From 2d86d22f2228188e4fefe86c75c5a96f35116287 Mon Sep 17 00:00:00 2001 From: CI Date: Wed, 13 Nov 2024 12:53:08 +0000 Subject: [PATCH] Build branch main with version main (a04f9ba) Build pipeline: viash-hub.rnaseq.main-xf2ql Source commit: https://github.com/viash-hub/rnaseq/commit/a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814 Source message: avoid generating STAR index if alignment is skipped --- src/workflows/prepare_genome/config.vsh.yaml | 3 +++ src/workflows/prepare_genome/main.nf | 2 +- src/workflows/rnaseq/main.nf | 3 ++- .../executable/bbmap_bbsplit/.config.vsh.yaml | 4 ++-- target/executable/bbmap_bbsplit/bbmap_bbsplit | 6 +++--- .../bedtools_genomecov/.config.vsh.yaml | 4 ++-- .../bedtools_genomecov/bedtools_genomecov | 6 +++--- .../cat_additional_fasta/.config.vsh.yaml | 4 ++-- .../cat_additional_fasta/cat_additional_fasta | 6 +++--- target/executable/cat_fastq/.config.vsh.yaml | 4 ++-- target/executable/cat_fastq/cat_fastq | 6 +++--- target/executable/deseq2_qc/.config.vsh.yaml | 4 ++-- target/executable/deseq2_qc/deseq2_qc | 6 +++--- target/executable/dupradar/.config.vsh.yaml | 4 ++-- target/executable/dupradar/dupradar | 6 +++--- target/executable/fastqc/.config.vsh.yaml | 4 ++-- target/executable/fastqc/fastqc | 6 +++--- .../executable/fq_subsample/.config.vsh.yaml | 4 ++-- target/executable/fq_subsample/fq_subsample | 6 +++--- .../executable/getchromsizes/.config.vsh.yaml | 4 ++-- target/executable/getchromsizes/getchromsizes | 6 +++--- target/executable/gtf2bed/.config.vsh.yaml | 4 ++-- target/executable/gtf2bed/gtf2bed | 6 +++--- target/executable/gtf_filter/.config.vsh.yaml | 4 ++-- target/executable/gtf_filter/gtf_filter | 6 +++--- target/executable/gunzip/.config.vsh.yaml | 4 ++-- target/executable/gunzip/gunzip | 6 +++--- .../kallisto/kallisto_index/.config.vsh.yaml | 4 ++-- .../kallisto/kallisto_index/kallisto_index | 6 +++--- .../kallisto/kallisto_quant/.config.vsh.yaml | 4 ++-- .../kallisto/kallisto_quant/kallisto_quant | 6 +++--- .../multiqc_custom_biotype/.config.vsh.yaml | 4 ++-- .../multiqc_custom_biotype | 6 +++--- .../picard_markduplicates/.config.vsh.yaml | 4 ++-- .../picard_markduplicates | 6 +++--- .../prepare_multiqc_input/.config.vsh.yaml | 4 ++-- .../prepare_multiqc_input | 6 +++--- .../.config.vsh.yaml | 4 ++-- .../preprocess_transcripts_fasta | 6 +++--- .../preseq_lcextrap/.config.vsh.yaml | 4 ++-- .../preseq_lcextrap/preseq_lcextrap | 6 +++--- target/executable/qualimap/.config.vsh.yaml | 4 ++-- target/executable/qualimap/qualimap | 6 +++--- .../.config.vsh.yaml | 4 ++-- .../rsem_calculate_expression | 6 +++--- .../rsem/rsem_merge_counts/.config.vsh.yaml | 4 ++-- .../rsem/rsem_merge_counts/rsem_merge_counts | 6 +++--- .../rseqc/rseqc_bamstat/.config.vsh.yaml | 4 ++-- .../rseqc/rseqc_bamstat/rseqc_bamstat | 6 +++--- .../rseqc_inferexperiment/.config.vsh.yaml | 4 ++-- .../rseqc_inferexperiment | 6 +++--- .../rseqc_innerdistance/.config.vsh.yaml | 4 ++-- .../rseqc_innerdistance/rseqc_innerdistance | 6 +++--- .../rseqc_junctionannotation/.config.vsh.yaml | 4 ++-- .../rseqc_junctionannotation | 6 +++--- .../rseqc_junctionsaturation/.config.vsh.yaml | 4 ++-- .../rseqc_junctionsaturation | 6 +++--- .../rseqc_readdistribution/.config.vsh.yaml | 4 ++-- .../rseqc_readdistribution | 6 +++--- .../rseqc_readduplication/.config.vsh.yaml | 4 ++-- .../rseqc_readduplication | 6 +++--- .../rseqc/rseqc_tin/.config.vsh.yaml | 4 ++-- target/executable/rseqc/rseqc_tin/rseqc_tin | 6 +++--- target/executable/sortmerna/.config.vsh.yaml | 4 ++-- target/executable/sortmerna/sortmerna | 6 +++--- target/executable/stringtie/.config.vsh.yaml | 4 ++-- target/executable/stringtie/stringtie | 6 +++--- .../summarizedexperiment/.config.vsh.yaml | 4 ++-- .../summarizedexperiment/summarizedexperiment | 6 +++--- target/executable/trimgalore/.config.vsh.yaml | 4 ++-- target/executable/trimgalore/trimgalore | 4 ++-- target/executable/tx2gene/.config.vsh.yaml | 4 ++-- target/executable/tx2gene/tx2gene | 6 +++--- target/executable/tximport/.config.vsh.yaml | 4 ++-- target/executable/tximport/tximport | 6 +++--- .../executable/ucsc/bedclip/.config.vsh.yaml | 4 ++-- target/executable/ucsc/bedclip/bedclip | 6 +++--- .../ucsc/bedgraphtobigwig/.config.vsh.yaml | 4 ++-- .../ucsc/bedgraphtobigwig/bedgraphtobigwig | 6 +++--- .../umitools/umitools_dedup/.config.vsh.yaml | 4 ++-- .../umitools/umitools_dedup/umitools_dedup | 6 +++--- .../umitools_extract/.config.vsh.yaml | 4 ++-- .../umitools_extract/umitools_extract | 6 +++--- .../umitools_prepareforquant/.config.vsh.yaml | 4 ++-- .../umitools_prepareforquant | 6 +++--- .../.config.vsh.yaml | 4 ++-- .../merge_quant_results/.config.vsh.yaml | 4 ++-- .../post_processing/.config.vsh.yaml | 4 ++-- .../workflows/pre_processing/.config.vsh.yaml | 4 ++-- .../workflows/prepare_genome/.config.vsh.yaml | 9 +++++++-- .../workflows/prepare_genome/prepare_genome | 20 ++++++++++++++++++- .../.config.vsh.yaml | 4 ++-- .../quality_control/.config.vsh.yaml | 4 ++-- .../workflows/rnaseq/.config.vsh.yaml | 4 ++-- target/executable/workflows/rnaseq/rnaseq | 3 ++- .../nextflow/bbmap_bbsplit/.config.vsh.yaml | 4 ++-- target/nextflow/bbmap_bbsplit/main.nf | 4 ++-- .../bedtools_genomecov/.config.vsh.yaml | 4 ++-- target/nextflow/bedtools_genomecov/main.nf | 4 ++-- .../cat_additional_fasta/.config.vsh.yaml | 4 ++-- target/nextflow/cat_additional_fasta/main.nf | 4 ++-- target/nextflow/cat_fastq/.config.vsh.yaml | 4 ++-- target/nextflow/cat_fastq/main.nf | 4 ++-- target/nextflow/deseq2_qc/.config.vsh.yaml | 4 ++-- target/nextflow/deseq2_qc/main.nf | 4 ++-- target/nextflow/dupradar/.config.vsh.yaml | 4 ++-- target/nextflow/dupradar/main.nf | 4 ++-- target/nextflow/fastqc/.config.vsh.yaml | 4 ++-- target/nextflow/fastqc/main.nf | 4 ++-- target/nextflow/fq_subsample/.config.vsh.yaml | 4 ++-- target/nextflow/fq_subsample/main.nf | 4 ++-- .../nextflow/getchromsizes/.config.vsh.yaml | 4 ++-- target/nextflow/getchromsizes/main.nf | 4 ++-- target/nextflow/gtf2bed/.config.vsh.yaml | 4 ++-- target/nextflow/gtf2bed/main.nf | 4 ++-- target/nextflow/gtf_filter/.config.vsh.yaml | 4 ++-- target/nextflow/gtf_filter/main.nf | 4 ++-- target/nextflow/gunzip/.config.vsh.yaml | 4 ++-- target/nextflow/gunzip/main.nf | 4 ++-- .../kallisto/kallisto_index/.config.vsh.yaml | 4 ++-- .../nextflow/kallisto/kallisto_index/main.nf | 4 ++-- .../kallisto/kallisto_quant/.config.vsh.yaml | 4 ++-- .../nextflow/kallisto/kallisto_quant/main.nf | 4 ++-- .../multiqc_custom_biotype/.config.vsh.yaml | 4 ++-- .../nextflow/multiqc_custom_biotype/main.nf | 4 ++-- .../picard_markduplicates/.config.vsh.yaml | 4 ++-- target/nextflow/picard_markduplicates/main.nf | 4 ++-- .../prepare_multiqc_input/.config.vsh.yaml | 4 ++-- target/nextflow/prepare_multiqc_input/main.nf | 4 ++-- .../.config.vsh.yaml | 4 ++-- .../preprocess_transcripts_fasta/main.nf | 4 ++-- .../nextflow/preseq_lcextrap/.config.vsh.yaml | 4 ++-- target/nextflow/preseq_lcextrap/main.nf | 4 ++-- target/nextflow/qualimap/.config.vsh.yaml | 4 ++-- target/nextflow/qualimap/main.nf | 4 ++-- .../.config.vsh.yaml | 4 ++-- .../rsem/rsem_calculate_expression/main.nf | 4 ++-- .../rsem/rsem_merge_counts/.config.vsh.yaml | 4 ++-- .../nextflow/rsem/rsem_merge_counts/main.nf | 4 ++-- .../rseqc/rseqc_bamstat/.config.vsh.yaml | 4 ++-- target/nextflow/rseqc/rseqc_bamstat/main.nf | 4 ++-- .../rseqc_inferexperiment/.config.vsh.yaml | 4 ++-- .../rseqc/rseqc_inferexperiment/main.nf | 4 ++-- .../rseqc_innerdistance/.config.vsh.yaml | 4 ++-- .../rseqc/rseqc_innerdistance/main.nf | 4 ++-- .../rseqc_junctionannotation/.config.vsh.yaml | 4 ++-- .../rseqc/rseqc_junctionannotation/main.nf | 4 ++-- .../rseqc_junctionsaturation/.config.vsh.yaml | 4 ++-- .../rseqc/rseqc_junctionsaturation/main.nf | 4 ++-- .../rseqc_readdistribution/.config.vsh.yaml | 4 ++-- .../rseqc/rseqc_readdistribution/main.nf | 4 ++-- .../rseqc_readduplication/.config.vsh.yaml | 4 ++-- .../rseqc/rseqc_readduplication/main.nf | 4 ++-- .../nextflow/rseqc/rseqc_tin/.config.vsh.yaml | 4 ++-- target/nextflow/rseqc/rseqc_tin/main.nf | 4 ++-- target/nextflow/sortmerna/.config.vsh.yaml | 4 ++-- target/nextflow/sortmerna/main.nf | 4 ++-- target/nextflow/stringtie/.config.vsh.yaml | 4 ++-- target/nextflow/stringtie/main.nf | 4 ++-- .../summarizedexperiment/.config.vsh.yaml | 4 ++-- target/nextflow/summarizedexperiment/main.nf | 4 ++-- target/nextflow/trimgalore/.config.vsh.yaml | 4 ++-- target/nextflow/trimgalore/main.nf | 4 ++-- target/nextflow/tx2gene/.config.vsh.yaml | 4 ++-- target/nextflow/tx2gene/main.nf | 4 ++-- target/nextflow/tximport/.config.vsh.yaml | 4 ++-- target/nextflow/tximport/main.nf | 4 ++-- target/nextflow/ucsc/bedclip/.config.vsh.yaml | 4 ++-- target/nextflow/ucsc/bedclip/main.nf | 4 ++-- .../ucsc/bedgraphtobigwig/.config.vsh.yaml | 4 ++-- target/nextflow/ucsc/bedgraphtobigwig/main.nf | 4 ++-- .../umitools/umitools_dedup/.config.vsh.yaml | 4 ++-- .../nextflow/umitools/umitools_dedup/main.nf | 4 ++-- .../umitools_extract/.config.vsh.yaml | 4 ++-- .../umitools/umitools_extract/main.nf | 4 ++-- .../umitools_prepareforquant/.config.vsh.yaml | 4 ++-- .../nextflow/umitools_prepareforquant/main.nf | 4 ++-- .../.config.vsh.yaml | 4 ++-- .../genome_alignment_and_quant/main.nf | 4 ++-- .../merge_quant_results/.config.vsh.yaml | 4 ++-- .../workflows/merge_quant_results/main.nf | 4 ++-- .../post_processing/.config.vsh.yaml | 4 ++-- .../workflows/post_processing/main.nf | 4 ++-- .../workflows/pre_processing/.config.vsh.yaml | 4 ++-- .../nextflow/workflows/pre_processing/main.nf | 4 ++-- .../workflows/prepare_genome/.config.vsh.yaml | 9 +++++++-- .../nextflow/workflows/prepare_genome/main.nf | 12 ++++++++--- .../prepare_genome/nextflow_schema.json | 11 ++++++++++ .../.config.vsh.yaml | 4 ++-- .../pseudo_alignment_and_quant/main.nf | 4 ++-- .../quality_control/.config.vsh.yaml | 4 ++-- .../workflows/quality_control/main.nf | 4 ++-- .../workflows/rnaseq/.config.vsh.yaml | 4 ++-- target/nextflow/workflows/rnaseq/main.nf | 7 ++++--- 194 files changed, 473 insertions(+), 422 deletions(-) diff --git a/src/workflows/prepare_genome/config.vsh.yaml b/src/workflows/prepare_genome/config.vsh.yaml index f50b6b5..a6f7566 100644 --- a/src/workflows/prepare_genome/config.vsh.yaml +++ b/src/workflows/prepare_genome/config.vsh.yaml @@ -80,6 +80,9 @@ argument_groups: description: Specifies the pseudo aligner to use - available options are 'salmon'. Runs in addition to '--aligner'. choices: [salmon, kallisto] default: "salmon" + - name: "--skip_alignment" + type: boolean_true + description: Skip all of the alignment-based processes within the pipeline. - name: "Output" arguments: diff --git a/src/workflows/prepare_genome/main.nf b/src/workflows/prepare_genome/main.nf index 1f23a45..34ecd3a 100644 --- a/src/workflows/prepare_genome/main.nf +++ b/src/workflows/prepare_genome/main.nf @@ -185,7 +185,7 @@ workflow run_wf { // TODO: Add to viah-hub or adapt star_align_reads to enable the generateGenome runMode | star_genome_generate.run ( - runIf: {id, state -> !state.star_index}, + runIf: {id, state -> !state.star_index && !state.skip_alignment}, fromState: [ "genome_fasta_files": "fasta", "sjdb_gtf_file": "gtf" diff --git a/src/workflows/rnaseq/main.nf b/src/workflows/rnaseq/main.nf index 70f1530..902974d 100644 --- a/src/workflows/rnaseq/main.nf +++ b/src/workflows/rnaseq/main.nf @@ -69,7 +69,8 @@ workflow run_wf { "biotype": "biotype", "filter_gtf": "filter_gtf", "aligner": "aligner", - "pseudo_aligner": "pseudo_aligner" + "pseudo_aligner": "pseudo_aligner", + "skip_alignment": "skip_alignment" ], toState: [ "fasta": "uncompressed_fasta", diff --git a/target/executable/bbmap_bbsplit/.config.vsh.yaml b/target/executable/bbmap_bbsplit/.config.vsh.yaml index cccec49..479c36c 100644 --- a/target/executable/bbmap_bbsplit/.config.vsh.yaml +++ b/target/executable/bbmap_bbsplit/.config.vsh.yaml @@ -238,8 +238,8 @@ build_info: output: "target/executable/bbmap_bbsplit" executable: "target/executable/bbmap_bbsplit/bbmap_bbsplit" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/bbmap_bbsplit/bbmap_bbsplit b/target/executable/bbmap_bbsplit/bbmap_bbsplit index a2b8546..7a19300 100755 --- a/target/executable/bbmap_bbsplit/bbmap_bbsplit +++ b/target/executable/bbmap_bbsplit/bbmap_bbsplit @@ -506,9 +506,9 @@ tar xzf BBMap_39.01.tar.gz && \ cp -r bbmap/* /usr/local/bin LABEL org.opencontainers.image.description="Companion container for running component bbmap_bbsplit" -LABEL org.opencontainers.image.created="2024-11-13T10:13:21Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a" +LABEL org.opencontainers.image.created="2024-11-13T12:42:23Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bedtools_genomecov/.config.vsh.yaml b/target/executable/bedtools_genomecov/.config.vsh.yaml index 1edd1ff..7e9dbb0 100644 --- a/target/executable/bedtools_genomecov/.config.vsh.yaml +++ b/target/executable/bedtools_genomecov/.config.vsh.yaml @@ -178,8 +178,8 @@ build_info: output: "target/executable/bedtools_genomecov" executable: "target/executable/bedtools_genomecov/bedtools_genomecov" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/bedtools_genomecov/bedtools_genomecov b/target/executable/bedtools_genomecov/bedtools_genomecov index feefc19..6863983 100755 --- a/target/executable/bedtools_genomecov/bedtools_genomecov +++ b/target/executable/bedtools_genomecov/bedtools_genomecov @@ -481,9 +481,9 @@ mv bedtools.static /usr/local/bin/bedtools && \ chmod a+x /usr/local/bin/bedtools LABEL org.opencontainers.image.description="Companion container for running component bedtools_genomecov" -LABEL org.opencontainers.image.created="2024-11-13T10:13:19Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a" +LABEL org.opencontainers.image.created="2024-11-13T12:42:22Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/cat_additional_fasta/.config.vsh.yaml b/target/executable/cat_additional_fasta/.config.vsh.yaml index 1f40b9f..d072318 100644 --- a/target/executable/cat_additional_fasta/.config.vsh.yaml +++ b/target/executable/cat_additional_fasta/.config.vsh.yaml @@ -182,8 +182,8 @@ build_info: output: "target/executable/cat_additional_fasta" executable: "target/executable/cat_additional_fasta/cat_additional_fasta" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/cat_additional_fasta/cat_additional_fasta b/target/executable/cat_additional_fasta/cat_additional_fasta index 92988d0..10b74f3 100755 --- a/target/executable/cat_additional_fasta/cat_additional_fasta +++ b/target/executable/cat_additional_fasta/cat_additional_fasta @@ -480,9 +480,9 @@ function ViashDockerfile { FROM python:latest ENTRYPOINT [] LABEL org.opencontainers.image.description="Companion container for running component cat_additional_fasta" -LABEL org.opencontainers.image.created="2024-11-13T10:13:18Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a" +LABEL org.opencontainers.image.created="2024-11-13T12:42:21Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/cat_fastq/.config.vsh.yaml b/target/executable/cat_fastq/.config.vsh.yaml index b50aac0..12077f9 100644 --- a/target/executable/cat_fastq/.config.vsh.yaml +++ b/target/executable/cat_fastq/.config.vsh.yaml @@ -169,8 +169,8 @@ build_info: output: "target/executable/cat_fastq" executable: "target/executable/cat_fastq/cat_fastq" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/cat_fastq/cat_fastq b/target/executable/cat_fastq/cat_fastq index 723c1de..e441b6b 100755 --- a/target/executable/cat_fastq/cat_fastq +++ b/target/executable/cat_fastq/cat_fastq @@ -472,9 +472,9 @@ function ViashDockerfile { FROM ubuntu:22.04 ENTRYPOINT [] LABEL org.opencontainers.image.description="Companion container for running component cat_fastq" -LABEL org.opencontainers.image.created="2024-11-13T10:13:17Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a" +LABEL org.opencontainers.image.created="2024-11-13T12:42:20Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/deseq2_qc/.config.vsh.yaml b/target/executable/deseq2_qc/.config.vsh.yaml index eff242a..878a163 100644 --- a/target/executable/deseq2_qc/.config.vsh.yaml +++ b/target/executable/deseq2_qc/.config.vsh.yaml @@ -237,8 +237,8 @@ build_info: output: "target/executable/deseq2_qc" executable: "target/executable/deseq2_qc/deseq2_qc" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/deseq2_qc/deseq2_qc b/target/executable/deseq2_qc/deseq2_qc index 3f9fc59..5875eaf 100755 --- a/target/executable/deseq2_qc/deseq2_qc +++ b/target/executable/deseq2_qc/deseq2_qc @@ -506,9 +506,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag Rscript -e 'remotes::install_cran(c("optparse", "ggplot2", "RColorBrewer", "pheatmap", "stringr", "matrixStats"), repos = "https://cran.rstudio.com")' LABEL org.opencontainers.image.description="Companion container for running component deseq2_qc" -LABEL org.opencontainers.image.created="2024-11-13T10:13:19Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a" +LABEL org.opencontainers.image.created="2024-11-13T12:42:22Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/dupradar/.config.vsh.yaml b/target/executable/dupradar/.config.vsh.yaml index 295e298..5457031 100644 --- a/target/executable/dupradar/.config.vsh.yaml +++ b/target/executable/dupradar/.config.vsh.yaml @@ -266,8 +266,8 @@ build_info: output: "target/executable/dupradar" executable: "target/executable/dupradar/dupradar" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/dupradar/dupradar b/target/executable/dupradar/dupradar index 4b7fc8f..cc0bb07 100755 --- a/target/executable/dupradar/dupradar +++ b/target/executable/dupradar/dupradar @@ -520,9 +520,9 @@ RUN Rscript -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.pa Rscript -e 'if (!requireNamespace("dupRadar", quietly = TRUE)) BiocManager::install("dupRadar")' LABEL org.opencontainers.image.description="Companion container for running component dupradar" -LABEL org.opencontainers.image.created="2024-11-13T10:13:20Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a" +LABEL org.opencontainers.image.created="2024-11-13T12:42:22Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/fastqc/.config.vsh.yaml b/target/executable/fastqc/.config.vsh.yaml index 8f04ba9..5417a35 100644 --- a/target/executable/fastqc/.config.vsh.yaml +++ b/target/executable/fastqc/.config.vsh.yaml @@ -198,8 +198,8 @@ build_info: output: "target/executable/fastqc" executable: "target/executable/fastqc/fastqc" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/fastqc/fastqc b/target/executable/fastqc/fastqc index 989beb3..58cda08 100755 --- a/target/executable/fastqc/fastqc +++ b/target/executable/fastqc/fastqc @@ -490,9 +490,9 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* LABEL org.opencontainers.image.description="Companion container for running component fastqc" -LABEL org.opencontainers.image.created="2024-11-13T10:13:22Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a" +LABEL org.opencontainers.image.created="2024-11-13T12:42:25Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/fq_subsample/.config.vsh.yaml b/target/executable/fq_subsample/.config.vsh.yaml index 1ce90c9..46713f0 100644 --- a/target/executable/fq_subsample/.config.vsh.yaml +++ b/target/executable/fq_subsample/.config.vsh.yaml @@ -177,8 +177,8 @@ build_info: output: "target/executable/fq_subsample" executable: "target/executable/fq_subsample/fq_subsample" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/fq_subsample/fq_subsample b/target/executable/fq_subsample/fq_subsample index 0b0eae0..b24a6d0 100755 --- a/target/executable/fq_subsample/fq_subsample +++ b/target/executable/fq_subsample/fq_subsample @@ -485,9 +485,9 @@ cargo install --locked --path . && \ mv /usr/local/fq/target/release/fq /usr/local/bin/ LABEL org.opencontainers.image.description="Companion container for running component fq_subsample" -LABEL org.opencontainers.image.created="2024-11-13T10:13:21Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a" +LABEL org.opencontainers.image.created="2024-11-13T12:42:23Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/getchromsizes/.config.vsh.yaml b/target/executable/getchromsizes/.config.vsh.yaml index c285b59..50b36ba 100644 --- a/target/executable/getchromsizes/.config.vsh.yaml +++ b/target/executable/getchromsizes/.config.vsh.yaml @@ -167,8 +167,8 @@ build_info: output: "target/executable/getchromsizes" executable: "target/executable/getchromsizes/getchromsizes" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/getchromsizes/getchromsizes b/target/executable/getchromsizes/getchromsizes index 43971e8..3248e54 100755 --- a/target/executable/getchromsizes/getchromsizes +++ b/target/executable/getchromsizes/getchromsizes @@ -480,9 +480,9 @@ make && \ make install LABEL org.opencontainers.image.description="Companion container for running component getchromsizes" -LABEL org.opencontainers.image.created="2024-11-13T10:13:18Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a" +LABEL org.opencontainers.image.created="2024-11-13T12:42:21Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/gtf2bed/.config.vsh.yaml b/target/executable/gtf2bed/.config.vsh.yaml index 7d58609..00aa0a9 100644 --- a/target/executable/gtf2bed/.config.vsh.yaml +++ b/target/executable/gtf2bed/.config.vsh.yaml @@ -145,8 +145,8 @@ build_info: output: "target/executable/gtf2bed" executable: "target/executable/gtf2bed/gtf2bed" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/gtf2bed/gtf2bed b/target/executable/gtf2bed/gtf2bed index 0fa76b1..a6c3ea9 100755 --- a/target/executable/gtf2bed/gtf2bed +++ b/target/executable/gtf2bed/gtf2bed @@ -466,9 +466,9 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* LABEL org.opencontainers.image.description="Companion container for running component gtf2bed" -LABEL org.opencontainers.image.created="2024-11-13T10:13:20Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a" +LABEL org.opencontainers.image.created="2024-11-13T12:42:23Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/gtf_filter/.config.vsh.yaml b/target/executable/gtf_filter/.config.vsh.yaml index 7bc762e..f25e871 100644 --- a/target/executable/gtf_filter/.config.vsh.yaml +++ b/target/executable/gtf_filter/.config.vsh.yaml @@ -155,8 +155,8 @@ build_info: output: "target/executable/gtf_filter" executable: "target/executable/gtf_filter/gtf_filter" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/gtf_filter/gtf_filter b/target/executable/gtf_filter/gtf_filter index ccc2b97..43a69ea 100755 --- a/target/executable/gtf_filter/gtf_filter +++ b/target/executable/gtf_filter/gtf_filter @@ -470,9 +470,9 @@ function ViashDockerfile { FROM python:latest ENTRYPOINT [] LABEL org.opencontainers.image.description="Companion container for running component gtf_filter" -LABEL org.opencontainers.image.created="2024-11-13T10:13:19Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a" +LABEL org.opencontainers.image.created="2024-11-13T12:42:21Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/gunzip/.config.vsh.yaml b/target/executable/gunzip/.config.vsh.yaml index f2796c7..1dc21d0 100644 --- a/target/executable/gunzip/.config.vsh.yaml +++ b/target/executable/gunzip/.config.vsh.yaml @@ -144,8 +144,8 @@ build_info: output: "target/executable/gunzip" executable: "target/executable/gunzip/gunzip" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/gunzip/gunzip b/target/executable/gunzip/gunzip index 0060c4d..050b1ec 100755 --- a/target/executable/gunzip/gunzip +++ b/target/executable/gunzip/gunzip @@ -466,9 +466,9 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* LABEL org.opencontainers.image.description="Companion container for running component gunzip" -LABEL org.opencontainers.image.created="2024-11-13T10:13:14Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a" +LABEL org.opencontainers.image.created="2024-11-13T12:42:16Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/kallisto/kallisto_index/.config.vsh.yaml b/target/executable/kallisto/kallisto_index/.config.vsh.yaml index 734f249..b0e980c 100644 --- a/target/executable/kallisto/kallisto_index/.config.vsh.yaml +++ b/target/executable/kallisto/kallisto_index/.config.vsh.yaml @@ -155,8 +155,8 @@ build_info: output: "target/executable/kallisto/kallisto_index" executable: "target/executable/kallisto/kallisto_index/kallisto_index" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/kallisto/kallisto_index/kallisto_index b/target/executable/kallisto/kallisto_index/kallisto_index index 9d22b75..64c1080 100755 --- a/target/executable/kallisto/kallisto_index/kallisto_index +++ b/target/executable/kallisto/kallisto_index/kallisto_index @@ -471,9 +471,9 @@ tar -xzf kallisto_linux-v0.50.1.tar.gz && \ mv kallisto/kallisto /usr/local/bin/ LABEL org.opencontainers.image.description="Companion container for running component kallisto kallisto_index" -LABEL org.opencontainers.image.created="2024-11-13T10:13:14Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a" +LABEL org.opencontainers.image.created="2024-11-13T12:42:17Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/kallisto/kallisto_quant/.config.vsh.yaml b/target/executable/kallisto/kallisto_quant/.config.vsh.yaml index 8276b4f..de1d107 100644 --- a/target/executable/kallisto/kallisto_quant/.config.vsh.yaml +++ b/target/executable/kallisto/kallisto_quant/.config.vsh.yaml @@ -253,8 +253,8 @@ build_info: output: "target/executable/kallisto/kallisto_quant" executable: "target/executable/kallisto/kallisto_quant/kallisto_quant" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/kallisto/kallisto_quant/kallisto_quant b/target/executable/kallisto/kallisto_quant/kallisto_quant index 5070bd9..6ea1cc1 100755 --- a/target/executable/kallisto/kallisto_quant/kallisto_quant +++ b/target/executable/kallisto/kallisto_quant/kallisto_quant @@ -515,9 +515,9 @@ tar -xzf kallisto_linux-v0.50.1.tar.gz && \ mv kallisto/kallisto /usr/local/bin/ LABEL org.opencontainers.image.description="Companion container for running component kallisto kallisto_quant" -LABEL org.opencontainers.image.created="2024-11-13T10:13:14Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a" +LABEL org.opencontainers.image.created="2024-11-13T12:42:17Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/multiqc_custom_biotype/.config.vsh.yaml b/target/executable/multiqc_custom_biotype/.config.vsh.yaml index b0fc698..ea18903 100644 --- a/target/executable/multiqc_custom_biotype/.config.vsh.yaml +++ b/target/executable/multiqc_custom_biotype/.config.vsh.yaml @@ -161,8 +161,8 @@ build_info: output: "target/executable/multiqc_custom_biotype" executable: "target/executable/multiqc_custom_biotype/multiqc_custom_biotype" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/multiqc_custom_biotype/multiqc_custom_biotype b/target/executable/multiqc_custom_biotype/multiqc_custom_biotype index 828b148..076eefa 100755 --- a/target/executable/multiqc_custom_biotype/multiqc_custom_biotype +++ b/target/executable/multiqc_custom_biotype/multiqc_custom_biotype @@ -476,9 +476,9 @@ function ViashDockerfile { FROM python:latest ENTRYPOINT [] LABEL org.opencontainers.image.description="Companion container for running component multiqc_custom_biotype" -LABEL org.opencontainers.image.created="2024-11-13T10:13:18Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a" +LABEL org.opencontainers.image.created="2024-11-13T12:42:20Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/picard_markduplicates/.config.vsh.yaml b/target/executable/picard_markduplicates/.config.vsh.yaml index b4da303..8403994 100644 --- a/target/executable/picard_markduplicates/.config.vsh.yaml +++ b/target/executable/picard_markduplicates/.config.vsh.yaml @@ -207,8 +207,8 @@ build_info: output: "target/executable/picard_markduplicates" executable: "target/executable/picard_markduplicates/picard_markduplicates" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/picard_markduplicates/picard_markduplicates b/target/executable/picard_markduplicates/picard_markduplicates index d36a251..1952963 100755 --- a/target/executable/picard_markduplicates/picard_markduplicates +++ b/target/executable/picard_markduplicates/picard_markduplicates @@ -494,9 +494,9 @@ wget --no-check-certificate https://github.com/broadinstitute/picard/releases/do mv picard.jar /usr/local/bin LABEL org.opencontainers.image.description="Companion container for running component picard_markduplicates" -LABEL org.opencontainers.image.created="2024-11-13T10:13:16Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a" +LABEL org.opencontainers.image.created="2024-11-13T12:42:18Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/prepare_multiqc_input/.config.vsh.yaml b/target/executable/prepare_multiqc_input/.config.vsh.yaml index edb174e..9d8aabd 100644 --- a/target/executable/prepare_multiqc_input/.config.vsh.yaml +++ b/target/executable/prepare_multiqc_input/.config.vsh.yaml @@ -409,8 +409,8 @@ build_info: output: "target/executable/prepare_multiqc_input" executable: "target/executable/prepare_multiqc_input/prepare_multiqc_input" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/prepare_multiqc_input/prepare_multiqc_input b/target/executable/prepare_multiqc_input/prepare_multiqc_input index 72afe91..29e724d 100755 --- a/target/executable/prepare_multiqc_input/prepare_multiqc_input +++ b/target/executable/prepare_multiqc_input/prepare_multiqc_input @@ -557,9 +557,9 @@ function ViashDockerfile { FROM ubuntu:22.04 ENTRYPOINT [] LABEL org.opencontainers.image.description="Companion container for running component prepare_multiqc_input" -LABEL org.opencontainers.image.created="2024-11-13T10:13:11Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a" +LABEL org.opencontainers.image.created="2024-11-13T12:42:14Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/preprocess_transcripts_fasta/.config.vsh.yaml b/target/executable/preprocess_transcripts_fasta/.config.vsh.yaml index 80cafb1..aa1fbe6 100644 --- a/target/executable/preprocess_transcripts_fasta/.config.vsh.yaml +++ b/target/executable/preprocess_transcripts_fasta/.config.vsh.yaml @@ -138,8 +138,8 @@ build_info: output: "target/executable/preprocess_transcripts_fasta" executable: "target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta b/target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta index 73b0a97..a57e69a 100755 --- a/target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta +++ b/target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta @@ -462,9 +462,9 @@ function ViashDockerfile { FROM ubuntu:22.04 ENTRYPOINT [] LABEL org.opencontainers.image.description="Companion container for running component preprocess_transcripts_fasta" -LABEL org.opencontainers.image.created="2024-11-13T10:13:16Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a" +LABEL org.opencontainers.image.created="2024-11-13T12:42:19Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/preseq_lcextrap/.config.vsh.yaml b/target/executable/preseq_lcextrap/.config.vsh.yaml index a2016e8..dba2f1e 100644 --- a/target/executable/preseq_lcextrap/.config.vsh.yaml +++ b/target/executable/preseq_lcextrap/.config.vsh.yaml @@ -191,8 +191,8 @@ build_info: output: "target/executable/preseq_lcextrap" executable: "target/executable/preseq_lcextrap/preseq_lcextrap" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/preseq_lcextrap/preseq_lcextrap b/target/executable/preseq_lcextrap/preseq_lcextrap index 29bae0c..f5c94b9 100755 --- a/target/executable/preseq_lcextrap/preseq_lcextrap +++ b/target/executable/preseq_lcextrap/preseq_lcextrap @@ -495,9 +495,9 @@ mkdir build && cd build && \ make && make install && make HAVE_HTSLIB=1 all LABEL org.opencontainers.image.description="Companion container for running component preseq_lcextrap" -LABEL org.opencontainers.image.created="2024-11-13T10:13:16Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a" +LABEL org.opencontainers.image.created="2024-11-13T12:42:18Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/qualimap/.config.vsh.yaml b/target/executable/qualimap/.config.vsh.yaml index f6c20c0..712e1b0 100644 --- a/target/executable/qualimap/.config.vsh.yaml +++ b/target/executable/qualimap/.config.vsh.yaml @@ -271,8 +271,8 @@ build_info: output: "target/executable/qualimap" executable: "target/executable/qualimap/qualimap" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/qualimap/qualimap b/target/executable/qualimap/qualimap index 99affad..21493b6 100755 --- a/target/executable/qualimap/qualimap +++ b/target/executable/qualimap/qualimap @@ -537,9 +537,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag Rscript -e 'remotes::install_cran(c("optparse"), repos = "https://cran.rstudio.com")' LABEL org.opencontainers.image.description="Companion container for running component qualimap" -LABEL org.opencontainers.image.created="2024-11-13T10:13:13Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a" +LABEL org.opencontainers.image.created="2024-11-13T12:42:16Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml b/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml index ba0cd06..3cddcbf 100644 --- a/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml +++ b/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml @@ -299,8 +299,8 @@ build_info: output: "target/executable/rsem/rsem_calculate_expression" executable: "target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression b/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression index b5557fb..24125fa 100755 --- a/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression +++ b/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression @@ -542,9 +542,9 @@ echo 'export PATH=$PATH:/usr/local/bin' >> ~/.bashrc && \ /bin/bash -c "source /etc/profile && source ~/.bashrc && echo $PATH && which STAR" LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_calculate_expression" -LABEL org.opencontainers.image.created="2024-11-13T10:13:13Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a" +LABEL org.opencontainers.image.created="2024-11-13T12:42:15Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/rsem/rsem_merge_counts/.config.vsh.yaml b/target/executable/rsem/rsem_merge_counts/.config.vsh.yaml index 3927f5d..3a7afb1 100644 --- a/target/executable/rsem/rsem_merge_counts/.config.vsh.yaml +++ b/target/executable/rsem/rsem_merge_counts/.config.vsh.yaml @@ -182,8 +182,8 @@ build_info: output: "target/executable/rsem/rsem_merge_counts" executable: "target/executable/rsem/rsem_merge_counts/rsem_merge_counts" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/rsem/rsem_merge_counts/rsem_merge_counts b/target/executable/rsem/rsem_merge_counts/rsem_merge_counts index 7f1bb9a..392395e 100755 --- a/target/executable/rsem/rsem_merge_counts/rsem_merge_counts +++ b/target/executable/rsem/rsem_merge_counts/rsem_merge_counts @@ -483,9 +483,9 @@ function ViashDockerfile { FROM ubuntu:22.04 ENTRYPOINT [] LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_merge_counts" -LABEL org.opencontainers.image.created="2024-11-13T10:13:12Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a" +LABEL org.opencontainers.image.created="2024-11-13T12:42:15Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml b/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml index ca06b05..2c910c4 100644 --- a/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml @@ -163,8 +163,8 @@ build_info: output: "target/executable/rseqc/rseqc_bamstat" executable: "target/executable/rseqc/rseqc_bamstat/rseqc_bamstat" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat b/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat index 4dd19a4..848a3da 100755 --- a/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat +++ b/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat @@ -477,9 +477,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "RSeQC" LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_bamstat" -LABEL org.opencontainers.image.created="2024-11-13T10:13:18Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a" +LABEL org.opencontainers.image.created="2024-11-13T12:42:20Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml b/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml index 89faa5b..76b8b28 100644 --- a/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml @@ -186,8 +186,8 @@ build_info: output: "target/executable/rseqc/rseqc_inferexperiment" executable: "target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment b/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment index 7078972..f107147 100755 --- a/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment +++ b/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment @@ -487,9 +487,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "RSeQC" LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_inferexperiment" -LABEL org.opencontainers.image.created="2024-11-13T10:13:19Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a" +LABEL org.opencontainers.image.created="2024-11-13T12:42:22Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml b/target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml index 98b0eb3..2c235f6 100644 --- a/target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml @@ -272,8 +272,8 @@ build_info: output: "target/executable/rseqc/rseqc_innerdistance" executable: "target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance b/target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance index b1271ea..9f9e8a2 100755 --- a/target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance +++ b/target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance @@ -529,9 +529,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "RSeQC" LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_innerdistance" -LABEL org.opencontainers.image.created="2024-11-13T10:13:17Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a" +LABEL org.opencontainers.image.created="2024-11-13T12:42:20Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml b/target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml index 6c4a0e2..58b01dc 100644 --- a/target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml @@ -260,8 +260,8 @@ build_info: output: "target/executable/rseqc/rseqc_junctionannotation" executable: "target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation b/target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation index 0c9e6f7..d0ad366 100755 --- a/target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation +++ b/target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation @@ -519,9 +519,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "RSeQC" LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_junctionannotation" -LABEL org.opencontainers.image.created="2024-11-13T10:13:17Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a" +LABEL org.opencontainers.image.created="2024-11-13T12:42:20Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_junctionsaturation/.config.vsh.yaml b/target/executable/rseqc/rseqc_junctionsaturation/.config.vsh.yaml index 352185d..5fa0a58 100644 --- a/target/executable/rseqc/rseqc_junctionsaturation/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_junctionsaturation/.config.vsh.yaml @@ -249,8 +249,8 @@ build_info: output: "target/executable/rseqc/rseqc_junctionsaturation" executable: "target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation b/target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation index efec96f..e1a34d6 100755 --- a/target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation +++ b/target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation @@ -522,9 +522,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "RSeQC" LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_junctionsaturation" -LABEL org.opencontainers.image.created="2024-11-13T10:13:19Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a" +LABEL org.opencontainers.image.created="2024-11-13T12:42:21Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_readdistribution/.config.vsh.yaml b/target/executable/rseqc/rseqc_readdistribution/.config.vsh.yaml index 366a5a9..10a7dd3 100644 --- a/target/executable/rseqc/rseqc_readdistribution/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_readdistribution/.config.vsh.yaml @@ -162,8 +162,8 @@ build_info: output: "target/executable/rseqc/rseqc_readdistribution" executable: "target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution b/target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution index d318e4e..f325d2c 100755 --- a/target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution +++ b/target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution @@ -474,9 +474,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "RSeQC" LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_readdistribution" -LABEL org.opencontainers.image.created="2024-11-13T10:13:18Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a" +LABEL org.opencontainers.image.created="2024-11-13T12:42:21Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_readduplication/.config.vsh.yaml b/target/executable/rseqc/rseqc_readduplication/.config.vsh.yaml index 75a5edd..2b7389e 100644 --- a/target/executable/rseqc/rseqc_readduplication/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_readduplication/.config.vsh.yaml @@ -211,8 +211,8 @@ build_info: output: "target/executable/rseqc/rseqc_readduplication" executable: "target/executable/rseqc/rseqc_readduplication/rseqc_readduplication" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/rseqc/rseqc_readduplication/rseqc_readduplication b/target/executable/rseqc/rseqc_readduplication/rseqc_readduplication index ea03355..0da3081 100755 --- a/target/executable/rseqc/rseqc_readduplication/rseqc_readduplication +++ b/target/executable/rseqc/rseqc_readduplication/rseqc_readduplication @@ -499,9 +499,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "RSeQC" LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_readduplication" -LABEL org.opencontainers.image.created="2024-11-13T10:13:17Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a" +LABEL org.opencontainers.image.created="2024-11-13T12:42:19Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_tin/.config.vsh.yaml b/target/executable/rseqc/rseqc_tin/.config.vsh.yaml index 53d51be..a6ded79 100644 --- a/target/executable/rseqc/rseqc_tin/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_tin/.config.vsh.yaml @@ -214,8 +214,8 @@ build_info: output: "target/executable/rseqc/rseqc_tin" executable: "target/executable/rseqc/rseqc_tin/rseqc_tin" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/rseqc/rseqc_tin/rseqc_tin b/target/executable/rseqc/rseqc_tin/rseqc_tin index a61c0b3..1b86556 100755 --- a/target/executable/rseqc/rseqc_tin/rseqc_tin +++ b/target/executable/rseqc/rseqc_tin/rseqc_tin @@ -501,9 +501,9 @@ RUN apt-get update && \ RUN pip3 install RSeQC LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_tin" -LABEL org.opencontainers.image.created="2024-11-13T10:13:18Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a" +LABEL org.opencontainers.image.created="2024-11-13T12:42:21Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/sortmerna/.config.vsh.yaml b/target/executable/sortmerna/.config.vsh.yaml index 1c89c83..ace3d51 100644 --- a/target/executable/sortmerna/.config.vsh.yaml +++ b/target/executable/sortmerna/.config.vsh.yaml @@ -192,8 +192,8 @@ build_info: output: "target/executable/sortmerna" executable: "target/executable/sortmerna/sortmerna" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/sortmerna/sortmerna b/target/executable/sortmerna/sortmerna index 0e52fea..1fc648c 100755 --- a/target/executable/sortmerna/sortmerna +++ b/target/executable/sortmerna/sortmerna @@ -486,9 +486,9 @@ function ViashDockerfile { FROM quay.io/biocontainers/sortmerna:4.3.6--h9ee0642_0 ENTRYPOINT [] LABEL org.opencontainers.image.description="Companion container for running component sortmerna" -LABEL org.opencontainers.image.created="2024-11-13T10:13:22Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a" +LABEL org.opencontainers.image.created="2024-11-13T12:42:24Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/stringtie/.config.vsh.yaml b/target/executable/stringtie/.config.vsh.yaml index 5170a7f..3048f24 100644 --- a/target/executable/stringtie/.config.vsh.yaml +++ b/target/executable/stringtie/.config.vsh.yaml @@ -216,8 +216,8 @@ build_info: output: "target/executable/stringtie" executable: "target/executable/stringtie/stringtie" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/stringtie/stringtie b/target/executable/stringtie/stringtie index 79d5acd..3f973b6 100755 --- a/target/executable/stringtie/stringtie +++ b/target/executable/stringtie/stringtie @@ -496,9 +496,9 @@ tar -xzf stringtie-2.2.1.Linux_x86_64.tar.gz && \ cp stringtie-2.2.1.Linux_x86_64/stringtie /usr/local/bin/ LABEL org.opencontainers.image.description="Companion container for running component stringtie" -LABEL org.opencontainers.image.created="2024-11-13T10:13:23Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a" +LABEL org.opencontainers.image.created="2024-11-13T12:42:25Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/summarizedexperiment/.config.vsh.yaml b/target/executable/summarizedexperiment/.config.vsh.yaml index f1f0991..4c0707a 100644 --- a/target/executable/summarizedexperiment/.config.vsh.yaml +++ b/target/executable/summarizedexperiment/.config.vsh.yaml @@ -199,8 +199,8 @@ build_info: output: "target/executable/summarizedexperiment" executable: "target/executable/summarizedexperiment/summarizedexperiment" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/summarizedexperiment/summarizedexperiment b/target/executable/summarizedexperiment/summarizedexperiment index 5cba212..13478e5 100755 --- a/target/executable/summarizedexperiment/summarizedexperiment +++ b/target/executable/summarizedexperiment/summarizedexperiment @@ -487,9 +487,9 @@ RUN Rscript -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.pa Rscript -e 'if (!requireNamespace("tximeta", quietly = TRUE)) BiocManager::install("tximeta")' LABEL org.opencontainers.image.description="Companion container for running component summarizedexperiment" -LABEL org.opencontainers.image.created="2024-11-13T10:13:20Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a" +LABEL org.opencontainers.image.created="2024-11-13T12:42:23Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/trimgalore/.config.vsh.yaml b/target/executable/trimgalore/.config.vsh.yaml index 8d89d27..4600848 100644 --- a/target/executable/trimgalore/.config.vsh.yaml +++ b/target/executable/trimgalore/.config.vsh.yaml @@ -788,8 +788,8 @@ build_info: output: "target/executable/trimgalore" executable: "target/executable/trimgalore/trimgalore" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/trimgalore/trimgalore b/target/executable/trimgalore/trimgalore index 0763e88..7902a28 100755 --- a/target/executable/trimgalore/trimgalore +++ b/target/executable/trimgalore/trimgalore @@ -858,9 +858,9 @@ ENTRYPOINT [] RUN echo "TrimGalore: `trim_galore --version | sed -n 's/.*version\s\+\([0-9]\+\.[0-9]\+\.[0-9]\+\).*/\1/p'`" > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component trimgalore" -LABEL org.opencontainers.image.created="2024-11-13T10:13:21Z" +LABEL org.opencontainers.image.created="2024-11-13T12:42:24Z" LABEL org.opencontainers.image.source="https://github.com/FelixKrueger/TrimGalore" -LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a" +LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/tx2gene/.config.vsh.yaml b/target/executable/tx2gene/.config.vsh.yaml index 6e22a1d..23183ac 100644 --- a/target/executable/tx2gene/.config.vsh.yaml +++ b/target/executable/tx2gene/.config.vsh.yaml @@ -192,8 +192,8 @@ build_info: output: "target/executable/tx2gene" executable: "target/executable/tx2gene/tx2gene" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/tx2gene/tx2gene b/target/executable/tx2gene/tx2gene index 1adbeff..e7f39ec 100755 --- a/target/executable/tx2gene/tx2gene +++ b/target/executable/tx2gene/tx2gene @@ -487,9 +487,9 @@ RUN apt-get update && \ RUN pip install --upgrade pip LABEL org.opencontainers.image.description="Companion container for running component tx2gene" -LABEL org.opencontainers.image.created="2024-11-13T10:13:20Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a" +LABEL org.opencontainers.image.created="2024-11-13T12:42:23Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/tximport/.config.vsh.yaml b/target/executable/tximport/.config.vsh.yaml index 8b8a1f0..2c5e0c1 100644 --- a/target/executable/tximport/.config.vsh.yaml +++ b/target/executable/tximport/.config.vsh.yaml @@ -247,8 +247,8 @@ build_info: output: "target/executable/tximport" executable: "target/executable/tximport/tximport" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/tximport/tximport b/target/executable/tximport/tximport index 288bc03..49aae23 100755 --- a/target/executable/tximport/tximport +++ b/target/executable/tximport/tximport @@ -508,9 +508,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag Rscript -e 'remotes::install_cran(c("jsonlite"), repos = "https://cran.rstudio.com")' LABEL org.opencontainers.image.description="Companion container for running component tximport" -LABEL org.opencontainers.image.created="2024-11-13T10:13:19Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a" +LABEL org.opencontainers.image.created="2024-11-13T12:42:22Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/ucsc/bedclip/.config.vsh.yaml b/target/executable/ucsc/bedclip/.config.vsh.yaml index 0135f7a..be1f4b0 100644 --- a/target/executable/ucsc/bedclip/.config.vsh.yaml +++ b/target/executable/ucsc/bedclip/.config.vsh.yaml @@ -164,8 +164,8 @@ build_info: output: "target/executable/ucsc/bedclip" executable: "target/executable/ucsc/bedclip/bedclip" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/ucsc/bedclip/bedclip b/target/executable/ucsc/bedclip/bedclip index 1eb7067..a7c8a86 100755 --- a/target/executable/ucsc/bedclip/bedclip +++ b/target/executable/ucsc/bedclip/bedclip @@ -473,9 +473,9 @@ RUN apt-get update && \ RUN rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/bedClip /usr/local/bin/ LABEL org.opencontainers.image.description="Companion container for running component ucsc bedclip" -LABEL org.opencontainers.image.created="2024-11-13T10:13:20Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a" +LABEL org.opencontainers.image.created="2024-11-13T12:42:22Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/ucsc/bedgraphtobigwig/.config.vsh.yaml b/target/executable/ucsc/bedgraphtobigwig/.config.vsh.yaml index 5ada2d8..f49ffb5 100644 --- a/target/executable/ucsc/bedgraphtobigwig/.config.vsh.yaml +++ b/target/executable/ucsc/bedgraphtobigwig/.config.vsh.yaml @@ -164,8 +164,8 @@ build_info: output: "target/executable/ucsc/bedgraphtobigwig" executable: "target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig b/target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig index 598e3a7..0779c4f 100755 --- a/target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig +++ b/target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig @@ -473,9 +473,9 @@ RUN apt-get update && \ RUN rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/bedGraphToBigWig /usr/local/bin/ LABEL org.opencontainers.image.description="Companion container for running component ucsc bedgraphtobigwig" -LABEL org.opencontainers.image.created="2024-11-13T10:13:20Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a" +LABEL org.opencontainers.image.created="2024-11-13T12:42:23Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/umitools/umitools_dedup/.config.vsh.yaml b/target/executable/umitools/umitools_dedup/.config.vsh.yaml index 398abdc..9152c17 100644 --- a/target/executable/umitools/umitools_dedup/.config.vsh.yaml +++ b/target/executable/umitools/umitools_dedup/.config.vsh.yaml @@ -195,8 +195,8 @@ build_info: output: "target/executable/umitools/umitools_dedup" executable: "target/executable/umitools/umitools_dedup/umitools_dedup" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/umitools/umitools_dedup/umitools_dedup b/target/executable/umitools/umitools_dedup/umitools_dedup index 9ac509b..c797bb9 100755 --- a/target/executable/umitools/umitools_dedup/umitools_dedup +++ b/target/executable/umitools/umitools_dedup/umitools_dedup @@ -489,9 +489,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "umi_tools" LABEL org.opencontainers.image.description="Companion container for running component umitools umitools_dedup" -LABEL org.opencontainers.image.created="2024-11-13T10:13:15Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a" +LABEL org.opencontainers.image.created="2024-11-13T12:42:18Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/umitools/umitools_extract/.config.vsh.yaml b/target/executable/umitools/umitools_extract/.config.vsh.yaml index 71df6fc..5fc2c10 100644 --- a/target/executable/umitools/umitools_extract/.config.vsh.yaml +++ b/target/executable/umitools/umitools_extract/.config.vsh.yaml @@ -253,8 +253,8 @@ build_info: output: "target/executable/umitools/umitools_extract" executable: "target/executable/umitools/umitools_extract/umitools_extract" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/umitools/umitools_extract/umitools_extract b/target/executable/umitools/umitools_extract/umitools_extract index 33573a2..4fd3d9b 100755 --- a/target/executable/umitools/umitools_extract/umitools_extract +++ b/target/executable/umitools/umitools_extract/umitools_extract @@ -521,9 +521,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "umi_tools" LABEL org.opencontainers.image.description="Companion container for running component umitools umitools_extract" -LABEL org.opencontainers.image.created="2024-11-13T10:13:15Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a" +LABEL org.opencontainers.image.created="2024-11-13T12:42:17Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/umitools_prepareforquant/.config.vsh.yaml b/target/executable/umitools_prepareforquant/.config.vsh.yaml index ef49f2d..e620701 100644 --- a/target/executable/umitools_prepareforquant/.config.vsh.yaml +++ b/target/executable/umitools_prepareforquant/.config.vsh.yaml @@ -156,8 +156,8 @@ build_info: output: "target/executable/umitools_prepareforquant" executable: "target/executable/umitools_prepareforquant/umitools_prepareforquant" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/umitools_prepareforquant/umitools_prepareforquant b/target/executable/umitools_prepareforquant/umitools_prepareforquant index b0a75f4..b9181d0 100755 --- a/target/executable/umitools_prepareforquant/umitools_prepareforquant +++ b/target/executable/umitools_prepareforquant/umitools_prepareforquant @@ -473,9 +473,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "umi_tools" "pysam" LABEL org.opencontainers.image.description="Companion container for running component umitools_prepareforquant" -LABEL org.opencontainers.image.created="2024-11-13T10:13:22Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a" +LABEL org.opencontainers.image.created="2024-11-13T12:42:24Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/workflows/genome_alignment_and_quant/.config.vsh.yaml b/target/executable/workflows/genome_alignment_and_quant/.config.vsh.yaml index 32643dd..a716ee8 100644 --- a/target/executable/workflows/genome_alignment_and_quant/.config.vsh.yaml +++ b/target/executable/workflows/genome_alignment_and_quant/.config.vsh.yaml @@ -603,8 +603,8 @@ build_info: output: "target/executable/workflows/genome_alignment_and_quant" executable: "target/executable/workflows/genome_alignment_and_quant/genome_alignment_and_quant" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" dependencies: - "target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_align_reads" - "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort" diff --git a/target/executable/workflows/merge_quant_results/.config.vsh.yaml b/target/executable/workflows/merge_quant_results/.config.vsh.yaml index f7c07bc..0782cff 100644 --- a/target/executable/workflows/merge_quant_results/.config.vsh.yaml +++ b/target/executable/workflows/merge_quant_results/.config.vsh.yaml @@ -278,8 +278,8 @@ build_info: output: "target/executable/workflows/merge_quant_results" executable: "target/executable/workflows/merge_quant_results/merge_quant_results" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/tx2gene" - "target/nextflow/tximport" diff --git a/target/executable/workflows/post_processing/.config.vsh.yaml b/target/executable/workflows/post_processing/.config.vsh.yaml index ca5d73d..195a2c9 100644 --- a/target/executable/workflows/post_processing/.config.vsh.yaml +++ b/target/executable/workflows/post_processing/.config.vsh.yaml @@ -486,8 +486,8 @@ build_info: output: "target/executable/workflows/post_processing" executable: "target/executable/workflows/post_processing/post_processing" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/picard_markduplicates" - "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort" diff --git a/target/executable/workflows/pre_processing/.config.vsh.yaml b/target/executable/workflows/pre_processing/.config.vsh.yaml index a1d2385..0d29799 100644 --- a/target/executable/workflows/pre_processing/.config.vsh.yaml +++ b/target/executable/workflows/pre_processing/.config.vsh.yaml @@ -673,8 +673,8 @@ build_info: output: "target/executable/workflows/pre_processing" executable: "target/executable/workflows/pre_processing/pre_processing" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/fastqc" - "target/nextflow/umitools/umitools_extract" diff --git a/target/executable/workflows/prepare_genome/.config.vsh.yaml b/target/executable/workflows/prepare_genome/.config.vsh.yaml index dc80f25..28331bb 100644 --- a/target/executable/workflows/prepare_genome/.config.vsh.yaml +++ b/target/executable/workflows/prepare_genome/.config.vsh.yaml @@ -221,6 +221,11 @@ argument_groups: direction: "input" multiple: false multiple_sep: ";" + - type: "boolean_true" + name: "--skip_alignment" + description: "Skip all of the alignment-based processes within the pipeline." + info: null + direction: "input" - name: "Output" arguments: - type: "file" @@ -496,8 +501,8 @@ build_info: output: "target/executable/workflows/prepare_genome" executable: "target/executable/workflows/prepare_genome/prepare_genome" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/gunzip" - "target/dependencies/vsh/vsh/biobox/main/nextflow/gffread" diff --git a/target/executable/workflows/prepare_genome/prepare_genome b/target/executable/workflows/prepare_genome/prepare_genome index 7a544be..a22ef3c 100755 --- a/target/executable/workflows/prepare_genome/prepare_genome +++ b/target/executable/workflows/prepare_genome/prepare_genome @@ -275,6 +275,10 @@ function ViashHelp { echo " Specifies the pseudo aligner to use - available options are 'salmon'." echo " Runs in addition to '--aligner'." echo "" + echo " --skip_alignment" + echo " type: boolean_true" + echo " Skip all of the alignment-based processes within the pipeline." + echo "" echo "Output:" echo " --fasta_uncompressed" echo " type: file, output, file must exist" @@ -577,6 +581,11 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_PSEUDO_ALIGNER=$(ViashRemoveFlags "$1") shift 1 ;; + --skip_alignment) + [ -n "$VIASH_PAR_SKIP_ALIGNMENT" ] && ViashError Bad arguments for option \'--skip_alignment\': \'$VIASH_PAR_SKIP_ALIGNMENT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_SKIP_ALIGNMENT=true + shift 1 + ;; --fasta_uncompressed) [ -n "$VIASH_PAR_FASTA_UNCOMPRESSED" ] && ViashError Bad arguments for option \'--fasta_uncompressed\': \'$VIASH_PAR_FASTA_UNCOMPRESSED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 VIASH_PAR_FASTA_UNCOMPRESSED="$2" @@ -846,6 +855,9 @@ fi if [ -z ${VIASH_PAR_PSEUDO_ALIGNER+x} ]; then VIASH_PAR_PSEUDO_ALIGNER="salmon" fi +if [ -z ${VIASH_PAR_SKIP_ALIGNMENT+x} ]; then + VIASH_PAR_SKIP_ALIGNMENT="false" +fi if [ -z ${VIASH_PAR_FASTA_UNCOMPRESSED+x} ]; then VIASH_PAR_FASTA_UNCOMPRESSED="reference_genome.fasta" fi @@ -959,6 +971,12 @@ if [[ -n "$VIASH_PAR_FILTER_GTF" ]]; then exit 1 fi fi +if [[ -n "$VIASH_PAR_SKIP_ALIGNMENT" ]]; then + if ! [[ "$VIASH_PAR_SKIP_ALIGNMENT" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then + ViashError '--skip_alignment' has to be a boolean_true. Use "--help" to get more information on the parameters. + exit 1 + fi +fi if [[ -n "$VIASH_META_CPUS" ]]; then if ! [[ "$VIASH_META_CPUS" =~ ^[-+]?[0-9]+$ ]]; then ViashError 'cpus' has to be an integer. Use "--help" to get more information on the parameters. @@ -1322,7 +1340,7 @@ workflow run_wf { // TODO: Add to viah-hub or adapt star_align_reads to enable the generateGenome runMode | star_genome_generate.run ( - runIf: {id, state -> !state.star_index}, + runIf: {id, state -> !state.star_index && !state.skip_alignment}, fromState: [ "genome_fasta_files": "fasta", "sjdb_gtf_file": "gtf" diff --git a/target/executable/workflows/pseudo_alignment_and_quant/.config.vsh.yaml b/target/executable/workflows/pseudo_alignment_and_quant/.config.vsh.yaml index fbc4b1a..3b27db7 100644 --- a/target/executable/workflows/pseudo_alignment_and_quant/.config.vsh.yaml +++ b/target/executable/workflows/pseudo_alignment_and_quant/.config.vsh.yaml @@ -283,8 +283,8 @@ build_info: output: "target/executable/workflows/pseudo_alignment_and_quant" executable: "target/executable/workflows/pseudo_alignment_and_quant/pseudo_alignment_and_quant" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" dependencies: - "target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant" - "target/nextflow/kallisto/kallisto_quant" diff --git a/target/executable/workflows/quality_control/.config.vsh.yaml b/target/executable/workflows/quality_control/.config.vsh.yaml index c353f41..5172217 100644 --- a/target/executable/workflows/quality_control/.config.vsh.yaml +++ b/target/executable/workflows/quality_control/.config.vsh.yaml @@ -1572,8 +1572,8 @@ build_info: output: "target/executable/workflows/quality_control" executable: "target/executable/workflows/quality_control/quality_control" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/rseqc/rseqc_bamstat" - "target/nextflow/rseqc/rseqc_inferexperiment" diff --git a/target/executable/workflows/rnaseq/.config.vsh.yaml b/target/executable/workflows/rnaseq/.config.vsh.yaml index 6c850f4..de17b18 100644 --- a/target/executable/workflows/rnaseq/.config.vsh.yaml +++ b/target/executable/workflows/rnaseq/.config.vsh.yaml @@ -2082,8 +2082,8 @@ build_info: output: "target/executable/workflows/rnaseq" executable: "target/executable/workflows/rnaseq/rnaseq" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/workflows/prepare_genome" - "target/nextflow/cat_fastq" diff --git a/target/executable/workflows/rnaseq/rnaseq b/target/executable/workflows/rnaseq/rnaseq index 5c34423..38a05eb 100755 --- a/target/executable/workflows/rnaseq/rnaseq +++ b/target/executable/workflows/rnaseq/rnaseq @@ -4471,7 +4471,8 @@ workflow run_wf { "biotype": "biotype", "filter_gtf": "filter_gtf", "aligner": "aligner", - "pseudo_aligner": "pseudo_aligner" + "pseudo_aligner": "pseudo_aligner", + "skip_alignment": "skip_alignment" ], toState: [ "fasta": "uncompressed_fasta", diff --git a/target/nextflow/bbmap_bbsplit/.config.vsh.yaml b/target/nextflow/bbmap_bbsplit/.config.vsh.yaml index 592ce00..ba8eec7 100644 --- a/target/nextflow/bbmap_bbsplit/.config.vsh.yaml +++ b/target/nextflow/bbmap_bbsplit/.config.vsh.yaml @@ -238,8 +238,8 @@ build_info: output: "target/nextflow/bbmap_bbsplit" executable: "target/nextflow/bbmap_bbsplit/main.nf" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/bbmap_bbsplit/main.nf b/target/nextflow/bbmap_bbsplit/main.nf index e052879..9ada2eb 100644 --- a/target/nextflow/bbmap_bbsplit/main.nf +++ b/target/nextflow/bbmap_bbsplit/main.nf @@ -3104,8 +3104,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/bbmap_bbsplit", "viash_version" : "0.9.0", - "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", - "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + "git_commit" : "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814", + "git_remote" : "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/bedtools_genomecov/.config.vsh.yaml b/target/nextflow/bedtools_genomecov/.config.vsh.yaml index ed06091..02d8b3b 100644 --- a/target/nextflow/bedtools_genomecov/.config.vsh.yaml +++ b/target/nextflow/bedtools_genomecov/.config.vsh.yaml @@ -178,8 +178,8 @@ build_info: output: "target/nextflow/bedtools_genomecov" executable: "target/nextflow/bedtools_genomecov/main.nf" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/bedtools_genomecov/main.nf b/target/nextflow/bedtools_genomecov/main.nf index 47bfd63..6438bea 100644 --- a/target/nextflow/bedtools_genomecov/main.nf +++ b/target/nextflow/bedtools_genomecov/main.nf @@ -3031,8 +3031,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/bedtools_genomecov", "viash_version" : "0.9.0", - "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", - "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + "git_commit" : "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814", + "git_remote" : "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/cat_additional_fasta/.config.vsh.yaml b/target/nextflow/cat_additional_fasta/.config.vsh.yaml index ac6928a..5b58f57 100644 --- a/target/nextflow/cat_additional_fasta/.config.vsh.yaml +++ b/target/nextflow/cat_additional_fasta/.config.vsh.yaml @@ -182,8 +182,8 @@ build_info: output: "target/nextflow/cat_additional_fasta" executable: "target/nextflow/cat_additional_fasta/main.nf" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/cat_additional_fasta/main.nf b/target/nextflow/cat_additional_fasta/main.nf index 3c6ac9c..512f2de 100644 --- a/target/nextflow/cat_additional_fasta/main.nf +++ b/target/nextflow/cat_additional_fasta/main.nf @@ -3032,8 +3032,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/cat_additional_fasta", "viash_version" : "0.9.0", - "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", - "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + "git_commit" : "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814", + "git_remote" : "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/cat_fastq/.config.vsh.yaml b/target/nextflow/cat_fastq/.config.vsh.yaml index 87501e2..902e107 100644 --- a/target/nextflow/cat_fastq/.config.vsh.yaml +++ b/target/nextflow/cat_fastq/.config.vsh.yaml @@ -169,8 +169,8 @@ build_info: output: "target/nextflow/cat_fastq" executable: "target/nextflow/cat_fastq/main.nf" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/cat_fastq/main.nf b/target/nextflow/cat_fastq/main.nf index 4412021..2719e76 100644 --- a/target/nextflow/cat_fastq/main.nf +++ b/target/nextflow/cat_fastq/main.nf @@ -3023,8 +3023,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/cat_fastq", "viash_version" : "0.9.0", - "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", - "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + "git_commit" : "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814", + "git_remote" : "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/deseq2_qc/.config.vsh.yaml b/target/nextflow/deseq2_qc/.config.vsh.yaml index 0b8af01..a02789d 100644 --- a/target/nextflow/deseq2_qc/.config.vsh.yaml +++ b/target/nextflow/deseq2_qc/.config.vsh.yaml @@ -237,8 +237,8 @@ build_info: output: "target/nextflow/deseq2_qc" executable: "target/nextflow/deseq2_qc/main.nf" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/deseq2_qc/main.nf b/target/nextflow/deseq2_qc/main.nf index bb2b736..a33245d 100644 --- a/target/nextflow/deseq2_qc/main.nf +++ b/target/nextflow/deseq2_qc/main.nf @@ -3104,8 +3104,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/deseq2_qc", "viash_version" : "0.9.0", - "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", - "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + "git_commit" : "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814", + "git_remote" : "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/dupradar/.config.vsh.yaml b/target/nextflow/dupradar/.config.vsh.yaml index 0896798..0188dba 100644 --- a/target/nextflow/dupradar/.config.vsh.yaml +++ b/target/nextflow/dupradar/.config.vsh.yaml @@ -266,8 +266,8 @@ build_info: output: "target/nextflow/dupradar" executable: "target/nextflow/dupradar/main.nf" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/dupradar/main.nf b/target/nextflow/dupradar/main.nf index cbe5f2d..b596f74 100644 --- a/target/nextflow/dupradar/main.nf +++ b/target/nextflow/dupradar/main.nf @@ -3136,8 +3136,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/dupradar", "viash_version" : "0.9.0", - "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", - "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + "git_commit" : "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814", + "git_remote" : "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/fastqc/.config.vsh.yaml b/target/nextflow/fastqc/.config.vsh.yaml index 70ae3cf..0338c1f 100644 --- a/target/nextflow/fastqc/.config.vsh.yaml +++ b/target/nextflow/fastqc/.config.vsh.yaml @@ -198,8 +198,8 @@ build_info: output: "target/nextflow/fastqc" executable: "target/nextflow/fastqc/main.nf" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/fastqc/main.nf b/target/nextflow/fastqc/main.nf index 6e308bd..0b9e236 100644 --- a/target/nextflow/fastqc/main.nf +++ b/target/nextflow/fastqc/main.nf @@ -3056,8 +3056,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/fastqc", "viash_version" : "0.9.0", - "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", - "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + "git_commit" : "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814", + "git_remote" : "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/fq_subsample/.config.vsh.yaml b/target/nextflow/fq_subsample/.config.vsh.yaml index 1a1decc..c77ff00 100644 --- a/target/nextflow/fq_subsample/.config.vsh.yaml +++ b/target/nextflow/fq_subsample/.config.vsh.yaml @@ -177,8 +177,8 @@ build_info: output: "target/nextflow/fq_subsample" executable: "target/nextflow/fq_subsample/main.nf" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/fq_subsample/main.nf b/target/nextflow/fq_subsample/main.nf index 6c6d4cf..fbca2d7 100644 --- a/target/nextflow/fq_subsample/main.nf +++ b/target/nextflow/fq_subsample/main.nf @@ -3027,8 +3027,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/fq_subsample", "viash_version" : "0.9.0", - "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", - "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + "git_commit" : "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814", + "git_remote" : "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/getchromsizes/.config.vsh.yaml b/target/nextflow/getchromsizes/.config.vsh.yaml index b141149..c577723 100644 --- a/target/nextflow/getchromsizes/.config.vsh.yaml +++ b/target/nextflow/getchromsizes/.config.vsh.yaml @@ -167,8 +167,8 @@ build_info: output: "target/nextflow/getchromsizes" executable: "target/nextflow/getchromsizes/main.nf" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/getchromsizes/main.nf b/target/nextflow/getchromsizes/main.nf index 3ae37ab..6692aef 100644 --- a/target/nextflow/getchromsizes/main.nf +++ b/target/nextflow/getchromsizes/main.nf @@ -3013,8 +3013,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/getchromsizes", "viash_version" : "0.9.0", - "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", - "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + "git_commit" : "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814", + "git_remote" : "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/gtf2bed/.config.vsh.yaml b/target/nextflow/gtf2bed/.config.vsh.yaml index 298a0d3..0070d00 100644 --- a/target/nextflow/gtf2bed/.config.vsh.yaml +++ b/target/nextflow/gtf2bed/.config.vsh.yaml @@ -145,8 +145,8 @@ build_info: output: "target/nextflow/gtf2bed" executable: "target/nextflow/gtf2bed/main.nf" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/gtf2bed/main.nf b/target/nextflow/gtf2bed/main.nf index 4356b89..476d2cb 100644 --- a/target/nextflow/gtf2bed/main.nf +++ b/target/nextflow/gtf2bed/main.nf @@ -2995,8 +2995,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/gtf2bed", "viash_version" : "0.9.0", - "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", - "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + "git_commit" : "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814", + "git_remote" : "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/gtf_filter/.config.vsh.yaml b/target/nextflow/gtf_filter/.config.vsh.yaml index 0185428..1669e4b 100644 --- a/target/nextflow/gtf_filter/.config.vsh.yaml +++ b/target/nextflow/gtf_filter/.config.vsh.yaml @@ -155,8 +155,8 @@ build_info: output: "target/nextflow/gtf_filter" executable: "target/nextflow/gtf_filter/main.nf" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/gtf_filter/main.nf b/target/nextflow/gtf_filter/main.nf index 163c699..42cb9ee 100644 --- a/target/nextflow/gtf_filter/main.nf +++ b/target/nextflow/gtf_filter/main.nf @@ -3003,8 +3003,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/gtf_filter", "viash_version" : "0.9.0", - "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", - "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + "git_commit" : "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814", + "git_remote" : "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/gunzip/.config.vsh.yaml b/target/nextflow/gunzip/.config.vsh.yaml index 5c49ded..68d9d17 100644 --- a/target/nextflow/gunzip/.config.vsh.yaml +++ b/target/nextflow/gunzip/.config.vsh.yaml @@ -144,8 +144,8 @@ build_info: output: "target/nextflow/gunzip" executable: "target/nextflow/gunzip/main.nf" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/gunzip/main.nf b/target/nextflow/gunzip/main.nf index baaedae..97b2107 100644 --- a/target/nextflow/gunzip/main.nf +++ b/target/nextflow/gunzip/main.nf @@ -2992,8 +2992,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/gunzip", "viash_version" : "0.9.0", - "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", - "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + "git_commit" : "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814", + "git_remote" : "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml b/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml index 4ae8f4d..3283a00 100644 --- a/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml +++ b/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml @@ -155,8 +155,8 @@ build_info: output: "target/nextflow/kallisto/kallisto_index" executable: "target/nextflow/kallisto/kallisto_index/main.nf" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/kallisto/kallisto_index/main.nf b/target/nextflow/kallisto/kallisto_index/main.nf index ea26f3c..ae9093c 100644 --- a/target/nextflow/kallisto/kallisto_index/main.nf +++ b/target/nextflow/kallisto/kallisto_index/main.nf @@ -3002,8 +3002,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/kallisto/kallisto_index", "viash_version" : "0.9.0", - "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", - "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + "git_commit" : "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814", + "git_remote" : "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml b/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml index 54f78eb..1b3f6ae 100644 --- a/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml +++ b/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml @@ -253,8 +253,8 @@ build_info: output: "target/nextflow/kallisto/kallisto_quant" executable: "target/nextflow/kallisto/kallisto_quant/main.nf" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/kallisto/kallisto_quant/main.nf b/target/nextflow/kallisto/kallisto_quant/main.nf index c88f1ea..ebb20e3 100644 --- a/target/nextflow/kallisto/kallisto_quant/main.nf +++ b/target/nextflow/kallisto/kallisto_quant/main.nf @@ -3114,8 +3114,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/kallisto/kallisto_quant", "viash_version" : "0.9.0", - "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", - "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + "git_commit" : "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814", + "git_remote" : "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/multiqc_custom_biotype/.config.vsh.yaml b/target/nextflow/multiqc_custom_biotype/.config.vsh.yaml index 3b6a184..188f319 100644 --- a/target/nextflow/multiqc_custom_biotype/.config.vsh.yaml +++ b/target/nextflow/multiqc_custom_biotype/.config.vsh.yaml @@ -161,8 +161,8 @@ build_info: output: "target/nextflow/multiqc_custom_biotype" executable: "target/nextflow/multiqc_custom_biotype/main.nf" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/multiqc_custom_biotype/main.nf b/target/nextflow/multiqc_custom_biotype/main.nf index c36d323..dd5f726 100644 --- a/target/nextflow/multiqc_custom_biotype/main.nf +++ b/target/nextflow/multiqc_custom_biotype/main.nf @@ -3005,8 +3005,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/multiqc_custom_biotype", "viash_version" : "0.9.0", - "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", - "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + "git_commit" : "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814", + "git_remote" : "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/picard_markduplicates/.config.vsh.yaml b/target/nextflow/picard_markduplicates/.config.vsh.yaml index 61af449..889b149 100644 --- a/target/nextflow/picard_markduplicates/.config.vsh.yaml +++ b/target/nextflow/picard_markduplicates/.config.vsh.yaml @@ -207,8 +207,8 @@ build_info: output: "target/nextflow/picard_markduplicates" executable: "target/nextflow/picard_markduplicates/main.nf" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/picard_markduplicates/main.nf b/target/nextflow/picard_markduplicates/main.nf index 6d35c57..c3b65ca 100644 --- a/target/nextflow/picard_markduplicates/main.nf +++ b/target/nextflow/picard_markduplicates/main.nf @@ -3063,8 +3063,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/picard_markduplicates", "viash_version" : "0.9.0", - "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", - "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + "git_commit" : "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814", + "git_remote" : "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/prepare_multiqc_input/.config.vsh.yaml b/target/nextflow/prepare_multiqc_input/.config.vsh.yaml index 6167e0f..66a93f4 100644 --- a/target/nextflow/prepare_multiqc_input/.config.vsh.yaml +++ b/target/nextflow/prepare_multiqc_input/.config.vsh.yaml @@ -409,8 +409,8 @@ build_info: output: "target/nextflow/prepare_multiqc_input" executable: "target/nextflow/prepare_multiqc_input/main.nf" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/prepare_multiqc_input/main.nf b/target/nextflow/prepare_multiqc_input/main.nf index c37b1d5..60bf059 100644 --- a/target/nextflow/prepare_multiqc_input/main.nf +++ b/target/nextflow/prepare_multiqc_input/main.nf @@ -3277,8 +3277,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/prepare_multiqc_input", "viash_version" : "0.9.0", - "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", - "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + "git_commit" : "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814", + "git_remote" : "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/preprocess_transcripts_fasta/.config.vsh.yaml b/target/nextflow/preprocess_transcripts_fasta/.config.vsh.yaml index 88ed5b0..2f6e510 100644 --- a/target/nextflow/preprocess_transcripts_fasta/.config.vsh.yaml +++ b/target/nextflow/preprocess_transcripts_fasta/.config.vsh.yaml @@ -138,8 +138,8 @@ build_info: output: "target/nextflow/preprocess_transcripts_fasta" executable: "target/nextflow/preprocess_transcripts_fasta/main.nf" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/preprocess_transcripts_fasta/main.nf b/target/nextflow/preprocess_transcripts_fasta/main.nf index 1d592f8..1ded5b9 100644 --- a/target/nextflow/preprocess_transcripts_fasta/main.nf +++ b/target/nextflow/preprocess_transcripts_fasta/main.nf @@ -2982,8 +2982,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/preprocess_transcripts_fasta", "viash_version" : "0.9.0", - "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", - "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + "git_commit" : "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814", + "git_remote" : "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/preseq_lcextrap/.config.vsh.yaml b/target/nextflow/preseq_lcextrap/.config.vsh.yaml index be413ef..3cffdd3 100644 --- a/target/nextflow/preseq_lcextrap/.config.vsh.yaml +++ b/target/nextflow/preseq_lcextrap/.config.vsh.yaml @@ -191,8 +191,8 @@ build_info: output: "target/nextflow/preseq_lcextrap" executable: "target/nextflow/preseq_lcextrap/main.nf" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/preseq_lcextrap/main.nf b/target/nextflow/preseq_lcextrap/main.nf index ae6c5c1..0830fea 100644 --- a/target/nextflow/preseq_lcextrap/main.nf +++ b/target/nextflow/preseq_lcextrap/main.nf @@ -3035,8 +3035,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/preseq_lcextrap", "viash_version" : "0.9.0", - "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", - "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + "git_commit" : "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814", + "git_remote" : "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/qualimap/.config.vsh.yaml b/target/nextflow/qualimap/.config.vsh.yaml index 3acdadc..62fbcc1 100644 --- a/target/nextflow/qualimap/.config.vsh.yaml +++ b/target/nextflow/qualimap/.config.vsh.yaml @@ -271,8 +271,8 @@ build_info: output: "target/nextflow/qualimap" executable: "target/nextflow/qualimap/main.nf" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/qualimap/main.nf b/target/nextflow/qualimap/main.nf index f99aac1..261678c 100644 --- a/target/nextflow/qualimap/main.nf +++ b/target/nextflow/qualimap/main.nf @@ -3144,8 +3144,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/qualimap", "viash_version" : "0.9.0", - "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", - "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + "git_commit" : "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814", + "git_remote" : "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml b/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml index c059f38..45355a2 100644 --- a/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml +++ b/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml @@ -299,8 +299,8 @@ build_info: output: "target/nextflow/rsem/rsem_calculate_expression" executable: "target/nextflow/rsem/rsem_calculate_expression/main.nf" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/rsem/rsem_calculate_expression/main.nf b/target/nextflow/rsem/rsem_calculate_expression/main.nf index 15a858f..06f299a 100644 --- a/target/nextflow/rsem/rsem_calculate_expression/main.nf +++ b/target/nextflow/rsem/rsem_calculate_expression/main.nf @@ -3163,8 +3163,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rsem/rsem_calculate_expression", "viash_version" : "0.9.0", - "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", - "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + "git_commit" : "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814", + "git_remote" : "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/rsem/rsem_merge_counts/.config.vsh.yaml b/target/nextflow/rsem/rsem_merge_counts/.config.vsh.yaml index ce8775e..40c145a 100644 --- a/target/nextflow/rsem/rsem_merge_counts/.config.vsh.yaml +++ b/target/nextflow/rsem/rsem_merge_counts/.config.vsh.yaml @@ -182,8 +182,8 @@ build_info: output: "target/nextflow/rsem/rsem_merge_counts" executable: "target/nextflow/rsem/rsem_merge_counts/main.nf" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/rsem/rsem_merge_counts/main.nf b/target/nextflow/rsem/rsem_merge_counts/main.nf index e50fb67..8e210af 100644 --- a/target/nextflow/rsem/rsem_merge_counts/main.nf +++ b/target/nextflow/rsem/rsem_merge_counts/main.nf @@ -3028,8 +3028,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rsem/rsem_merge_counts", "viash_version" : "0.9.0", - "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", - "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + "git_commit" : "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814", + "git_remote" : "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml index b3dc052..509119e 100644 --- a/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml @@ -163,8 +163,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_bamstat" executable: "target/nextflow/rseqc/rseqc_bamstat/main.nf" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/rseqc/rseqc_bamstat/main.nf b/target/nextflow/rseqc/rseqc_bamstat/main.nf index 3a0cb94..bb71971 100644 --- a/target/nextflow/rseqc/rseqc_bamstat/main.nf +++ b/target/nextflow/rseqc/rseqc_bamstat/main.nf @@ -3016,8 +3016,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_bamstat", "viash_version" : "0.9.0", - "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", - "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + "git_commit" : "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814", + "git_remote" : "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml index f639b73..ce875a7 100644 --- a/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml @@ -186,8 +186,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_inferexperiment" executable: "target/nextflow/rseqc/rseqc_inferexperiment/main.nf" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/rseqc/rseqc_inferexperiment/main.nf b/target/nextflow/rseqc/rseqc_inferexperiment/main.nf index d90cfb1..a2bcf83 100644 --- a/target/nextflow/rseqc/rseqc_inferexperiment/main.nf +++ b/target/nextflow/rseqc/rseqc_inferexperiment/main.nf @@ -3044,8 +3044,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_inferexperiment", "viash_version" : "0.9.0", - "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", - "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + "git_commit" : "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814", + "git_remote" : "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/rseqc/rseqc_innerdistance/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_innerdistance/.config.vsh.yaml index 63b6390..d869dac 100644 --- a/target/nextflow/rseqc/rseqc_innerdistance/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_innerdistance/.config.vsh.yaml @@ -272,8 +272,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_innerdistance" executable: "target/nextflow/rseqc/rseqc_innerdistance/main.nf" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/rseqc/rseqc_innerdistance/main.nf b/target/nextflow/rseqc/rseqc_innerdistance/main.nf index e48faf1..b18b51e 100644 --- a/target/nextflow/rseqc/rseqc_innerdistance/main.nf +++ b/target/nextflow/rseqc/rseqc_innerdistance/main.nf @@ -3137,8 +3137,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_innerdistance", "viash_version" : "0.9.0", - "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", - "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + "git_commit" : "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814", + "git_remote" : "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/rseqc/rseqc_junctionannotation/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_junctionannotation/.config.vsh.yaml index 373bf70..ef59e31 100644 --- a/target/nextflow/rseqc/rseqc_junctionannotation/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_junctionannotation/.config.vsh.yaml @@ -260,8 +260,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_junctionannotation" executable: "target/nextflow/rseqc/rseqc_junctionannotation/main.nf" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/rseqc/rseqc_junctionannotation/main.nf b/target/nextflow/rseqc/rseqc_junctionannotation/main.nf index 94dce62..47273db 100644 --- a/target/nextflow/rseqc/rseqc_junctionannotation/main.nf +++ b/target/nextflow/rseqc/rseqc_junctionannotation/main.nf @@ -3128,8 +3128,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_junctionannotation", "viash_version" : "0.9.0", - "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", - "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + "git_commit" : "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814", + "git_remote" : "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/rseqc/rseqc_junctionsaturation/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_junctionsaturation/.config.vsh.yaml index c61da3c..65d33c1 100644 --- a/target/nextflow/rseqc/rseqc_junctionsaturation/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_junctionsaturation/.config.vsh.yaml @@ -249,8 +249,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_junctionsaturation" executable: "target/nextflow/rseqc/rseqc_junctionsaturation/main.nf" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/rseqc/rseqc_junctionsaturation/main.nf b/target/nextflow/rseqc/rseqc_junctionsaturation/main.nf index e6f0e84..bf3d455 100644 --- a/target/nextflow/rseqc/rseqc_junctionsaturation/main.nf +++ b/target/nextflow/rseqc/rseqc_junctionsaturation/main.nf @@ -3113,8 +3113,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_junctionsaturation", "viash_version" : "0.9.0", - "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", - "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + "git_commit" : "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814", + "git_remote" : "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/rseqc/rseqc_readdistribution/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_readdistribution/.config.vsh.yaml index 25476eb..b9fb75c 100644 --- a/target/nextflow/rseqc/rseqc_readdistribution/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_readdistribution/.config.vsh.yaml @@ -162,8 +162,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_readdistribution" executable: "target/nextflow/rseqc/rseqc_readdistribution/main.nf" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/rseqc/rseqc_readdistribution/main.nf b/target/nextflow/rseqc/rseqc_readdistribution/main.nf index 818bcb3..a0228c5 100644 --- a/target/nextflow/rseqc/rseqc_readdistribution/main.nf +++ b/target/nextflow/rseqc/rseqc_readdistribution/main.nf @@ -3017,8 +3017,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_readdistribution", "viash_version" : "0.9.0", - "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", - "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + "git_commit" : "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814", + "git_remote" : "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/rseqc/rseqc_readduplication/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_readduplication/.config.vsh.yaml index cdefc5e..32862b3 100644 --- a/target/nextflow/rseqc/rseqc_readduplication/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_readduplication/.config.vsh.yaml @@ -211,8 +211,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_readduplication" executable: "target/nextflow/rseqc/rseqc_readduplication/main.nf" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/rseqc/rseqc_readduplication/main.nf b/target/nextflow/rseqc/rseqc_readduplication/main.nf index 43e57a1..af9bfdd 100644 --- a/target/nextflow/rseqc/rseqc_readduplication/main.nf +++ b/target/nextflow/rseqc/rseqc_readduplication/main.nf @@ -3071,8 +3071,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_readduplication", "viash_version" : "0.9.0", - "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", - "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + "git_commit" : "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814", + "git_remote" : "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/rseqc/rseqc_tin/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_tin/.config.vsh.yaml index 69c8fb4..baacd3e 100644 --- a/target/nextflow/rseqc/rseqc_tin/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_tin/.config.vsh.yaml @@ -214,8 +214,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_tin" executable: "target/nextflow/rseqc/rseqc_tin/main.nf" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/rseqc/rseqc_tin/main.nf b/target/nextflow/rseqc/rseqc_tin/main.nf index 56d2276..80771ad 100644 --- a/target/nextflow/rseqc/rseqc_tin/main.nf +++ b/target/nextflow/rseqc/rseqc_tin/main.nf @@ -3076,8 +3076,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_tin", "viash_version" : "0.9.0", - "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", - "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + "git_commit" : "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814", + "git_remote" : "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/sortmerna/.config.vsh.yaml b/target/nextflow/sortmerna/.config.vsh.yaml index 47f48b9..d6e3892 100644 --- a/target/nextflow/sortmerna/.config.vsh.yaml +++ b/target/nextflow/sortmerna/.config.vsh.yaml @@ -192,8 +192,8 @@ build_info: output: "target/nextflow/sortmerna" executable: "target/nextflow/sortmerna/main.nf" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/sortmerna/main.nf b/target/nextflow/sortmerna/main.nf index 75cb58e..633f4fc 100644 --- a/target/nextflow/sortmerna/main.nf +++ b/target/nextflow/sortmerna/main.nf @@ -3042,8 +3042,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/sortmerna", "viash_version" : "0.9.0", - "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", - "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + "git_commit" : "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814", + "git_remote" : "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/stringtie/.config.vsh.yaml b/target/nextflow/stringtie/.config.vsh.yaml index 6732cf9..fb46058 100644 --- a/target/nextflow/stringtie/.config.vsh.yaml +++ b/target/nextflow/stringtie/.config.vsh.yaml @@ -216,8 +216,8 @@ build_info: output: "target/nextflow/stringtie" executable: "target/nextflow/stringtie/main.nf" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/stringtie/main.nf b/target/nextflow/stringtie/main.nf index bfff52d..54980ce 100644 --- a/target/nextflow/stringtie/main.nf +++ b/target/nextflow/stringtie/main.nf @@ -3073,8 +3073,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/stringtie", "viash_version" : "0.9.0", - "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", - "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + "git_commit" : "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814", + "git_remote" : "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/summarizedexperiment/.config.vsh.yaml b/target/nextflow/summarizedexperiment/.config.vsh.yaml index 01add5c..ff1589c 100644 --- a/target/nextflow/summarizedexperiment/.config.vsh.yaml +++ b/target/nextflow/summarizedexperiment/.config.vsh.yaml @@ -199,8 +199,8 @@ build_info: output: "target/nextflow/summarizedexperiment" executable: "target/nextflow/summarizedexperiment/main.nf" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/summarizedexperiment/main.nf b/target/nextflow/summarizedexperiment/main.nf index 4cf0d29..bb1dee0 100644 --- a/target/nextflow/summarizedexperiment/main.nf +++ b/target/nextflow/summarizedexperiment/main.nf @@ -3054,8 +3054,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/summarizedexperiment", "viash_version" : "0.9.0", - "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", - "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + "git_commit" : "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814", + "git_remote" : "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/trimgalore/.config.vsh.yaml b/target/nextflow/trimgalore/.config.vsh.yaml index e254ddc..65ec78c 100644 --- a/target/nextflow/trimgalore/.config.vsh.yaml +++ b/target/nextflow/trimgalore/.config.vsh.yaml @@ -788,8 +788,8 @@ build_info: output: "target/nextflow/trimgalore" executable: "target/nextflow/trimgalore/main.nf" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/trimgalore/main.nf b/target/nextflow/trimgalore/main.nf index efdffea..a1b083b 100644 --- a/target/nextflow/trimgalore/main.nf +++ b/target/nextflow/trimgalore/main.nf @@ -3576,8 +3576,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/trimgalore", "viash_version" : "0.9.0", - "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", - "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + "git_commit" : "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814", + "git_remote" : "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/tx2gene/.config.vsh.yaml b/target/nextflow/tx2gene/.config.vsh.yaml index ae637d3..e01a0c1 100644 --- a/target/nextflow/tx2gene/.config.vsh.yaml +++ b/target/nextflow/tx2gene/.config.vsh.yaml @@ -192,8 +192,8 @@ build_info: output: "target/nextflow/tx2gene" executable: "target/nextflow/tx2gene/main.nf" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/tx2gene/main.nf b/target/nextflow/tx2gene/main.nf index 535f873..1211d09 100644 --- a/target/nextflow/tx2gene/main.nf +++ b/target/nextflow/tx2gene/main.nf @@ -3049,8 +3049,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/tx2gene", "viash_version" : "0.9.0", - "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", - "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + "git_commit" : "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814", + "git_remote" : "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/tximport/.config.vsh.yaml b/target/nextflow/tximport/.config.vsh.yaml index 0189f9d..ed5c14c 100644 --- a/target/nextflow/tximport/.config.vsh.yaml +++ b/target/nextflow/tximport/.config.vsh.yaml @@ -247,8 +247,8 @@ build_info: output: "target/nextflow/tximport" executable: "target/nextflow/tximport/main.nf" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/tximport/main.nf b/target/nextflow/tximport/main.nf index f2b63df..fedb04c 100644 --- a/target/nextflow/tximport/main.nf +++ b/target/nextflow/tximport/main.nf @@ -3114,8 +3114,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/tximport", "viash_version" : "0.9.0", - "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", - "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + "git_commit" : "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814", + "git_remote" : "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/ucsc/bedclip/.config.vsh.yaml b/target/nextflow/ucsc/bedclip/.config.vsh.yaml index 61ba071..65fe928 100644 --- a/target/nextflow/ucsc/bedclip/.config.vsh.yaml +++ b/target/nextflow/ucsc/bedclip/.config.vsh.yaml @@ -164,8 +164,8 @@ build_info: output: "target/nextflow/ucsc/bedclip" executable: "target/nextflow/ucsc/bedclip/main.nf" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/ucsc/bedclip/main.nf b/target/nextflow/ucsc/bedclip/main.nf index eb3f994..3223daa 100644 --- a/target/nextflow/ucsc/bedclip/main.nf +++ b/target/nextflow/ucsc/bedclip/main.nf @@ -3018,8 +3018,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/ucsc/bedclip", "viash_version" : "0.9.0", - "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", - "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + "git_commit" : "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814", + "git_remote" : "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/ucsc/bedgraphtobigwig/.config.vsh.yaml b/target/nextflow/ucsc/bedgraphtobigwig/.config.vsh.yaml index 22c6a2e..c2541bb 100644 --- a/target/nextflow/ucsc/bedgraphtobigwig/.config.vsh.yaml +++ b/target/nextflow/ucsc/bedgraphtobigwig/.config.vsh.yaml @@ -164,8 +164,8 @@ build_info: output: "target/nextflow/ucsc/bedgraphtobigwig" executable: "target/nextflow/ucsc/bedgraphtobigwig/main.nf" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/ucsc/bedgraphtobigwig/main.nf b/target/nextflow/ucsc/bedgraphtobigwig/main.nf index dd016e4..a6f0a42 100644 --- a/target/nextflow/ucsc/bedgraphtobigwig/main.nf +++ b/target/nextflow/ucsc/bedgraphtobigwig/main.nf @@ -3018,8 +3018,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/ucsc/bedgraphtobigwig", "viash_version" : "0.9.0", - "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", - "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + "git_commit" : "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814", + "git_remote" : "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/umitools/umitools_dedup/.config.vsh.yaml b/target/nextflow/umitools/umitools_dedup/.config.vsh.yaml index 6b1bedd..962c0b7 100644 --- a/target/nextflow/umitools/umitools_dedup/.config.vsh.yaml +++ b/target/nextflow/umitools/umitools_dedup/.config.vsh.yaml @@ -195,8 +195,8 @@ build_info: output: "target/nextflow/umitools/umitools_dedup" executable: "target/nextflow/umitools/umitools_dedup/main.nf" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/umitools/umitools_dedup/main.nf b/target/nextflow/umitools/umitools_dedup/main.nf index 4ef21a1..6e0d94c 100644 --- a/target/nextflow/umitools/umitools_dedup/main.nf +++ b/target/nextflow/umitools/umitools_dedup/main.nf @@ -3054,8 +3054,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/umitools/umitools_dedup", "viash_version" : "0.9.0", - "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", - "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + "git_commit" : "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814", + "git_remote" : "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/umitools/umitools_extract/.config.vsh.yaml b/target/nextflow/umitools/umitools_extract/.config.vsh.yaml index f0316a0..09fd4b7 100644 --- a/target/nextflow/umitools/umitools_extract/.config.vsh.yaml +++ b/target/nextflow/umitools/umitools_extract/.config.vsh.yaml @@ -253,8 +253,8 @@ build_info: output: "target/nextflow/umitools/umitools_extract" executable: "target/nextflow/umitools/umitools_extract/main.nf" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/umitools/umitools_extract/main.nf b/target/nextflow/umitools/umitools_extract/main.nf index 00cffd0..223131d 100644 --- a/target/nextflow/umitools/umitools_extract/main.nf +++ b/target/nextflow/umitools/umitools_extract/main.nf @@ -3119,8 +3119,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/umitools/umitools_extract", "viash_version" : "0.9.0", - "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", - "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + "git_commit" : "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814", + "git_remote" : "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/umitools_prepareforquant/.config.vsh.yaml b/target/nextflow/umitools_prepareforquant/.config.vsh.yaml index 94e0c85..9ee8458 100644 --- a/target/nextflow/umitools_prepareforquant/.config.vsh.yaml +++ b/target/nextflow/umitools_prepareforquant/.config.vsh.yaml @@ -156,8 +156,8 @@ build_info: output: "target/nextflow/umitools_prepareforquant" executable: "target/nextflow/umitools_prepareforquant/main.nf" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/umitools_prepareforquant/main.nf b/target/nextflow/umitools_prepareforquant/main.nf index ecbb5f1..03bf805 100644 --- a/target/nextflow/umitools_prepareforquant/main.nf +++ b/target/nextflow/umitools_prepareforquant/main.nf @@ -3007,8 +3007,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/umitools_prepareforquant", "viash_version" : "0.9.0", - "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", - "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + "git_commit" : "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814", + "git_remote" : "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/workflows/genome_alignment_and_quant/.config.vsh.yaml b/target/nextflow/workflows/genome_alignment_and_quant/.config.vsh.yaml index 1dcaa01..5092b17 100644 --- a/target/nextflow/workflows/genome_alignment_and_quant/.config.vsh.yaml +++ b/target/nextflow/workflows/genome_alignment_and_quant/.config.vsh.yaml @@ -603,8 +603,8 @@ build_info: output: "target/nextflow/workflows/genome_alignment_and_quant" executable: "target/nextflow/workflows/genome_alignment_and_quant/main.nf" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" dependencies: - "target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_align_reads" - "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort" diff --git a/target/nextflow/workflows/genome_alignment_and_quant/main.nf b/target/nextflow/workflows/genome_alignment_and_quant/main.nf index 6146e4e..3322b7c 100644 --- a/target/nextflow/workflows/genome_alignment_and_quant/main.nf +++ b/target/nextflow/workflows/genome_alignment_and_quant/main.nf @@ -3531,8 +3531,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/genome_alignment_and_quant", "viash_version" : "0.9.0", - "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", - "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + "git_commit" : "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814", + "git_remote" : "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/workflows/merge_quant_results/.config.vsh.yaml b/target/nextflow/workflows/merge_quant_results/.config.vsh.yaml index fe9b4b1..ad4f770 100644 --- a/target/nextflow/workflows/merge_quant_results/.config.vsh.yaml +++ b/target/nextflow/workflows/merge_quant_results/.config.vsh.yaml @@ -278,8 +278,8 @@ build_info: output: "target/nextflow/workflows/merge_quant_results" executable: "target/nextflow/workflows/merge_quant_results/main.nf" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/tx2gene" - "target/nextflow/tximport" diff --git a/target/nextflow/workflows/merge_quant_results/main.nf b/target/nextflow/workflows/merge_quant_results/main.nf index 65abfa6..79e2c33 100644 --- a/target/nextflow/workflows/merge_quant_results/main.nf +++ b/target/nextflow/workflows/merge_quant_results/main.nf @@ -3149,8 +3149,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/merge_quant_results", "viash_version" : "0.9.0", - "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", - "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + "git_commit" : "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814", + "git_remote" : "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/workflows/post_processing/.config.vsh.yaml b/target/nextflow/workflows/post_processing/.config.vsh.yaml index 9d8fe59..a2c811b 100644 --- a/target/nextflow/workflows/post_processing/.config.vsh.yaml +++ b/target/nextflow/workflows/post_processing/.config.vsh.yaml @@ -486,8 +486,8 @@ build_info: output: "target/nextflow/workflows/post_processing" executable: "target/nextflow/workflows/post_processing/main.nf" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/picard_markduplicates" - "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort" diff --git a/target/nextflow/workflows/post_processing/main.nf b/target/nextflow/workflows/post_processing/main.nf index b1184b4..8807215 100644 --- a/target/nextflow/workflows/post_processing/main.nf +++ b/target/nextflow/workflows/post_processing/main.nf @@ -3397,8 +3397,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/post_processing", "viash_version" : "0.9.0", - "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", - "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + "git_commit" : "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814", + "git_remote" : "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/workflows/pre_processing/.config.vsh.yaml b/target/nextflow/workflows/pre_processing/.config.vsh.yaml index cead340..1f61d2a 100644 --- a/target/nextflow/workflows/pre_processing/.config.vsh.yaml +++ b/target/nextflow/workflows/pre_processing/.config.vsh.yaml @@ -673,8 +673,8 @@ build_info: output: "target/nextflow/workflows/pre_processing" executable: "target/nextflow/workflows/pre_processing/main.nf" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/fastqc" - "target/nextflow/umitools/umitools_extract" diff --git a/target/nextflow/workflows/pre_processing/main.nf b/target/nextflow/workflows/pre_processing/main.nf index 766f3d4..394e71c 100644 --- a/target/nextflow/workflows/pre_processing/main.nf +++ b/target/nextflow/workflows/pre_processing/main.nf @@ -3626,8 +3626,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/pre_processing", "viash_version" : "0.9.0", - "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", - "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + "git_commit" : "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814", + "git_remote" : "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/workflows/prepare_genome/.config.vsh.yaml b/target/nextflow/workflows/prepare_genome/.config.vsh.yaml index 72a9354..e944e16 100644 --- a/target/nextflow/workflows/prepare_genome/.config.vsh.yaml +++ b/target/nextflow/workflows/prepare_genome/.config.vsh.yaml @@ -221,6 +221,11 @@ argument_groups: direction: "input" multiple: false multiple_sep: ";" + - type: "boolean_true" + name: "--skip_alignment" + description: "Skip all of the alignment-based processes within the pipeline." + info: null + direction: "input" - name: "Output" arguments: - type: "file" @@ -496,8 +501,8 @@ build_info: output: "target/nextflow/workflows/prepare_genome" executable: "target/nextflow/workflows/prepare_genome/main.nf" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/gunzip" - "target/dependencies/vsh/vsh/biobox/main/nextflow/gffread" diff --git a/target/nextflow/workflows/prepare_genome/main.nf b/target/nextflow/workflows/prepare_genome/main.nf index e40a4ff..ad3cba6 100644 --- a/target/nextflow/workflows/prepare_genome/main.nf +++ b/target/nextflow/workflows/prepare_genome/main.nf @@ -3043,6 +3043,12 @@ meta = [ "direction" : "input", "multiple" : false, "multiple_sep" : ";" + }, + { + "type" : "boolean_true", + "name" : "--skip_alignment", + "description" : "Skip all of the alignment-based processes within the pipeline.", + "direction" : "input" } ] }, @@ -3407,8 +3413,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/prepare_genome", "viash_version" : "0.9.0", - "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", - "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + "git_commit" : "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814", + "git_remote" : "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", @@ -3654,7 +3660,7 @@ workflow run_wf { // TODO: Add to viah-hub or adapt star_align_reads to enable the generateGenome runMode | star_genome_generate.run ( - runIf: {id, state -> !state.star_index}, + runIf: {id, state -> !state.star_index && !state.skip_alignment}, fromState: [ "genome_fasta_files": "fasta", "sjdb_gtf_file": "gtf" diff --git a/target/nextflow/workflows/prepare_genome/nextflow_schema.json b/target/nextflow/workflows/prepare_genome/nextflow_schema.json index 97fadef..e56ab59 100644 --- a/target/nextflow/workflows/prepare_genome/nextflow_schema.json +++ b/target/nextflow/workflows/prepare_genome/nextflow_schema.json @@ -230,6 +230,17 @@ } + , + "skip_alignment": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Skip all of the alignment-based processes within the pipeline", + "help_text": "Type: `boolean_true`, default: `false`. Skip all of the alignment-based processes within the pipeline." + , + "default": "False" + } + + } }, diff --git a/target/nextflow/workflows/pseudo_alignment_and_quant/.config.vsh.yaml b/target/nextflow/workflows/pseudo_alignment_and_quant/.config.vsh.yaml index 75517a4..bc3ae70 100644 --- a/target/nextflow/workflows/pseudo_alignment_and_quant/.config.vsh.yaml +++ b/target/nextflow/workflows/pseudo_alignment_and_quant/.config.vsh.yaml @@ -283,8 +283,8 @@ build_info: output: "target/nextflow/workflows/pseudo_alignment_and_quant" executable: "target/nextflow/workflows/pseudo_alignment_and_quant/main.nf" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" dependencies: - "target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant" - "target/nextflow/kallisto/kallisto_quant" diff --git a/target/nextflow/workflows/pseudo_alignment_and_quant/main.nf b/target/nextflow/workflows/pseudo_alignment_and_quant/main.nf index 53de4aa..fb39d48 100644 --- a/target/nextflow/workflows/pseudo_alignment_and_quant/main.nf +++ b/target/nextflow/workflows/pseudo_alignment_and_quant/main.nf @@ -3143,8 +3143,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/pseudo_alignment_and_quant", "viash_version" : "0.9.0", - "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", - "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + "git_commit" : "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814", + "git_remote" : "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/workflows/quality_control/.config.vsh.yaml b/target/nextflow/workflows/quality_control/.config.vsh.yaml index 9c586d2..16efd8d 100644 --- a/target/nextflow/workflows/quality_control/.config.vsh.yaml +++ b/target/nextflow/workflows/quality_control/.config.vsh.yaml @@ -1572,8 +1572,8 @@ build_info: output: "target/nextflow/workflows/quality_control" executable: "target/nextflow/workflows/quality_control/main.nf" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/rseqc/rseqc_bamstat" - "target/nextflow/rseqc/rseqc_inferexperiment" diff --git a/target/nextflow/workflows/quality_control/main.nf b/target/nextflow/workflows/quality_control/main.nf index 8ad591b..536e944 100644 --- a/target/nextflow/workflows/quality_control/main.nf +++ b/target/nextflow/workflows/quality_control/main.nf @@ -4648,8 +4648,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/quality_control", "viash_version" : "0.9.0", - "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", - "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + "git_commit" : "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814", + "git_remote" : "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/workflows/rnaseq/.config.vsh.yaml b/target/nextflow/workflows/rnaseq/.config.vsh.yaml index 1d2db70..991477a 100644 --- a/target/nextflow/workflows/rnaseq/.config.vsh.yaml +++ b/target/nextflow/workflows/rnaseq/.config.vsh.yaml @@ -2082,8 +2082,8 @@ build_info: output: "target/nextflow/workflows/rnaseq" executable: "target/nextflow/workflows/rnaseq/main.nf" viash_version: "0.9.0" - git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" - git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814" + git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/workflows/prepare_genome" - "target/nextflow/cat_fastq" diff --git a/target/nextflow/workflows/rnaseq/main.nf b/target/nextflow/workflows/rnaseq/main.nf index 62caa0a..51b4f6a 100644 --- a/target/nextflow/workflows/rnaseq/main.nf +++ b/target/nextflow/workflows/rnaseq/main.nf @@ -5242,8 +5242,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/rnaseq", "viash_version" : "0.9.0", - "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", - "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" + "git_commit" : "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814", + "git_remote" : "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", @@ -5367,7 +5367,8 @@ workflow run_wf { "biotype": "biotype", "filter_gtf": "filter_gtf", "aligner": "aligner", - "pseudo_aligner": "pseudo_aligner" + "pseudo_aligner": "pseudo_aligner", + "skip_alignment": "skip_alignment" ], toState: [ "fasta": "uncompressed_fasta",