `out.bam.bai`. Output file name" - , - "default": "$id.$key.output.bai" - } - - -} -}, - - - "options" : { - "title": "Options", - "type": "object", - "description": "No description", - "properties": { - - - "bai": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Generate BAM index", - "help_text": "Type: `boolean_true`, default: `false`. Generate BAM index" - , - "default": "False" - } - - - , - "csi": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Create a CSI index for BAM files instead of the traditional BAI \nindex", - "help_text": "Type: `boolean_true`, default: `false`. Create a CSI index for BAM files instead of the traditional BAI \nindex. This will be required for genomes with larger chromosome \nsizes.\n" - , - "default": "False" - } - - - , - "min_shift": { - "type": - "integer", - "description": "Type: `integer`. Create a CSI index, with a minimum interval size of 2^INT", - "help_text": "Type: `integer`. Create a CSI index, with a minimum interval size of 2^INT.\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_sort/.config.vsh.yaml b/target/nextflow/samtools/samtools_sort/.config.vsh.yaml index 39d5c2c0..67c9c4a6 100644 --- a/target/nextflow/samtools/samtools_sort/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_sort/.config.vsh.yaml @@ -318,7 +318,7 @@ build_info: output: "target/nextflow/samtools/samtools_sort" executable: "target/nextflow/samtools/samtools_sort/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" 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 20753ee4..0392cdeb 100644 --- a/target/nextflow/samtools/samtools_sort/main.nf +++ b/target/nextflow/samtools/samtools_sort/main.nf @@ -3173,7 +3173,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_sort", "viash_version" : "0.9.0-RC6", - "git_commit" : "d0c648fb7eefe067f5b5b3d402a204354bb37198", + "git_commit" : "3481750f6e2d77defa28423d832ff251da3a1f9e", "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 7aefbe46..de3880ab 100644 --- a/target/nextflow/samtools/samtools_stats/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_stats/.config.vsh.yaml @@ -380,7 +380,7 @@ build_info: output: "target/nextflow/samtools/samtools_stats" executable: "target/nextflow/samtools/samtools_stats/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" 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 1099dec9..21e071db 100644 --- a/target/nextflow/samtools/samtools_stats/main.nf +++ b/target/nextflow/samtools/samtools_stats/main.nf @@ -3238,7 +3238,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_stats", "viash_version" : "0.9.0-RC6", - "git_commit" : "d0c648fb7eefe067f5b5b3d402a204354bb37198", + "git_commit" : "3481750f6e2d77defa28423d832ff251da3a1f9e", "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 cfb1632b..723560e0 100644 --- a/target/nextflow/samtools/samtools_view/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_view/.config.vsh.yaml @@ -651,7 +651,7 @@ build_info: output: "target/nextflow/samtools/samtools_view" executable: "target/nextflow/samtools/samtools_view/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" 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 d00e913b..590d63d5 100644 --- a/target/nextflow/samtools/samtools_view/main.nf +++ b/target/nextflow/samtools/samtools_view/main.nf @@ -3424,7 +3424,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_view", "viash_version" : "0.9.0-RC6", - "git_commit" : "d0c648fb7eefe067f5b5b3d402a204354bb37198", + "git_commit" : "3481750f6e2d77defa28423d832ff251da3a1f9e", "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 2bf8a55e..57ae4316 100644 --- a/target/nextflow/star/star_align_reads/.config.vsh.yaml +++ b/target/nextflow/star/star_align_reads/.config.vsh.yaml @@ -1966,6 +1966,19 @@ argument_groups: direction: "output" multiple: false multiple_sep: ";" + - type: "file" + name: "--reads_aligned_to_transcriptome" + description: "The output file containing the alignments to transcriptome in BAM\ + \ formats. This file is generated when --quantMode is set to TranscriptomeSAM." + info: null + example: + - "transcriptome_aligned.bam" + must_exist: true + create_parent: true + required: false + direction: "output" + multiple: false + multiple_sep: ";" resources: - type: "python_script" path: "script.py" @@ -2095,7 +2108,7 @@ build_info: output: "target/nextflow/star/star_align_reads" executable: "target/nextflow/star/star_align_reads/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" 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 e2d1828c..77c6d6fb 100644 --- a/target/nextflow/star/star_align_reads/main.nf +++ b/target/nextflow/star/star_align_reads/main.nf @@ -4848,6 +4848,20 @@ meta = [ "direction" : "output", "multiple" : false, "multiple_sep" : ";" + }, + { + "type" : "file", + "name" : "--reads_aligned_to_transcriptome", + "description" : "The output file containing the alignments to transcriptome in BAM formats. This file is generated when --quantMode is set to TranscriptomeSAM.", + "example" : [ + "transcriptome_aligned.bam" + ], + "must_exist" : true, + "create_parent" : true, + "required" : false, + "direction" : "output", + "multiple" : false, + "multiple_sep" : ";" } ] } @@ -5009,7 +5023,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/star/star_align_reads", "viash_version" : "0.9.0-RC6", - "git_commit" : "d0c648fb7eefe067f5b5b3d402a204354bb37198", + "git_commit" : "3481750f6e2d77defa28423d832ff251da3a1f9e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { @@ -5221,7 +5235,8 @@ par = { 'unmapped_r2': $( if [ ! -z ${VIASH_PAR_UNMAPPED_R2+x} ]; then echo "r'${VIASH_PAR_UNMAPPED_R2//\\'/\\'\\"\\'\\"r\\'}'"; else echo None; fi ), 'chimeric_junctions': $( if [ ! -z ${VIASH_PAR_CHIMERIC_JUNCTIONS+x} ]; then echo "r'${VIASH_PAR_CHIMERIC_JUNCTIONS//\\'/\\'\\"\\'\\"r\\'}'"; else echo None; fi ), 'log': $( if [ ! -z ${VIASH_PAR_LOG+x} ]; then echo "r'${VIASH_PAR_LOG//\\'/\\'\\"\\'\\"r\\'}'"; else echo None; fi ), - 'splice_junctions': $( if [ ! -z ${VIASH_PAR_SPLICE_JUNCTIONS+x} ]; then echo "r'${VIASH_PAR_SPLICE_JUNCTIONS//\\'/\\'\\"\\'\\"r\\'}'"; else echo None; fi ) + 'splice_junctions': $( if [ ! -z ${VIASH_PAR_SPLICE_JUNCTIONS+x} ]; then echo "r'${VIASH_PAR_SPLICE_JUNCTIONS//\\'/\\'\\"\\'\\"r\\'}'"; else echo None; fi ), + 'reads_aligned_to_transcriptome': $( if [ ! -z ${VIASH_PAR_READS_ALIGNED_TO_TRANSCRIPTOME+x} ]; then echo "r'${VIASH_PAR_READS_ALIGNED_TO_TRANSCRIPTOME//\\'/\\'\\"\\'\\"r\\'}'"; else echo None; fi ) } meta = { 'name': $( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "r'${VIASH_META_NAME//\\'/\\'\\"\\'\\"r\\'}'"; else echo None; fi ), @@ -5285,7 +5300,8 @@ expected_outputs = { "log": "Log.final.out", "splice_junctions": "SJ.out.tab", "unmapped": "Unmapped.out.mate1", - "unmapped_r2": "Unmapped.out.mate2" + "unmapped_r2": "Unmapped.out.mate2", + "reads_aligned_to_transcriptome": "Aligned.toTranscriptome.out.bam" } output_paths = {name: par[name] for name in expected_outputs.keys()} for name in expected_outputs.keys(): diff --git a/target/nextflow/star/star_align_reads/nextflow_schema.json b/target/nextflow/star/star_align_reads/nextflow_schema.json index 6c1dc148..82127551 100644 --- a/target/nextflow/star/star_align_reads/nextflow_schema.json +++ b/target/nextflow/star/star_align_reads/nextflow_schema.json @@ -120,6 +120,17 @@ } + , + "reads_aligned_to_transcriptome": { + "type": + "string", + "description": "Type: `file`, default: `$id.$key.reads_aligned_to_transcriptome.bam`, example: `transcriptome_aligned.bam`. The output file containing the alignments to transcriptome in BAM formats", + "help_text": "Type: `file`, default: `$id.$key.reads_aligned_to_transcriptome.bam`, example: `transcriptome_aligned.bam`. The output file containing the alignments to transcriptome in BAM formats. This file is generated when --quantMode is set to TranscriptomeSAM." + , + "default": "$id.$key.reads_aligned_to_transcriptome.bam" + } + + } }, diff --git a/target/nextflow/star/star_genome_generate/.config.vsh.yaml b/target/nextflow/star/star_genome_generate/.config.vsh.yaml index a174da7b..7d2a5e5f 100644 --- a/target/nextflow/star/star_genome_generate/.config.vsh.yaml +++ b/target/nextflow/star/star_genome_generate/.config.vsh.yaml @@ -319,7 +319,7 @@ build_info: output: "target/nextflow/star/star_genome_generate" executable: "target/nextflow/star/star_genome_generate/main.nf" viash_version: "0.9.0-RC6" - git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198" + git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e" 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 95b263e3..924cfe54 100644 --- a/target/nextflow/star/star_genome_generate/main.nf +++ b/target/nextflow/star/star_genome_generate/main.nf @@ -3143,7 +3143,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/star/star_genome_generate", "viash_version" : "0.9.0-RC6", - "git_commit" : "d0c648fb7eefe067f5b5b3d402a204354bb37198", + "git_commit" : "3481750f6e2d77defa28423d832ff251da3a1f9e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : {