From bc17b94cd5e09b61a5b9ced1d30de0e37f883faa Mon Sep 17 00:00:00 2001 From: CI Date: Wed, 13 Nov 2024 10:26:31 +0000 Subject: [PATCH] Build branch main with version main (5fbd530) Build pipeline: viash-hub.rnaseq.main-rfpzb Source commit: https://github.com/viash-hub/rnaseq/commit/5fbd530a7cf631bcc2930747d4712993ee19f07a Source message: add arguments to skip qc components --- src/deseq2_qc/config.vsh.yaml | 3 +- src/workflows/quality_control/config.vsh.yaml | 9 ++ src/workflows/quality_control/main.nf | 34 +++--- src/workflows/rnaseq/config.vsh.yaml | 9 +- src/workflows/rnaseq/main.nf | 7 +- .../main/nextflow/fastp/.config.vsh.yaml | 6 +- .../vsh/biobox/main/nextflow/fastp/main.nf | 6 +- .../nextflow/featurecounts/.config.vsh.yaml | 6 +- .../main/nextflow/featurecounts/main.nf | 6 +- .../main/nextflow/gffread/.config.vsh.yaml | 6 +- .../vsh/biobox/main/nextflow/gffread/main.nf | 6 +- .../main/nextflow/multiqc/.config.vsh.yaml | 6 +- .../vsh/biobox/main/nextflow/multiqc/main.nf | 6 +- .../rsem_prepare_reference/.config.vsh.yaml | 6 +- .../rsem/rsem_prepare_reference/main.nf | 6 +- .../salmon/salmon_index/.config.vsh.yaml | 6 +- .../main/nextflow/salmon/salmon_index/main.nf | 6 +- .../salmon/salmon_quant/.config.vsh.yaml | 6 +- .../main/nextflow/salmon/salmon_quant/main.nf | 6 +- .../samtools_flagstat/.config.vsh.yaml | 6 +- .../samtools/samtools_flagstat/main.nf | 6 +- .../samtools_idxstats/.config.vsh.yaml | 6 +- .../samtools/samtools_idxstats/main.nf | 6 +- .../samtools/samtools_index/.config.vsh.yaml | 6 +- .../nextflow/samtools/samtools_index/main.nf | 6 +- .../samtools/samtools_sort/.config.vsh.yaml | 6 +- .../nextflow/samtools/samtools_sort/main.nf | 6 +- .../samtools/samtools_stats/.config.vsh.yaml | 6 +- .../nextflow/samtools/samtools_stats/main.nf | 6 +- .../star/star_align_reads/.config.vsh.yaml | 6 +- .../nextflow/star/star_align_reads/main.nf | 6 +- .../star_genome_generate/.config.vsh.yaml | 6 +- .../star/star_genome_generate/main.nf | 6 +- .../umi_tools_extract/.config.vsh.yaml | 23 +--- .../umi_tools/umi_tools_extract/main.nf | 36 +------ .../umi_tools_extract/nextflow_schema.json | 12 --- .../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 | 7 +- target/executable/deseq2_qc/deseq2_qc | 9 +- 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 | 4 +- .../.config.vsh.yaml | 4 +- .../quality_control/.config.vsh.yaml | 20 +++- .../workflows/quality_control/quality_control | 102 +++++++++++++++--- .../workflows/rnaseq/.config.vsh.yaml | 15 ++- target/executable/workflows/rnaseq/rnaseq | 66 ++++++++---- .../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 | 7 +- target/nextflow/deseq2_qc/main.nf | 10 +- 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 | 4 +- .../nextflow/workflows/prepare_genome/main.nf | 4 +- .../.config.vsh.yaml | 4 +- .../pseudo_alignment_and_quant/main.nf | 4 +- .../quality_control/.config.vsh.yaml | 20 +++- .../workflows/quality_control/main.nf | 58 +++++++--- .../quality_control/nextflow_schema.json | 44 ++++++++ .../workflows/rnaseq/.config.vsh.yaml | 15 ++- target/nextflow/workflows/rnaseq/main.nf | 27 +++-- .../workflows/rnaseq/nextflow_schema.json | 11 ++ 228 files changed, 846 insertions(+), 656 deletions(-) diff --git a/src/deseq2_qc/config.vsh.yaml b/src/deseq2_qc/config.vsh.yaml index 807781d..56b557d 100644 --- a/src/deseq2_qc/config.vsh.yaml +++ b/src/deseq2_qc/config.vsh.yaml @@ -71,9 +71,8 @@ engines: image: rocker/r2u:22.04 setup: - type: r - cran: [ optparse, ggplot2, RColorBrewer, pheatmap, stringr ] + cran: [ optparse, ggplot2, RColorBrewer, pheatmap, stringr, matrixStats ] bioc: [ DESeq2 ] - url: https://cran.r-project.org/src/contrib/Archive/matrixStats/matrixStats_1.1.0.tar.gz runners: - type: executable - type: nextflow diff --git a/src/workflows/quality_control/config.vsh.yaml b/src/workflows/quality_control/config.vsh.yaml index 7cc65e4..c57a781 100644 --- a/src/workflows/quality_control/config.vsh.yaml +++ b/src/workflows/quality_control/config.vsh.yaml @@ -77,6 +77,15 @@ argument_groups: default: false - name: "--skip_pseudo_align" type: boolean + - name: "--skip_dupradar" + type: boolean_true + - name: "--skip_qualimap" + type: boolean_true + - name: "--skip_rseqc" + type: boolean_true + - name: "--skip_multiqc" + type: boolean_true + # Component specific options # preseq diff --git a/src/workflows/quality_control/main.nf b/src/workflows/quality_control/main.nf index 54908f3..35ba2e9 100644 --- a/src/workflows/quality_control/main.nf +++ b/src/workflows/quality_control/main.nf @@ -16,7 +16,7 @@ workflow run_wf { } | featurecounts.run ( - runIf: { id, state -> !state.skip_qc && !state.skip_biotype_qc && state.biotype && state.biotype_in_gtf }, + runIf: { id, state -> !state.skip_qc && !state.skip_biotype_qc && state.biotype && state.biotype_in_gtf && !state.skip_align }, fromState: [ "paired": "paired", "strand": "strand", @@ -37,7 +37,7 @@ workflow run_wf { ) | multiqc_custom_biotype.run ( - runIf: { id, state -> !state.skip_qc && !state.skip_biotype_qc && state.biotype && state.featurecounts }, + runIf: { id, state -> !state.skip_qc && !state.skip_biotype_qc && state.biotype && state.featurecounts && !state.skip_align }, fromState: [ "id": "id", "biocounts": "featurecounts", @@ -50,7 +50,7 @@ workflow run_wf { ) | preseq_lcextrap.run ( - runIf: { id, state -> !state.skip_qc && !state.skip_preseq }, + runIf: { id, state -> !state.skip_qc && !state.skip_preseq && !state.skip_align }, fromState: [ "paired": "paired", "input": "genome_bam", @@ -60,7 +60,7 @@ workflow run_wf { ) | rseqc_bamstat.run ( - runIf: { id, state -> "bam_stat" in state.rseqc_modules }, + runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "bam_stat" in state.rseqc_modules && !state.skip_align }, fromState: [ "input": "genome_bam", "map_qual": "map_qual" @@ -68,7 +68,7 @@ workflow run_wf { toState: [ "bamstat_output": "output" ] ) | rseqc_inferexperiment.run( - runIf: { id, state -> "infer_experiment" in state.rseqc_modules }, + runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "infer_experiment" in state.rseqc_modules && !state.skip_align }, fromState: [ "input": "genome_bam", "refgene": "gene_bed", @@ -84,7 +84,7 @@ workflow run_wf { [ id, state + [ inferred_strand: inferred_strand, passed_strand_check: passed_strand_check ] ] } | rseqc_innerdistance.run( - runIf: { id, state -> state.paired && "inner_distance" in state.rseqc_modules }, + runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && state.paired && "inner_distance" in state.rseqc_modules && !state.skip_align }, key: "inner_distance", fromState: [ "input": "genome_bam", @@ -104,7 +104,7 @@ workflow run_wf { ] ) | rseqc_junctionannotation.run( - runIf: { id, state -> "junction_annotation" in state.rseqc_modules }, + runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "junction_annotation" in state.rseqc_modules && !state.skip_align }, fromState: [ "input": "genome_bam", "refgene": "gene_bed", @@ -122,7 +122,7 @@ workflow run_wf { ] ) | rseqc_junctionsaturation.run( - runIf: { id, state -> "junction_saturation" in state.rseqc_modules }, + runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "junction_saturation" in state.rseqc_modules && !state.skip_align }, fromState: [ "input": "genome_bam", "refgene": "gene_bed", @@ -139,7 +139,7 @@ workflow run_wf { ] ) | rseqc_readdistribution.run( - runIf: { id, state -> "read_distribution" in state.rseqc_modules }, + runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "read_distribution" in state.rseqc_modules && !state.skip_align }, fromState: [ "input": "genome_bam", "refgene": "gene_bed", @@ -147,7 +147,7 @@ workflow run_wf { toState: [ "read_distribution_output": "output" ] ) | rseqc_readduplication.run( - runIf: { id, state -> "read_duplication" in state.rseqc_modules }, + runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "read_duplication" in state.rseqc_modules && !state.skip_align }, fromState: [ "input": "genome_bam", "read_count_upper_limit": "read_count_upper_limit", @@ -161,7 +161,7 @@ workflow run_wf { ] ) | rseqc_tin.run( - runIf: { id, state -> "tin" in state.rseqc_modules }, + runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "tin" in state.rseqc_modules && !state.skip_align }, fromState: [ "bam_input": "genome_bam", "bai_input": "genome_bam_index", @@ -177,6 +177,7 @@ workflow run_wf { ) | dupradar.run( + runIf: { id, state -> !state.skip_qc && !state.skip_dupradar && !state.skip_align }, fromState: [ "id": "id", "input": "genome_bam", @@ -196,6 +197,7 @@ workflow run_wf { ) | qualimap.run( + runIf: { id, state -> !state.skip_qc && !state.skip_qualimap && !state.skip_align }, fromState: [ "input": "genome_bam", "gtf": "gtf", @@ -216,7 +218,7 @@ workflow run_wf { | toSortedList | map { list -> - def ids = list.collect { id, state -> state.id } + def ids = list.collect { id, state -> id } def strandedness = list.collect { id, state -> state.strandedness } def num_trimmed_reads = list.collect { id, state -> state.num_trimmed_reads } def passed_trimmed_reads = list.collect { id, state -> state.passed_trimmed_reads } @@ -522,7 +524,7 @@ workflow run_wf { | deseq2_qc.run ( runIf: { id, state -> !state.skip_qc && !state.skip_deseq2_qc && !state.skip_pseudo_align }, fromState: [ - "counts": "counts", + "counts": "pseudo_counts_gene_length_scaled", "vst": "deseq2_vst", "label": "pseudo_aligner" ], @@ -534,7 +536,7 @@ workflow run_wf { ], key: "deseq2_qc_pseuso_align_quant" ) - + | niceView() // Get list of samples that failed trimming, mapping, and strand check for MultiQC report | map { id, state -> def fail_trimming_header = ["Sample", "Reads after trimming"] @@ -557,7 +559,7 @@ workflow run_wf { fail_mapping_multiqc += tsv_data.join('\n') } if (!state.passed_strand_check[i]) { - tsv_data = ([ids[i], state.strandedness[i]] + state.inferred_strand[i]).join('\t') + tsv_data = ([state.ids[i], state.strandedness[i]] + state.inferred_strand[i]).join('\t') fail_strand_multiqc += tsv_data.join('\n') } } @@ -577,6 +579,7 @@ workflow run_wf { } | prepare_multiqc_input.run( + runIf: { id, state -> !state.skip_qc && !state.skip_multiqc }, fromState: [ "fail_trimming_multiqc": "fail_trimming_multiqc", "fail_mapping_multiqc": "fail_mapping_multiqc", @@ -617,6 +620,7 @@ workflow run_wf { ) | multiqc.run ( + runIf: { id, state -> !state.skip_qc && !state.skip_multiqc }, fromState: [ "title": "multiqc_title", "input": "multiqc_input", diff --git a/src/workflows/rnaseq/config.vsh.yaml b/src/workflows/rnaseq/config.vsh.yaml index c6af61b..664bbe5 100644 --- a/src/workflows/rnaseq/config.vsh.yaml +++ b/src/workflows/rnaseq/config.vsh.yaml @@ -276,13 +276,16 @@ argument_groups: - name: "--skip_deseq2_qc" type: boolean_true description: Skip DESeq2 PCA and heatmap plotting. - - name: skip_dupradar + - name: --skip_dupradar type: boolean_true description: Skip dupRadar. - - name: skip_rseqc + - name: --skip_qualimap + type: boolean_true + description: Skip Qualimap. + - name: --skip_rseqc type: boolean_true description: Skip RSeQC. - - name: skip_multiqc + - name: --skip_multiqc type: boolean_true description: Skip MultiQC. diff --git a/src/workflows/rnaseq/main.nf b/src/workflows/rnaseq/main.nf index dc3f42a..70f1530 100644 --- a/src/workflows/rnaseq/main.nf +++ b/src/workflows/rnaseq/main.nf @@ -241,7 +241,7 @@ workflow run_wf { // Filter channels to get samples that passed STAR minimum mapping percentage | map { id, state -> - def percent_mapped = getStarPercentMapped(state.star_multiqc) + def percent_mapped = (!state.skip_alignment) ? getStarPercentMapped(state.star_multiqc) : 0.0 def passed_mapping = (percent_mapped >= state.min_mapped_reads) ? true : false [ id, state + [percent_mapped: percent_mapped, passed_mapping: passed_mapping] ] } @@ -336,6 +336,11 @@ workflow run_wf { "strandedness": "strandedness", "skip_align": "skip_alignment", "skip_pseudo_align": "skip_pseudo_alignment", + "skip_dupradar": "skip_dupradar", + "skip_qualimap": "skip_qualimap", + "skip_rseqc": "skip_rseqc", + "skip_multiqc": "skip_multiqc", + "skip_preseq": "skip_preseq", "gtf": "gtf", "num_trimmed_reads": "num_trimmed_reads", "passed_trimmed_reads": "passed_trimmed_reads", diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/fastp/.config.vsh.yaml b/target/dependencies/vsh/vsh/biobox/main/nextflow/fastp/.config.vsh.yaml index 7c4cda3..dc59589 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/fastp/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/fastp/.config.vsh.yaml @@ -1083,9 +1083,9 @@ build_info: output: "target/nextflow/fastp" executable: "target/nextflow/fastp/main.nf" viash_version: "0.9.0" - git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7" - git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox" - git_tag: "v0.2.0-11-g7fb67a9" + git_commit: "1d17ce01e25569c8e898b8160af1480ad22fc986" + git_remote: "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox" + git_tag: "v0.2.0-24-g1d17ce0" package_config: name: "biobox" version: "main" diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/fastp/main.nf b/target/dependencies/vsh/vsh/biobox/main/nextflow/fastp/main.nf index b50efec..92e05da 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/fastp/main.nf +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/fastp/main.nf @@ -4023,9 +4023,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/fastp", "viash_version" : "0.9.0", - "git_commit" : "7fb67a98539868b9af788338fb5f46d34ab742f7", - "git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-11-g7fb67a9" + "git_commit" : "1d17ce01e25569c8e898b8160af1480ad22fc986", + "git_remote" : "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-24-g1d17ce0" }, "package_config" : { "name" : "biobox", diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/featurecounts/.config.vsh.yaml b/target/dependencies/vsh/vsh/biobox/main/nextflow/featurecounts/.config.vsh.yaml index a542225..f76f3c4 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/featurecounts/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/featurecounts/.config.vsh.yaml @@ -645,9 +645,9 @@ build_info: output: "target/nextflow/featurecounts" executable: "target/nextflow/featurecounts/main.nf" viash_version: "0.9.0" - git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7" - git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox" - git_tag: "v0.2.0-11-g7fb67a9" + git_commit: "1d17ce01e25569c8e898b8160af1480ad22fc986" + git_remote: "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox" + git_tag: "v0.2.0-24-g1d17ce0" package_config: name: "biobox" version: "main" diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/featurecounts/main.nf b/target/dependencies/vsh/vsh/biobox/main/nextflow/featurecounts/main.nf index 667c27d..0850e9b 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/featurecounts/main.nf +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/featurecounts/main.nf @@ -3549,9 +3549,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/featurecounts", "viash_version" : "0.9.0", - "git_commit" : "7fb67a98539868b9af788338fb5f46d34ab742f7", - "git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-11-g7fb67a9" + "git_commit" : "1d17ce01e25569c8e898b8160af1480ad22fc986", + "git_remote" : "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-24-g1d17ce0" }, "package_config" : { "name" : "biobox", diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/gffread/.config.vsh.yaml b/target/dependencies/vsh/vsh/biobox/main/nextflow/gffread/.config.vsh.yaml index aa08967..1885da2 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/gffread/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/gffread/.config.vsh.yaml @@ -685,9 +685,9 @@ build_info: output: "target/nextflow/gffread" executable: "target/nextflow/gffread/main.nf" viash_version: "0.9.0" - git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7" - git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox" - git_tag: "v0.2.0-11-g7fb67a9" + git_commit: "1d17ce01e25569c8e898b8160af1480ad22fc986" + git_remote: "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox" + git_tag: "v0.2.0-24-g1d17ce0" package_config: name: "biobox" version: "main" diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/gffread/main.nf b/target/dependencies/vsh/vsh/biobox/main/nextflow/gffread/main.nf index 739241d..29cd13a 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/gffread/main.nf +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/gffread/main.nf @@ -3606,9 +3606,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/gffread", "viash_version" : "0.9.0", - "git_commit" : "7fb67a98539868b9af788338fb5f46d34ab742f7", - "git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-11-g7fb67a9" + "git_commit" : "1d17ce01e25569c8e898b8160af1480ad22fc986", + "git_remote" : "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-24-g1d17ce0" }, "package_config" : { "name" : "biobox", diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/multiqc/.config.vsh.yaml b/target/dependencies/vsh/vsh/biobox/main/nextflow/multiqc/.config.vsh.yaml index 0ec1371..beccf81 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/multiqc/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/multiqc/.config.vsh.yaml @@ -456,9 +456,9 @@ build_info: output: "target/nextflow/multiqc" executable: "target/nextflow/multiqc/main.nf" viash_version: "0.9.0" - git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7" - git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox" - git_tag: "v0.2.0-11-g7fb67a9" + git_commit: "1d17ce01e25569c8e898b8160af1480ad22fc986" + git_remote: "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox" + git_tag: "v0.2.0-24-g1d17ce0" package_config: name: "biobox" version: "main" diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/multiqc/main.nf b/target/dependencies/vsh/vsh/biobox/main/nextflow/multiqc/main.nf index 49798d2..e55ed7d 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/multiqc/main.nf +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/multiqc/main.nf @@ -3366,9 +3366,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/multiqc", "viash_version" : "0.9.0", - "git_commit" : "7fb67a98539868b9af788338fb5f46d34ab742f7", - "git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-11-g7fb67a9" + "git_commit" : "1d17ce01e25569c8e898b8160af1480ad22fc986", + "git_remote" : "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-24-g1d17ce0" }, "package_config" : { "name" : "biobox", diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml b/target/dependencies/vsh/vsh/biobox/main/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml index 69add8a..12a63ad 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml @@ -416,9 +416,9 @@ build_info: output: "target/nextflow/rsem/rsem_prepare_reference" executable: "target/nextflow/rsem/rsem_prepare_reference/main.nf" viash_version: "0.9.0" - git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7" - git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox" - git_tag: "v0.2.0-11-g7fb67a9" + git_commit: "1d17ce01e25569c8e898b8160af1480ad22fc986" + git_remote: "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox" + git_tag: "v0.2.0-24-g1d17ce0" package_config: name: "biobox" version: "main" diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/rsem/rsem_prepare_reference/main.nf b/target/dependencies/vsh/vsh/biobox/main/nextflow/rsem/rsem_prepare_reference/main.nf index 6ff7f8e..d953e17 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/rsem/rsem_prepare_reference/main.nf +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/rsem/rsem_prepare_reference/main.nf @@ -3245,9 +3245,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/rsem/rsem_prepare_reference", "viash_version" : "0.9.0", - "git_commit" : "7fb67a98539868b9af788338fb5f46d34ab742f7", - "git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-11-g7fb67a9" + "git_commit" : "1d17ce01e25569c8e898b8160af1480ad22fc986", + "git_remote" : "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-24-g1d17ce0" }, "package_config" : { "name" : "biobox", diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_index/.config.vsh.yaml b/target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_index/.config.vsh.yaml index d1ae754..f54b5d5 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_index/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_index/.config.vsh.yaml @@ -277,9 +277,9 @@ build_info: output: "target/nextflow/salmon/salmon_index" executable: "target/nextflow/salmon/salmon_index/main.nf" viash_version: "0.9.0" - git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7" - git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox" - git_tag: "v0.2.0-11-g7fb67a9" + git_commit: "1d17ce01e25569c8e898b8160af1480ad22fc986" + git_remote: "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox" + git_tag: "v0.2.0-24-g1d17ce0" package_config: name: "biobox" version: "main" diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_index/main.nf b/target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_index/main.nf index c7ba9c9..6467e13 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_index/main.nf +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_index/main.nf @@ -3129,9 +3129,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/salmon/salmon_index", "viash_version" : "0.9.0", - "git_commit" : "7fb67a98539868b9af788338fb5f46d34ab742f7", - "git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-11-g7fb67a9" + "git_commit" : "1d17ce01e25569c8e898b8160af1480ad22fc986", + "git_remote" : "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-24-g1d17ce0" }, "package_config" : { "name" : "biobox", diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant/.config.vsh.yaml b/target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant/.config.vsh.yaml index 3058d9d..7607eb8 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant/.config.vsh.yaml @@ -1173,9 +1173,9 @@ build_info: output: "target/nextflow/salmon/salmon_quant" executable: "target/nextflow/salmon/salmon_quant/main.nf" viash_version: "0.9.0" - git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7" - git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox" - git_tag: "v0.2.0-11-g7fb67a9" + git_commit: "1d17ce01e25569c8e898b8160af1480ad22fc986" + git_remote: "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox" + git_tag: "v0.2.0-24-g1d17ce0" package_config: name: "biobox" version: "main" diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant/main.nf b/target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant/main.nf index a477022..0d5c49f 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant/main.nf +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant/main.nf @@ -3964,9 +3964,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/salmon/salmon_quant", "viash_version" : "0.9.0", - "git_commit" : "7fb67a98539868b9af788338fb5f46d34ab742f7", - "git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-11-g7fb67a9" + "git_commit" : "1d17ce01e25569c8e898b8160af1480ad22fc986", + "git_remote" : "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-24-g1d17ce0" }, "package_config" : { "name" : "biobox", diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_flagstat/.config.vsh.yaml b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_flagstat/.config.vsh.yaml index 0bd3ec4..293585f 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_flagstat/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_flagstat/.config.vsh.yaml @@ -173,9 +173,9 @@ build_info: output: "target/nextflow/samtools/samtools_flagstat" executable: "target/nextflow/samtools/samtools_flagstat/main.nf" viash_version: "0.9.0" - git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7" - git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox" - git_tag: "v0.2.0-11-g7fb67a9" + git_commit: "1d17ce01e25569c8e898b8160af1480ad22fc986" + git_remote: "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox" + git_tag: "v0.2.0-24-g1d17ce0" package_config: name: "biobox" version: "main" diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_flagstat/main.nf b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_flagstat/main.nf index a16f5f5..c7f53c0 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_flagstat/main.nf +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_flagstat/main.nf @@ -3028,9 +3028,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_flagstat", "viash_version" : "0.9.0", - "git_commit" : "7fb67a98539868b9af788338fb5f46d34ab742f7", - "git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-11-g7fb67a9" + "git_commit" : "1d17ce01e25569c8e898b8160af1480ad22fc986", + "git_remote" : "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-24-g1d17ce0" }, "package_config" : { "name" : "biobox", diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_idxstats/.config.vsh.yaml b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_idxstats/.config.vsh.yaml index ea9b52f..c342835 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_idxstats/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_idxstats/.config.vsh.yaml @@ -183,9 +183,9 @@ build_info: output: "target/nextflow/samtools/samtools_idxstats" executable: "target/nextflow/samtools/samtools_idxstats/main.nf" viash_version: "0.9.0" - git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7" - git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox" - git_tag: "v0.2.0-11-g7fb67a9" + git_commit: "1d17ce01e25569c8e898b8160af1480ad22fc986" + git_remote: "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox" + git_tag: "v0.2.0-24-g1d17ce0" package_config: name: "biobox" version: "main" diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_idxstats/main.nf b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_idxstats/main.nf index 7d4ff1d..faddb41 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_idxstats/main.nf +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_idxstats/main.nf @@ -3040,9 +3040,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_idxstats", "viash_version" : "0.9.0", - "git_commit" : "7fb67a98539868b9af788338fb5f46d34ab742f7", - "git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-11-g7fb67a9" + "git_commit" : "1d17ce01e25569c8e898b8160af1480ad22fc986", + "git_remote" : "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-24-g1d17ce0" }, "package_config" : { "name" : "biobox", diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_index/.config.vsh.yaml b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_index/.config.vsh.yaml index 3595201..94d7b6f 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_index/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_index/.config.vsh.yaml @@ -189,9 +189,9 @@ build_info: output: "target/nextflow/samtools/samtools_index" executable: "target/nextflow/samtools/samtools_index/main.nf" viash_version: "0.9.0" - git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7" - git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox" - git_tag: "v0.2.0-11-g7fb67a9" + git_commit: "1d17ce01e25569c8e898b8160af1480ad22fc986" + git_remote: "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox" + git_tag: "v0.2.0-24-g1d17ce0" package_config: name: "biobox" version: "main" diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_index/main.nf b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_index/main.nf index 9a1210d..39aefa3 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_index/main.nf +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_index/main.nf @@ -3053,9 +3053,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_index", "viash_version" : "0.9.0", - "git_commit" : "7fb67a98539868b9af788338fb5f46d34ab742f7", - "git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-11-g7fb67a9" + "git_commit" : "1d17ce01e25569c8e898b8160af1480ad22fc986", + "git_remote" : "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-24-g1d17ce0" }, "package_config" : { "name" : "biobox", diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort/.config.vsh.yaml b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort/.config.vsh.yaml index 2c6bfe2..a232b07 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort/.config.vsh.yaml @@ -332,9 +332,9 @@ build_info: output: "target/nextflow/samtools/samtools_sort" executable: "target/nextflow/samtools/samtools_sort/main.nf" viash_version: "0.9.0" - git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7" - git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox" - git_tag: "v0.2.0-11-g7fb67a9" + git_commit: "1d17ce01e25569c8e898b8160af1480ad22fc986" + git_remote: "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox" + git_tag: "v0.2.0-24-g1d17ce0" package_config: name: "biobox" version: "main" diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort/main.nf b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort/main.nf index 5355dd3..13fbc6f 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort/main.nf +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort/main.nf @@ -3225,9 +3225,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_sort", "viash_version" : "0.9.0", - "git_commit" : "7fb67a98539868b9af788338fb5f46d34ab742f7", - "git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-11-g7fb67a9" + "git_commit" : "1d17ce01e25569c8e898b8160af1480ad22fc986", + "git_remote" : "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-24-g1d17ce0" }, "package_config" : { "name" : "biobox", diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_stats/.config.vsh.yaml b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_stats/.config.vsh.yaml index 43ff922..5b67ca2 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_stats/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_stats/.config.vsh.yaml @@ -401,9 +401,9 @@ build_info: output: "target/nextflow/samtools/samtools_stats" executable: "target/nextflow/samtools/samtools_stats/main.nf" viash_version: "0.9.0" - git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7" - git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox" - git_tag: "v0.2.0-11-g7fb67a9" + git_commit: "1d17ce01e25569c8e898b8160af1480ad22fc986" + git_remote: "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox" + git_tag: "v0.2.0-24-g1d17ce0" package_config: name: "biobox" version: "main" diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_stats/main.nf b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_stats/main.nf index b8fa106..093dc9d 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_stats/main.nf +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_stats/main.nf @@ -3295,9 +3295,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_stats", "viash_version" : "0.9.0", - "git_commit" : "7fb67a98539868b9af788338fb5f46d34ab742f7", - "git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-11-g7fb67a9" + "git_commit" : "1d17ce01e25569c8e898b8160af1480ad22fc986", + "git_remote" : "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-24-g1d17ce0" }, "package_config" : { "name" : "biobox", diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_align_reads/.config.vsh.yaml b/target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_align_reads/.config.vsh.yaml index 5dac6c1..3ad5856 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_align_reads/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_align_reads/.config.vsh.yaml @@ -2663,9 +2663,9 @@ build_info: output: "target/nextflow/star/star_align_reads" executable: "target/nextflow/star/star_align_reads/main.nf" viash_version: "0.9.0" - git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7" - git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox" - git_tag: "v0.2.0-11-g7fb67a9" + git_commit: "1d17ce01e25569c8e898b8160af1480ad22fc986" + git_remote: "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox" + git_tag: "v0.2.0-24-g1d17ce0" package_config: name: "biobox" version: "main" diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_align_reads/main.nf b/target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_align_reads/main.nf index bfda8f2..fc36f07 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_align_reads/main.nf +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_align_reads/main.nf @@ -5943,9 +5943,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/star/star_align_reads", "viash_version" : "0.9.0", - "git_commit" : "7fb67a98539868b9af788338fb5f46d34ab742f7", - "git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-11-g7fb67a9" + "git_commit" : "1d17ce01e25569c8e898b8160af1480ad22fc986", + "git_remote" : "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-24-g1d17ce0" }, "package_config" : { "name" : "biobox", diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_genome_generate/.config.vsh.yaml b/target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_genome_generate/.config.vsh.yaml index 47b2520..0536e87 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_genome_generate/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_genome_generate/.config.vsh.yaml @@ -333,9 +333,9 @@ build_info: output: "target/nextflow/star/star_genome_generate" executable: "target/nextflow/star/star_genome_generate/main.nf" viash_version: "0.9.0" - git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7" - git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox" - git_tag: "v0.2.0-11-g7fb67a9" + git_commit: "1d17ce01e25569c8e898b8160af1480ad22fc986" + git_remote: "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox" + git_tag: "v0.2.0-24-g1d17ce0" package_config: name: "biobox" version: "main" diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_genome_generate/main.nf b/target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_genome_generate/main.nf index 07933cd..33cb90a 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_genome_generate/main.nf +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_genome_generate/main.nf @@ -3195,9 +3195,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/star/star_genome_generate", "viash_version" : "0.9.0", - "git_commit" : "7fb67a98539868b9af788338fb5f46d34ab742f7", - "git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-11-g7fb67a9" + "git_commit" : "1d17ce01e25569c8e898b8160af1480ad22fc986", + "git_remote" : "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-24-g1d17ce0" }, "package_config" : { "name" : "biobox", diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml b/target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml index 6b26b47..c04a85e 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml @@ -228,21 +228,6 @@ argument_groups: direction: "input" multiple: false multiple_sep: ";" - - type: "integer" - name: "--umi_discard_read" - description: "After UMI barcode extraction discard either R1 or R2 by setting\ - \ this parameter to 1 or 2, respectively. Default: `0`\n" - info: null - example: - - 0 - required: false - choices: - - 0 - - 1 - - 2 - direction: "input" - multiple: false - multiple_sep: ";" - name: "Common Options" arguments: - type: "file" @@ -259,7 +244,7 @@ argument_groups: name: "--log2stderr" description: "Send logging information to stderr." info: null - direction: "output" + direction: "input" - type: "integer" name: "--verbose" description: "Log level. The higher, the more output." @@ -449,9 +434,9 @@ build_info: output: "target/nextflow/umi_tools/umi_tools_extract" executable: "target/nextflow/umi_tools/umi_tools_extract/main.nf" viash_version: "0.9.0" - git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7" - git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox" - git_tag: "v0.2.0-11-g7fb67a9" + git_commit: "1d17ce01e25569c8e898b8160af1480ad22fc986" + git_remote: "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox" + git_tag: "v0.2.0-24-g1d17ce0" package_config: name: "biobox" version: "main" diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_extract/main.nf b/target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_extract/main.nf index 48f436f..52c67ff 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_extract/main.nf +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_extract/main.nf @@ -3050,23 +3050,6 @@ meta = [ "direction" : "input", "multiple" : false, "multiple_sep" : ";" - }, - { - "type" : "integer", - "name" : "--umi_discard_read", - "description" : "After UMI barcode extraction discard either R1 or R2 by setting this parameter to 1 or 2, respectively. Default: `0`\n", - "example" : [ - 0 - ], - "required" : false, - "choices" : [ - 0, - 1, - 2 - ], - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" } ] }, @@ -3088,7 +3071,7 @@ meta = [ "type" : "boolean_true", "name" : "--log2stderr", "description" : "Send logging information to stderr.", - "direction" : "output" + "direction" : "input" }, { "type" : "integer", @@ -3316,9 +3299,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/umi_tools/umi_tools_extract", "viash_version" : "0.9.0", - "git_commit" : "7fb67a98539868b9af788338fb5f46d34ab742f7", - "git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-11-g7fb67a9" + "git_commit" : "1d17ce01e25569c8e898b8160af1480ad22fc986", + "git_remote" : "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-24-g1d17ce0" }, "package_config" : { "name" : "biobox", @@ -3382,8 +3365,8 @@ $( if [ ! -z ${VIASH_PAR_THREE_PRIME+x} ]; then echo "${VIASH_PAR_THREE_PRIME}" $( if [ ! -z ${VIASH_PAR_IGNORE_READ_PAIR_SUFFIXES+x} ]; then echo "${VIASH_PAR_IGNORE_READ_PAIR_SUFFIXES}" | sed "s#'#'\\"'\\"'#g;s#.*#par_ignore_read_pair_suffixes='&'#" ; else echo "# par_ignore_read_pair_suffixes="; fi ) $( if [ ! -z ${VIASH_PAR_UMI_SEPARATOR+x} ]; then echo "${VIASH_PAR_UMI_SEPARATOR}" | sed "s#'#'\\"'\\"'#g;s#.*#par_umi_separator='&'#" ; else echo "# par_umi_separator="; fi ) $( if [ ! -z ${VIASH_PAR_GROUPING_METHOD+x} ]; then echo "${VIASH_PAR_GROUPING_METHOD}" | sed "s#'#'\\"'\\"'#g;s#.*#par_grouping_method='&'#" ; else echo "# par_grouping_method="; fi ) -$( if [ ! -z ${VIASH_PAR_UMI_DISCARD_READ+x} ]; then echo "${VIASH_PAR_UMI_DISCARD_READ}" | sed "s#'#'\\"'\\"'#g;s#.*#par_umi_discard_read='&'#" ; else echo "# par_umi_discard_read="; fi ) $( if [ ! -z ${VIASH_PAR_LOG+x} ]; then echo "${VIASH_PAR_LOG}" | sed "s#'#'\\"'\\"'#g;s#.*#par_log='&'#" ; else echo "# par_log="; fi ) +$( if [ ! -z ${VIASH_PAR_LOG2STDERR+x} ]; then echo "${VIASH_PAR_LOG2STDERR}" | sed "s#'#'\\"'\\"'#g;s#.*#par_log2stderr='&'#" ; else echo "# par_log2stderr="; fi ) $( if [ ! -z ${VIASH_PAR_VERBOSE+x} ]; then echo "${VIASH_PAR_VERBOSE}" | sed "s#'#'\\"'\\"'#g;s#.*#par_verbose='&'#" ; else echo "# par_verbose="; fi ) $( if [ ! -z ${VIASH_PAR_ERROR+x} ]; then echo "${VIASH_PAR_ERROR}" | sed "s#'#'\\"'\\"'#g;s#.*#par_error='&'#" ; else echo "# par_error="; fi ) $( if [ ! -z ${VIASH_PAR_TEMP_DIR+x} ]; then echo "${VIASH_PAR_TEMP_DIR}" | sed "s#'#'\\"'\\"'#g;s#.*#par_temp_dir='&'#" ; else echo "# par_temp_dir="; fi ) @@ -3492,15 +3475,6 @@ umi_tools extract \\\\ \\${par_log2stderr:+--log2stderr} \\\\ \\${par_verbose:+--verbose "\\$par_verbose"} \\\\ \\${par_error:+--error "\\$par_error"} - - -if [ "\\$par_umi_discard_read" == 1 ]; then - # discard read 1 - rm "\\$par_read1_out" -elif [ "\\$par_umi_discard_read" == 2 ]; then - # discard read 2 (-f to bypass file existence check) - rm -f "\\$par_read2_out" -fi VIASHMAIN bash "$tempscript" ''' diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_extract/nextflow_schema.json b/target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_extract/nextflow_schema.json index 438881f..aacd7d1 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_extract/nextflow_schema.json +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_extract/nextflow_schema.json @@ -255,18 +255,6 @@ } - , - "umi_discard_read": { - "type": - "integer", - "description": "Type: `integer`, example: `0`, choices: ``0`, `1`, `2``. After UMI barcode extraction discard either R1 or R2 by setting this parameter to 1 or 2, respectively", - "help_text": "Type: `integer`, example: `0`, choices: ``0`, `1`, `2``. After UMI barcode extraction discard either R1 or R2 by setting this parameter to 1 or 2, respectively. Default: `0`\n", - "enum": [0, 1, 2] - - - } - - } }, diff --git a/target/executable/bbmap_bbsplit/.config.vsh.yaml b/target/executable/bbmap_bbsplit/.config.vsh.yaml index ef355c9..cccec49 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 0f2f447..a2b8546 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="2024-10-25T08:58:48Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7" +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.version="main" VIASHDOCKER diff --git a/target/executable/bedtools_genomecov/.config.vsh.yaml b/target/executable/bedtools_genomecov/.config.vsh.yaml index 8001466..1edd1ff 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 c8d29b4..feefc19 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="2024-10-25T08:58:42Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7" +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.version="main" VIASHDOCKER diff --git a/target/executable/cat_additional_fasta/.config.vsh.yaml b/target/executable/cat_additional_fasta/.config.vsh.yaml index f3c68a9..1f40b9f 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 623e059..92988d0 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="2024-10-25T08:58:38Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7" +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.version="main" VIASHDOCKER diff --git a/target/executable/cat_fastq/.config.vsh.yaml b/target/executable/cat_fastq/.config.vsh.yaml index 2e3889d..b50aac0 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 569ef19..723c1de 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="2024-10-25T08:58:43Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7" +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.version="main" VIASHDOCKER diff --git a/target/executable/deseq2_qc/.config.vsh.yaml b/target/executable/deseq2_qc/.config.vsh.yaml index 43303d1..eff242a 100644 --- a/target/executable/deseq2_qc/.config.vsh.yaml +++ b/target/executable/deseq2_qc/.config.vsh.yaml @@ -222,10 +222,9 @@ engines: - "RColorBrewer" - "pheatmap" - "stringr" + - "matrixStats" bioc: - "DESeq2" - url: - - "https://cran.r-project.org/src/contrib/Archive/matrixStats/matrixStats_1.1.0.tar.gz" bioc_force_install: false entrypoint: [] cmd: null @@ -238,8 +237,8 @@ build_info: output: "target/executable/deseq2_qc" executable: "target/executable/deseq2_qc/deseq2_qc" viash_version: "0.9.0" - git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 ec5b27c..3f9fc59 100755 --- a/target/executable/deseq2_qc/deseq2_qc +++ b/target/executable/deseq2_qc/deseq2_qc @@ -503,13 +503,12 @@ ENTRYPOINT [] RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packages("remotes")' && \ Rscript -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")' && \ Rscript -e 'if (!requireNamespace("DESeq2", quietly = TRUE)) BiocManager::install("DESeq2")' && \ - Rscript -e 'remotes::install_cran(c("optparse", "ggplot2", "RColorBrewer", "pheatmap", "stringr"), repos = "https://cran.rstudio.com")' && \ - Rscript -e 'remotes::install_url(c("https://cran.r-project.org/src/contrib/Archive/matrixStats/matrixStats_1.1.0.tar.gz"), repos = "https://cran.rstudio.com")' + 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="2024-10-25T08:58:45Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7" +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.version="main" VIASHDOCKER diff --git a/target/executable/dupradar/.config.vsh.yaml b/target/executable/dupradar/.config.vsh.yaml index f3d74ec..295e298 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/dupradar/dupradar b/target/executable/dupradar/dupradar index 8bbcd49..4b7fc8f 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="2024-10-25T08:58:45Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7" +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.version="main" VIASHDOCKER diff --git a/target/executable/fastqc/.config.vsh.yaml b/target/executable/fastqc/.config.vsh.yaml index 0d73192..8f04ba9 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/fastqc/fastqc b/target/executable/fastqc/fastqc index 90eadff..989beb3 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="2024-10-25T08:58:41Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7" +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.version="main" VIASHDOCKER diff --git a/target/executable/fq_subsample/.config.vsh.yaml b/target/executable/fq_subsample/.config.vsh.yaml index 9c02921..1ce90c9 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 d825e4f..0b0eae0 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="2024-10-25T08:58:42Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7" +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.version="main" VIASHDOCKER diff --git a/target/executable/getchromsizes/.config.vsh.yaml b/target/executable/getchromsizes/.config.vsh.yaml index 811316c..c285b59 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/getchromsizes/getchromsizes b/target/executable/getchromsizes/getchromsizes index eb42d9c..43971e8 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="2024-10-25T08:58:40Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7" +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.version="main" VIASHDOCKER diff --git a/target/executable/gtf2bed/.config.vsh.yaml b/target/executable/gtf2bed/.config.vsh.yaml index b71a87d..7d58609 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/gtf2bed/gtf2bed b/target/executable/gtf2bed/gtf2bed index e89c6da..0fa76b1 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="2024-10-25T08:58:39Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7" +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.version="main" VIASHDOCKER diff --git a/target/executable/gtf_filter/.config.vsh.yaml b/target/executable/gtf_filter/.config.vsh.yaml index 6dd0990..7bc762e 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 7a3dd6b..ccc2b97 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="2024-10-25T08:58:45Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7" +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.version="main" VIASHDOCKER diff --git a/target/executable/gunzip/.config.vsh.yaml b/target/executable/gunzip/.config.vsh.yaml index d3e37de..f2796c7 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/gunzip/gunzip b/target/executable/gunzip/gunzip index 4fe63c6..0060c4d 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="2024-10-25T08:58:43Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7" +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.version="main" VIASHDOCKER diff --git a/target/executable/kallisto/kallisto_index/.config.vsh.yaml b/target/executable/kallisto/kallisto_index/.config.vsh.yaml index 801c013..734f249 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 5a1bbb9..9d22b75 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="2024-10-25T08:58:46Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7" +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.version="main" VIASHDOCKER diff --git a/target/executable/kallisto/kallisto_quant/.config.vsh.yaml b/target/executable/kallisto/kallisto_quant/.config.vsh.yaml index a6a5c19..8276b4f 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 da7b07b..5070bd9 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="2024-10-25T08:58:46Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7" +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.version="main" VIASHDOCKER diff --git a/target/executable/multiqc_custom_biotype/.config.vsh.yaml b/target/executable/multiqc_custom_biotype/.config.vsh.yaml index bacf7c5..b0fc698 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 b5c6829..828b148 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="2024-10-25T08:58:43Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7" +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.version="main" VIASHDOCKER diff --git a/target/executable/picard_markduplicates/.config.vsh.yaml b/target/executable/picard_markduplicates/.config.vsh.yaml index 7e9cb91..b4da303 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 fd4b9f8..d36a251 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="2024-10-25T08:58:41Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7" +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.version="main" VIASHDOCKER diff --git a/target/executable/prepare_multiqc_input/.config.vsh.yaml b/target/executable/prepare_multiqc_input/.config.vsh.yaml index c9de613..edb174e 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 75f1de1..72afe91 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="2024-10-25T08:58:39Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7" +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.version="main" VIASHDOCKER diff --git a/target/executable/preprocess_transcripts_fasta/.config.vsh.yaml b/target/executable/preprocess_transcripts_fasta/.config.vsh.yaml index 832222e..80cafb1 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 59184b9..73b0a97 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="2024-10-25T08:58:40Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7" +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.version="main" VIASHDOCKER diff --git a/target/executable/preseq_lcextrap/.config.vsh.yaml b/target/executable/preseq_lcextrap/.config.vsh.yaml index 9385b34..a2016e8 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 ccc8555..29bae0c 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="2024-10-25T08:58:41Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7" +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.version="main" VIASHDOCKER diff --git a/target/executable/qualimap/.config.vsh.yaml b/target/executable/qualimap/.config.vsh.yaml index 79f87f3..f6c20c0 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/qualimap/qualimap b/target/executable/qualimap/qualimap index 377eb6e..99affad 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="2024-10-25T08:58:44Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7" +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.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 e81f533..ba0cd06 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 71e5fee..b5557fb 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="2024-10-25T08:58:40Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7" +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.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 7492be8..3927f5d 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 ae9ea90..7f1bb9a 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="2024-10-25T08:58:39Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7" +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.version="main" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml b/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml index a23b549..ca06b05 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 e580d65..4dd19a4 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="2024-10-25T08:58:44Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7" +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.version="main" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml b/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml index d32cdcd..89faa5b 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 ab39069..7078972 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="2024-10-25T08:58:43Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7" +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.version="main" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml b/target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml index d8e020f..98b0eb3 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 a597fcf..b1271ea 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="2024-10-25T08:58:43Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7" +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.version="main" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml b/target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml index ccc4507..6c4a0e2 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 42038fb..0c9e6f7 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="2024-10-25T08:58:44Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7" +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.version="main" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_junctionsaturation/.config.vsh.yaml b/target/executable/rseqc/rseqc_junctionsaturation/.config.vsh.yaml index d99c7f4..352185d 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 1b71bda..efec96f 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="2024-10-25T08:58:45Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7" +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.version="main" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_readdistribution/.config.vsh.yaml b/target/executable/rseqc/rseqc_readdistribution/.config.vsh.yaml index 2ee0a7a..366a5a9 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 d97fc21..d318e4e 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="2024-10-25T08:58:42Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7" +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.version="main" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_readduplication/.config.vsh.yaml b/target/executable/rseqc/rseqc_readduplication/.config.vsh.yaml index a7f54d7..75a5edd 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 1b750fb..ea03355 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="2024-10-25T08:58:44Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7" +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.version="main" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_tin/.config.vsh.yaml b/target/executable/rseqc/rseqc_tin/.config.vsh.yaml index e02d49a..53d51be 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 9157123..a61c0b3 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="2024-10-25T08:58:43Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7" +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.version="main" VIASHDOCKER diff --git a/target/executable/sortmerna/.config.vsh.yaml b/target/executable/sortmerna/.config.vsh.yaml index b52bfe6..1c89c83 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/sortmerna/sortmerna b/target/executable/sortmerna/sortmerna index 71af8f1..0e52fea 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="2024-10-25T08:58:42Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7" +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.version="main" VIASHDOCKER diff --git a/target/executable/stringtie/.config.vsh.yaml b/target/executable/stringtie/.config.vsh.yaml index 89f2016..5170a7f 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/stringtie/stringtie b/target/executable/stringtie/stringtie index 2bab19e..79d5acd 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="2024-10-25T08:58:44Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7" +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.version="main" VIASHDOCKER diff --git a/target/executable/summarizedexperiment/.config.vsh.yaml b/target/executable/summarizedexperiment/.config.vsh.yaml index c52be4b..f1f0991 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/summarizedexperiment/summarizedexperiment b/target/executable/summarizedexperiment/summarizedexperiment index 0ef2d99..5cba212 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="2024-10-25T08:58:41Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7" +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.version="main" VIASHDOCKER diff --git a/target/executable/trimgalore/.config.vsh.yaml b/target/executable/trimgalore/.config.vsh.yaml index 5623af6..8d89d27 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/trimgalore/trimgalore b/target/executable/trimgalore/trimgalore index 792630b..0763e88 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="2024-10-25T08:58:42Z" +LABEL org.opencontainers.image.created="2024-11-13T10:13:21Z" LABEL org.opencontainers.image.source="https://github.com/FelixKrueger/TrimGalore" -LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7" +LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/tx2gene/.config.vsh.yaml b/target/executable/tx2gene/.config.vsh.yaml index d9f16e7..6e22a1d 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/tx2gene/tx2gene b/target/executable/tx2gene/tx2gene index c4125b7..1adbeff 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="2024-10-25T08:58:44Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7" +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.version="main" VIASHDOCKER diff --git a/target/executable/tximport/.config.vsh.yaml b/target/executable/tximport/.config.vsh.yaml index 9db327c..8b8a1f0 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/tximport/tximport b/target/executable/tximport/tximport index a0d5b81..288bc03 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="2024-10-25T08:58:38Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7" +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.version="main" VIASHDOCKER diff --git a/target/executable/ucsc/bedclip/.config.vsh.yaml b/target/executable/ucsc/bedclip/.config.vsh.yaml index 254e76c..0135f7a 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 0e73b21..1eb7067 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="2024-10-25T08:58:46Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7" +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.version="main" VIASHDOCKER diff --git a/target/executable/ucsc/bedgraphtobigwig/.config.vsh.yaml b/target/executable/ucsc/bedgraphtobigwig/.config.vsh.yaml index c60bb84..5ada2d8 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 c3b7488..598e3a7 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="2024-10-25T08:58:47Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7" +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.version="main" VIASHDOCKER diff --git a/target/executable/umitools/umitools_dedup/.config.vsh.yaml b/target/executable/umitools/umitools_dedup/.config.vsh.yaml index 6f89cd0..398abdc 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 f528045..9ac509b 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="2024-10-25T08:58:47Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7" +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.version="main" VIASHDOCKER diff --git a/target/executable/umitools/umitools_extract/.config.vsh.yaml b/target/executable/umitools/umitools_extract/.config.vsh.yaml index 1becbbe..71df6fc 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 7b5779a..33573a2 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="2024-10-25T08:58:47Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7" +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.version="main" VIASHDOCKER diff --git a/target/executable/umitools_prepareforquant/.config.vsh.yaml b/target/executable/umitools_prepareforquant/.config.vsh.yaml index e2cb4f1..ef49f2d 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 e30745e..b0a75f4 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="2024-10-25T08:58:42Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7" +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.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 92d13ce..32643dd 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 2be1a3a..f7c07bc 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 eca2670..ca5d73d 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 4df8876..a1d2385 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 dc397a9..dc80f25 100644 --- a/target/executable/workflows/prepare_genome/.config.vsh.yaml +++ b/target/executable/workflows/prepare_genome/.config.vsh.yaml @@ -496,8 +496,8 @@ build_info: output: "target/executable/workflows/prepare_genome" executable: "target/executable/workflows/prepare_genome/prepare_genome" viash_version: "0.9.0" - git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/gunzip" - "target/dependencies/vsh/vsh/biobox/main/nextflow/gffread" 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 4b11fb0..fbc4b1a 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 6e9dc49..c353f41 100644 --- a/target/executable/workflows/quality_control/.config.vsh.yaml +++ b/target/executable/workflows/quality_control/.config.vsh.yaml @@ -213,6 +213,22 @@ argument_groups: direction: "input" multiple: false multiple_sep: ";" + - type: "boolean_true" + name: "--skip_dupradar" + info: null + direction: "input" + - type: "boolean_true" + name: "--skip_qualimap" + info: null + direction: "input" + - type: "boolean_true" + name: "--skip_rseqc" + info: null + direction: "input" + - type: "boolean_true" + name: "--skip_multiqc" + info: null + direction: "input" - type: "boolean" name: "--skip_preseq" info: null @@ -1556,8 +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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/rseqc/rseqc_bamstat" - "target/nextflow/rseqc/rseqc_inferexperiment" diff --git a/target/executable/workflows/quality_control/quality_control b/target/executable/workflows/quality_control/quality_control index f3070e4..257f785 100755 --- a/target/executable/workflows/quality_control/quality_control +++ b/target/executable/workflows/quality_control/quality_control @@ -270,6 +270,18 @@ function ViashHelp { echo " --skip_pseudo_align" echo " type: boolean" echo "" + echo " --skip_dupradar" + echo " type: boolean_true" + echo "" + echo " --skip_qualimap" + echo " type: boolean_true" + echo "" + echo " --skip_rseqc" + echo " type: boolean_true" + echo "" + echo " --skip_multiqc" + echo " type: boolean_true" + echo "" echo " --skip_preseq" echo " type: boolean" echo " default: false" @@ -1063,6 +1075,26 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_SKIP_PSEUDO_ALIGN=$(ViashRemoveFlags "$1") shift 1 ;; + --skip_dupradar) + [ -n "$VIASH_PAR_SKIP_DUPRADAR" ] && ViashError Bad arguments for option \'--skip_dupradar\': \'$VIASH_PAR_SKIP_DUPRADAR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_SKIP_DUPRADAR=true + shift 1 + ;; + --skip_qualimap) + [ -n "$VIASH_PAR_SKIP_QUALIMAP" ] && ViashError Bad arguments for option \'--skip_qualimap\': \'$VIASH_PAR_SKIP_QUALIMAP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_SKIP_QUALIMAP=true + shift 1 + ;; + --skip_rseqc) + [ -n "$VIASH_PAR_SKIP_RSEQC" ] && ViashError Bad arguments for option \'--skip_rseqc\': \'$VIASH_PAR_SKIP_RSEQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_SKIP_RSEQC=true + shift 1 + ;; + --skip_multiqc) + [ -n "$VIASH_PAR_SKIP_MULTIQC" ] && ViashError Bad arguments for option \'--skip_multiqc\': \'$VIASH_PAR_SKIP_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_SKIP_MULTIQC=true + shift 1 + ;; --skip_preseq) [ -n "$VIASH_PAR_SKIP_PRESEQ" ] && ViashError Bad arguments for option \'--skip_preseq\': \'$VIASH_PAR_SKIP_PRESEQ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 VIASH_PAR_SKIP_PRESEQ="$2" @@ -2404,6 +2436,18 @@ fi if [ -z ${VIASH_PAR_SKIP_ALIGN+x} ]; then VIASH_PAR_SKIP_ALIGN="false" fi +if [ -z ${VIASH_PAR_SKIP_DUPRADAR+x} ]; then + VIASH_PAR_SKIP_DUPRADAR="false" +fi +if [ -z ${VIASH_PAR_SKIP_QUALIMAP+x} ]; then + VIASH_PAR_SKIP_QUALIMAP="false" +fi +if [ -z ${VIASH_PAR_SKIP_RSEQC+x} ]; then + VIASH_PAR_SKIP_RSEQC="false" +fi +if [ -z ${VIASH_PAR_SKIP_MULTIQC+x} ]; then + VIASH_PAR_SKIP_MULTIQC="false" +fi if [ -z ${VIASH_PAR_SKIP_PRESEQ+x} ]; then VIASH_PAR_SKIP_PRESEQ="false" fi @@ -2747,6 +2791,30 @@ if [[ -n "$VIASH_PAR_SKIP_PSEUDO_ALIGN" ]]; then exit 1 fi fi +if [[ -n "$VIASH_PAR_SKIP_DUPRADAR" ]]; then + if ! [[ "$VIASH_PAR_SKIP_DUPRADAR" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then + ViashError '--skip_dupradar' has to be a boolean_true. Use "--help" to get more information on the parameters. + exit 1 + fi +fi +if [[ -n "$VIASH_PAR_SKIP_QUALIMAP" ]]; then + if ! [[ "$VIASH_PAR_SKIP_QUALIMAP" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then + ViashError '--skip_qualimap' has to be a boolean_true. Use "--help" to get more information on the parameters. + exit 1 + fi +fi +if [[ -n "$VIASH_PAR_SKIP_RSEQC" ]]; then + if ! [[ "$VIASH_PAR_SKIP_RSEQC" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then + ViashError '--skip_rseqc' has to be a boolean_true. Use "--help" to get more information on the parameters. + exit 1 + fi +fi +if [[ -n "$VIASH_PAR_SKIP_MULTIQC" ]]; then + if ! [[ "$VIASH_PAR_SKIP_MULTIQC" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then + ViashError '--skip_multiqc' has to be a boolean_true. Use "--help" to get more information on the parameters. + exit 1 + fi +fi if [[ -n "$VIASH_PAR_SKIP_PRESEQ" ]]; then if ! [[ "$VIASH_PAR_SKIP_PRESEQ" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then ViashError '--skip_preseq' has to be a boolean. Use "--help" to get more information on the parameters. @@ -3305,7 +3373,7 @@ workflow run_wf { } | featurecounts.run ( - runIf: { id, state -> !state.skip_qc && !state.skip_biotype_qc && state.biotype && state.biotype_in_gtf }, + runIf: { id, state -> !state.skip_qc && !state.skip_biotype_qc && state.biotype && state.biotype_in_gtf && !state.skip_align }, fromState: [ "paired": "paired", "strand": "strand", @@ -3326,7 +3394,7 @@ workflow run_wf { ) | multiqc_custom_biotype.run ( - runIf: { id, state -> !state.skip_qc && !state.skip_biotype_qc && state.biotype && state.featurecounts }, + runIf: { id, state -> !state.skip_qc && !state.skip_biotype_qc && state.biotype && state.featurecounts && !state.skip_align }, fromState: [ "id": "id", "biocounts": "featurecounts", @@ -3339,7 +3407,7 @@ workflow run_wf { ) | preseq_lcextrap.run ( - runIf: { id, state -> !state.skip_qc && !state.skip_preseq }, + runIf: { id, state -> !state.skip_qc && !state.skip_preseq && !state.skip_align }, fromState: [ "paired": "paired", "input": "genome_bam", @@ -3349,7 +3417,7 @@ workflow run_wf { ) | rseqc_bamstat.run ( - runIf: { id, state -> "bam_stat" in state.rseqc_modules }, + runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "bam_stat" in state.rseqc_modules && !state.skip_align }, fromState: [ "input": "genome_bam", "map_qual": "map_qual" @@ -3357,7 +3425,7 @@ workflow run_wf { toState: [ "bamstat_output": "output" ] ) | rseqc_inferexperiment.run( - runIf: { id, state -> "infer_experiment" in state.rseqc_modules }, + runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "infer_experiment" in state.rseqc_modules && !state.skip_align }, fromState: [ "input": "genome_bam", "refgene": "gene_bed", @@ -3373,7 +3441,7 @@ workflow run_wf { [ id, state + [ inferred_strand: inferred_strand, passed_strand_check: passed_strand_check ] ] } | rseqc_innerdistance.run( - runIf: { id, state -> state.paired && "inner_distance" in state.rseqc_modules }, + runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && state.paired && "inner_distance" in state.rseqc_modules && !state.skip_align }, key: "inner_distance", fromState: [ "input": "genome_bam", @@ -3393,7 +3461,7 @@ workflow run_wf { ] ) | rseqc_junctionannotation.run( - runIf: { id, state -> "junction_annotation" in state.rseqc_modules }, + runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "junction_annotation" in state.rseqc_modules && !state.skip_align }, fromState: [ "input": "genome_bam", "refgene": "gene_bed", @@ -3411,7 +3479,7 @@ workflow run_wf { ] ) | rseqc_junctionsaturation.run( - runIf: { id, state -> "junction_saturation" in state.rseqc_modules }, + runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "junction_saturation" in state.rseqc_modules && !state.skip_align }, fromState: [ "input": "genome_bam", "refgene": "gene_bed", @@ -3428,7 +3496,7 @@ workflow run_wf { ] ) | rseqc_readdistribution.run( - runIf: { id, state -> "read_distribution" in state.rseqc_modules }, + runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "read_distribution" in state.rseqc_modules && !state.skip_align }, fromState: [ "input": "genome_bam", "refgene": "gene_bed", @@ -3436,7 +3504,7 @@ workflow run_wf { toState: [ "read_distribution_output": "output" ] ) | rseqc_readduplication.run( - runIf: { id, state -> "read_duplication" in state.rseqc_modules }, + runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "read_duplication" in state.rseqc_modules && !state.skip_align }, fromState: [ "input": "genome_bam", "read_count_upper_limit": "read_count_upper_limit", @@ -3450,7 +3518,7 @@ workflow run_wf { ] ) | rseqc_tin.run( - runIf: { id, state -> "tin" in state.rseqc_modules }, + runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "tin" in state.rseqc_modules && !state.skip_align }, fromState: [ "bam_input": "genome_bam", "bai_input": "genome_bam_index", @@ -3466,6 +3534,7 @@ workflow run_wf { ) | dupradar.run( + runIf: { id, state -> !state.skip_qc && !state.skip_dupradar && !state.skip_align }, fromState: [ "id": "id", "input": "genome_bam", @@ -3485,6 +3554,7 @@ workflow run_wf { ) | qualimap.run( + runIf: { id, state -> !state.skip_qc && !state.skip_qualimap && !state.skip_align }, fromState: [ "input": "genome_bam", "gtf": "gtf", @@ -3505,7 +3575,7 @@ workflow run_wf { | toSortedList | map { list -> - def ids = list.collect { id, state -> state.id } + def ids = list.collect { id, state -> id } def strandedness = list.collect { id, state -> state.strandedness } def num_trimmed_reads = list.collect { id, state -> state.num_trimmed_reads } def passed_trimmed_reads = list.collect { id, state -> state.passed_trimmed_reads } @@ -3811,7 +3881,7 @@ workflow run_wf { | deseq2_qc.run ( runIf: { id, state -> !state.skip_qc && !state.skip_deseq2_qc && !state.skip_pseudo_align }, fromState: [ - "counts": "counts", + "counts": "pseudo_counts_gene_length_scaled", "vst": "deseq2_vst", "label": "pseudo_aligner" ], @@ -3823,7 +3893,7 @@ workflow run_wf { ], key: "deseq2_qc_pseuso_align_quant" ) - + | niceView() // Get list of samples that failed trimming, mapping, and strand check for MultiQC report | map { id, state -> def fail_trimming_header = ["Sample", "Reads after trimming"] @@ -3846,7 +3916,7 @@ workflow run_wf { fail_mapping_multiqc += tsv_data.join('\\n') } if (!state.passed_strand_check[i]) { - tsv_data = ([ids[i], state.strandedness[i]] + state.inferred_strand[i]).join('\\t') + tsv_data = ([state.ids[i], state.strandedness[i]] + state.inferred_strand[i]).join('\\t') fail_strand_multiqc += tsv_data.join('\\n') } } @@ -3866,6 +3936,7 @@ workflow run_wf { } | prepare_multiqc_input.run( + runIf: { id, state -> !state.skip_qc && !state.skip_multiqc }, fromState: [ "fail_trimming_multiqc": "fail_trimming_multiqc", "fail_mapping_multiqc": "fail_mapping_multiqc", @@ -3906,6 +3977,7 @@ workflow run_wf { ) | multiqc.run ( + runIf: { id, state -> !state.skip_qc && !state.skip_multiqc }, fromState: [ "title": "multiqc_title", "input": "multiqc_input", diff --git a/target/executable/workflows/rnaseq/.config.vsh.yaml b/target/executable/workflows/rnaseq/.config.vsh.yaml index 1ffd9a5..6c850f4 100644 --- a/target/executable/workflows/rnaseq/.config.vsh.yaml +++ b/target/executable/workflows/rnaseq/.config.vsh.yaml @@ -607,17 +607,22 @@ argument_groups: info: null direction: "input" - type: "boolean_true" - name: "skip_dupradar" + name: "--skip_dupradar" description: "Skip dupRadar." info: null direction: "input" - type: "boolean_true" - name: "skip_rseqc" + name: "--skip_qualimap" + description: "Skip Qualimap." + info: null + direction: "input" + - type: "boolean_true" + name: "--skip_rseqc" description: "Skip RSeQC." info: null direction: "input" - type: "boolean_true" - name: "skip_multiqc" + name: "--skip_multiqc" description: "Skip MultiQC." info: null direction: "input" @@ -2077,8 +2082,8 @@ build_info: output: "target/executable/workflows/rnaseq" executable: "target/executable/workflows/rnaseq/rnaseq" viash_version: "0.9.0" - git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 4d0a269..5c34423 100755 --- a/target/executable/workflows/rnaseq/rnaseq +++ b/target/executable/workflows/rnaseq/rnaseq @@ -499,15 +499,19 @@ function ViashHelp { echo " type: boolean_true" echo " Skip DESeq2 PCA and heatmap plotting." echo "" - echo " skip_dupradar" + echo " --skip_dupradar" echo " type: boolean_true" echo " Skip dupRadar." echo "" - echo " skip_rseqc" + echo " --skip_qualimap" + echo " type: boolean_true" + echo " Skip Qualimap." + echo "" + echo " --skip_rseqc" echo " type: boolean_true" echo " Skip RSeQC." echo "" - echo " skip_multiqc" + echo " --skip_multiqc" echo " type: boolean_true" echo " Skip MultiQC." echo "" @@ -1675,6 +1679,26 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_SKIP_DESEQ2_QC=true shift 1 ;; + --skip_dupradar) + [ -n "$VIASH_PAR_SKIP_DUPRADAR" ] && ViashError Bad arguments for option \'--skip_dupradar\': \'$VIASH_PAR_SKIP_DUPRADAR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_SKIP_DUPRADAR=true + shift 1 + ;; + --skip_qualimap) + [ -n "$VIASH_PAR_SKIP_QUALIMAP" ] && ViashError Bad arguments for option \'--skip_qualimap\': \'$VIASH_PAR_SKIP_QUALIMAP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_SKIP_QUALIMAP=true + shift 1 + ;; + --skip_rseqc) + [ -n "$VIASH_PAR_SKIP_RSEQC" ] && ViashError Bad arguments for option \'--skip_rseqc\': \'$VIASH_PAR_SKIP_RSEQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_SKIP_RSEQC=true + shift 1 + ;; + --skip_multiqc) + [ -n "$VIASH_PAR_SKIP_MULTIQC" ] && ViashError Bad arguments for option \'--skip_multiqc\': \'$VIASH_PAR_SKIP_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_SKIP_MULTIQC=true + shift 1 + ;; --extra_fq_subsample_args) [ -n "$VIASH_PAR_EXTRA_FQ_SUBSAMPLE_ARGS" ] && ViashError Bad arguments for option \'--extra_fq_subsample_args\': \'$VIASH_PAR_EXTRA_FQ_SUBSAMPLE_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 VIASH_PAR_EXTRA_FQ_SUBSAMPLE_ARGS="$2" @@ -3059,20 +3083,6 @@ if [ -z "$VIASH_META_CPUS" ]; then fi -# storing leftover values in positionals -if [[ $# -gt 0 ]]; then - VIASH_PAR_SKIP_DUPRADAR="$1" - shift 1 -fi -if [[ $# -gt 0 ]]; then - VIASH_PAR_SKIP_RSEQC="$1" - shift 1 -fi -if [[ $# -gt 0 ]]; then - VIASH_PAR_SKIP_MULTIQC="$1" - shift 1 -fi - # check whether required parameters exist if [ -z ${VIASH_PAR_ID+x} ]; then ViashError '--id' is a required argument. Use "--help" to get more information on the parameters. @@ -3235,6 +3245,9 @@ fi if [ -z ${VIASH_PAR_SKIP_DUPRADAR+x} ]; then VIASH_PAR_SKIP_DUPRADAR="false" fi +if [ -z ${VIASH_PAR_SKIP_QUALIMAP+x} ]; then + VIASH_PAR_SKIP_QUALIMAP="false" +fi if [ -z ${VIASH_PAR_SKIP_RSEQC+x} ]; then VIASH_PAR_SKIP_RSEQC="false" fi @@ -3827,19 +3840,25 @@ if [[ -n "$VIASH_PAR_SKIP_DESEQ2_QC" ]]; then fi if [[ -n "$VIASH_PAR_SKIP_DUPRADAR" ]]; then if ! [[ "$VIASH_PAR_SKIP_DUPRADAR" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then - ViashError 'skip_dupradar' has to be a boolean_true. Use "--help" to get more information on the parameters. + ViashError '--skip_dupradar' has to be a boolean_true. Use "--help" to get more information on the parameters. + exit 1 + fi +fi +if [[ -n "$VIASH_PAR_SKIP_QUALIMAP" ]]; then + if ! [[ "$VIASH_PAR_SKIP_QUALIMAP" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then + ViashError '--skip_qualimap' has to be a boolean_true. Use "--help" to get more information on the parameters. exit 1 fi fi if [[ -n "$VIASH_PAR_SKIP_RSEQC" ]]; then if ! [[ "$VIASH_PAR_SKIP_RSEQC" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then - ViashError 'skip_rseqc' has to be a boolean_true. Use "--help" to get more information on the parameters. + ViashError '--skip_rseqc' has to be a boolean_true. Use "--help" to get more information on the parameters. exit 1 fi fi if [[ -n "$VIASH_PAR_SKIP_MULTIQC" ]]; then if ! [[ "$VIASH_PAR_SKIP_MULTIQC" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then - ViashError 'skip_multiqc' has to be a boolean_true. Use "--help" to get more information on the parameters. + ViashError '--skip_multiqc' has to be a boolean_true. Use "--help" to get more information on the parameters. exit 1 fi fi @@ -4624,7 +4643,7 @@ workflow run_wf { // Filter channels to get samples that passed STAR minimum mapping percentage | map { id, state -> - def percent_mapped = getStarPercentMapped(state.star_multiqc) + def percent_mapped = (!state.skip_alignment) ? getStarPercentMapped(state.star_multiqc) : 0.0 def passed_mapping = (percent_mapped >= state.min_mapped_reads) ? true : false [ id, state + [percent_mapped: percent_mapped, passed_mapping: passed_mapping] ] } @@ -4719,6 +4738,11 @@ workflow run_wf { "strandedness": "strandedness", "skip_align": "skip_alignment", "skip_pseudo_align": "skip_pseudo_alignment", + "skip_dupradar": "skip_dupradar", + "skip_qualimap": "skip_qualimap", + "skip_rseqc": "skip_rseqc", + "skip_multiqc": "skip_multiqc", + "skip_preseq": "skip_preseq", "gtf": "gtf", "num_trimmed_reads": "num_trimmed_reads", "passed_trimmed_reads": "passed_trimmed_reads", diff --git a/target/nextflow/bbmap_bbsplit/.config.vsh.yaml b/target/nextflow/bbmap_bbsplit/.config.vsh.yaml index 9abd3a5..592ce00 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 7748942..e052879 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" : "05d48ac2f802e6510893b0966727b56adf2d5bf7", - "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", + "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 09e84aa..ed06091 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 8f590ca..47bfd63 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" : "05d48ac2f802e6510893b0966727b56adf2d5bf7", - "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", + "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 d2dde9e..ac6928a 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 e14bd51..3c6ac9c 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" : "05d48ac2f802e6510893b0966727b56adf2d5bf7", - "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", + "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 7088d75..87501e2 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 f7b6f69..4412021 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" : "05d48ac2f802e6510893b0966727b56adf2d5bf7", - "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", + "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 68a6489..0b8af01 100644 --- a/target/nextflow/deseq2_qc/.config.vsh.yaml +++ b/target/nextflow/deseq2_qc/.config.vsh.yaml @@ -222,10 +222,9 @@ engines: - "RColorBrewer" - "pheatmap" - "stringr" + - "matrixStats" bioc: - "DESeq2" - url: - - "https://cran.r-project.org/src/contrib/Archive/matrixStats/matrixStats_1.1.0.tar.gz" bioc_force_install: false entrypoint: [] cmd: null @@ -238,8 +237,8 @@ build_info: output: "target/nextflow/deseq2_qc" executable: "target/nextflow/deseq2_qc/main.nf" viash_version: "0.9.0" - git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 bb511cf..bb2b736 100644 --- a/target/nextflow/deseq2_qc/main.nf +++ b/target/nextflow/deseq2_qc/main.nf @@ -3083,14 +3083,12 @@ meta = [ "ggplot2", "RColorBrewer", "pheatmap", - "stringr" + "stringr", + "matrixStats" ], "bioc" : [ "DESeq2" ], - "url" : [ - "https://cran.r-project.org/src/contrib/Archive/matrixStats/matrixStats_1.1.0.tar.gz" - ], "bioc_force_install" : false } ] @@ -3106,8 +3104,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/deseq2_qc", "viash_version" : "0.9.0", - "git_commit" : "05d48ac2f802e6510893b0966727b56adf2d5bf7", - "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", + "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 b7e3e5f..0896798 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 2c0f761..cbe5f2d 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" : "05d48ac2f802e6510893b0966727b56adf2d5bf7", - "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", + "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 7739e8b..70ae3cf 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 47707df..6e308bd 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" : "05d48ac2f802e6510893b0966727b56adf2d5bf7", - "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", + "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 19de8c9..1a1decc 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 f08bc22..6c6d4cf 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" : "05d48ac2f802e6510893b0966727b56adf2d5bf7", - "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", + "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 304e329..b141149 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 bf9a6b6..3ae37ab 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" : "05d48ac2f802e6510893b0966727b56adf2d5bf7", - "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", + "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 870342f..298a0d3 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 b71ef73..4356b89 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" : "05d48ac2f802e6510893b0966727b56adf2d5bf7", - "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", + "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 34a3750..0185428 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 a318145..163c699 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" : "05d48ac2f802e6510893b0966727b56adf2d5bf7", - "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", + "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 a8ea96c..5c49ded 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 ba16eb8..baaedae 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" : "05d48ac2f802e6510893b0966727b56adf2d5bf7", - "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", + "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 9f123f1..4ae8f4d 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 a7eadea..ea26f3c 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" : "05d48ac2f802e6510893b0966727b56adf2d5bf7", - "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", + "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 29b5b02..54f78eb 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 30f0e69..c88f1ea 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" : "05d48ac2f802e6510893b0966727b56adf2d5bf7", - "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", + "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 d3ab3bf..3b6a184 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 d9db1c6..c36d323 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" : "05d48ac2f802e6510893b0966727b56adf2d5bf7", - "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", + "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 3e089c9..61af449 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 1d42591..6d35c57 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" : "05d48ac2f802e6510893b0966727b56adf2d5bf7", - "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", + "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 3c80e2f..6167e0f 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 0e353b2..c37b1d5 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" : "05d48ac2f802e6510893b0966727b56adf2d5bf7", - "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", + "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 30a1e82..88ed5b0 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 8a45229..1d592f8 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" : "05d48ac2f802e6510893b0966727b56adf2d5bf7", - "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", + "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 75d1025..be413ef 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 f3f910e..ae6c5c1 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" : "05d48ac2f802e6510893b0966727b56adf2d5bf7", - "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", + "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 e1bfa04..3acdadc 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 1754b0f..f99aac1 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" : "05d48ac2f802e6510893b0966727b56adf2d5bf7", - "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", + "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 51c333c..c059f38 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 5e9344d..15a858f 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" : "05d48ac2f802e6510893b0966727b56adf2d5bf7", - "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", + "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 bc98fa5..ce8775e 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 55aec36..e50fb67 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" : "05d48ac2f802e6510893b0966727b56adf2d5bf7", - "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", + "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 d81267e..b3dc052 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 c5335d8..3a0cb94 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" : "05d48ac2f802e6510893b0966727b56adf2d5bf7", - "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", + "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 97fcbe6..f639b73 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 0d0b721..d90cfb1 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" : "05d48ac2f802e6510893b0966727b56adf2d5bf7", - "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", + "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 5b70a59..63b6390 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 3098e60..e48faf1 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" : "05d48ac2f802e6510893b0966727b56adf2d5bf7", - "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", + "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 a5cb1a8..373bf70 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 55e2fd7..94dce62 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" : "05d48ac2f802e6510893b0966727b56adf2d5bf7", - "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", + "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 3252c1f..c61da3c 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 76078b0..e6f0e84 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" : "05d48ac2f802e6510893b0966727b56adf2d5bf7", - "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", + "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 737b8ab..25476eb 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 08c99de..818bcb3 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" : "05d48ac2f802e6510893b0966727b56adf2d5bf7", - "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", + "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 c2ea28a..cdefc5e 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 1b4ec95..43e57a1 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" : "05d48ac2f802e6510893b0966727b56adf2d5bf7", - "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", + "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 af13ec1..69c8fb4 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 f7741f2..56d2276 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" : "05d48ac2f802e6510893b0966727b56adf2d5bf7", - "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", + "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 4bf2305..47f48b9 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 1e8ac4e..75cb58e 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" : "05d48ac2f802e6510893b0966727b56adf2d5bf7", - "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", + "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 708eca7..6732cf9 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 9763694..bfff52d 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" : "05d48ac2f802e6510893b0966727b56adf2d5bf7", - "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", + "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 893f4b4..01add5c 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 f550cf9..4cf0d29 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" : "05d48ac2f802e6510893b0966727b56adf2d5bf7", - "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", + "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 25eef96..e254ddc 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 316ca1e..efdffea 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" : "05d48ac2f802e6510893b0966727b56adf2d5bf7", - "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", + "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 26078b3..ae637d3 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 e2f4197..535f873 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" : "05d48ac2f802e6510893b0966727b56adf2d5bf7", - "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", + "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 96a0189..0189f9d 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 0241651..f2b63df 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" : "05d48ac2f802e6510893b0966727b56adf2d5bf7", - "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", + "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 52d0dbf..61ba071 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 540a755..eb3f994 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" : "05d48ac2f802e6510893b0966727b56adf2d5bf7", - "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", + "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 b5a26d1..22c6a2e 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 ab86e20..dd016e4 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" : "05d48ac2f802e6510893b0966727b56adf2d5bf7", - "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", + "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 48cef49..6b1bedd 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 9b11bf8..4ef21a1 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" : "05d48ac2f802e6510893b0966727b56adf2d5bf7", - "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", + "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 c2d7c3d..f0316a0 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 e37c57f..00cffd0 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" : "05d48ac2f802e6510893b0966727b56adf2d5bf7", - "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", + "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 5de53e5..94e0c85 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 3bbcbe8..ecbb5f1 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" : "05d48ac2f802e6510893b0966727b56adf2d5bf7", - "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", + "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 1994ddd..1dcaa01 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 b3c1288..6146e4e 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" : "05d48ac2f802e6510893b0966727b56adf2d5bf7", - "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", + "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 d2f7721..fe9b4b1 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 969d4c9..65abfa6 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" : "05d48ac2f802e6510893b0966727b56adf2d5bf7", - "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", + "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 d18c8cd..9d8fe59 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 e4c459b..b1184b4 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" : "05d48ac2f802e6510893b0966727b56adf2d5bf7", - "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", + "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 d2f2b7a..cead340 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 f89581d..766f3d4 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" : "05d48ac2f802e6510893b0966727b56adf2d5bf7", - "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", + "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 041b68a..72a9354 100644 --- a/target/nextflow/workflows/prepare_genome/.config.vsh.yaml +++ b/target/nextflow/workflows/prepare_genome/.config.vsh.yaml @@ -496,8 +496,8 @@ build_info: output: "target/nextflow/workflows/prepare_genome" executable: "target/nextflow/workflows/prepare_genome/main.nf" viash_version: "0.9.0" - git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 e4ff9c1..e40a4ff 100644 --- a/target/nextflow/workflows/prepare_genome/main.nf +++ b/target/nextflow/workflows/prepare_genome/main.nf @@ -3407,8 +3407,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/prepare_genome", "viash_version" : "0.9.0", - "git_commit" : "05d48ac2f802e6510893b0966727b56adf2d5bf7", - "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", + "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", 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 a6d8c3f..75517a4 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 be62b69..53de4aa 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" : "05d48ac2f802e6510893b0966727b56adf2d5bf7", - "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", + "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 7bc5c92..9c586d2 100644 --- a/target/nextflow/workflows/quality_control/.config.vsh.yaml +++ b/target/nextflow/workflows/quality_control/.config.vsh.yaml @@ -213,6 +213,22 @@ argument_groups: direction: "input" multiple: false multiple_sep: ";" + - type: "boolean_true" + name: "--skip_dupradar" + info: null + direction: "input" + - type: "boolean_true" + name: "--skip_qualimap" + info: null + direction: "input" + - type: "boolean_true" + name: "--skip_rseqc" + info: null + direction: "input" + - type: "boolean_true" + name: "--skip_multiqc" + info: null + direction: "input" - type: "boolean" name: "--skip_preseq" info: null @@ -1556,8 +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: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 8959420..8ad591b 100644 --- a/target/nextflow/workflows/quality_control/main.nf +++ b/target/nextflow/workflows/quality_control/main.nf @@ -3045,6 +3045,26 @@ meta = [ "multiple" : false, "multiple_sep" : ";" }, + { + "type" : "boolean_true", + "name" : "--skip_dupradar", + "direction" : "input" + }, + { + "type" : "boolean_true", + "name" : "--skip_qualimap", + "direction" : "input" + }, + { + "type" : "boolean_true", + "name" : "--skip_rseqc", + "direction" : "input" + }, + { + "type" : "boolean_true", + "name" : "--skip_multiqc", + "direction" : "input" + }, { "type" : "boolean", "name" : "--skip_preseq", @@ -4628,8 +4648,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/quality_control", "viash_version" : "0.9.0", - "git_commit" : "05d48ac2f802e6510893b0966727b56adf2d5bf7", - "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", + "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", @@ -4711,7 +4731,7 @@ workflow run_wf { } | featurecounts.run ( - runIf: { id, state -> !state.skip_qc && !state.skip_biotype_qc && state.biotype && state.biotype_in_gtf }, + runIf: { id, state -> !state.skip_qc && !state.skip_biotype_qc && state.biotype && state.biotype_in_gtf && !state.skip_align }, fromState: [ "paired": "paired", "strand": "strand", @@ -4732,7 +4752,7 @@ workflow run_wf { ) | multiqc_custom_biotype.run ( - runIf: { id, state -> !state.skip_qc && !state.skip_biotype_qc && state.biotype && state.featurecounts }, + runIf: { id, state -> !state.skip_qc && !state.skip_biotype_qc && state.biotype && state.featurecounts && !state.skip_align }, fromState: [ "id": "id", "biocounts": "featurecounts", @@ -4745,7 +4765,7 @@ workflow run_wf { ) | preseq_lcextrap.run ( - runIf: { id, state -> !state.skip_qc && !state.skip_preseq }, + runIf: { id, state -> !state.skip_qc && !state.skip_preseq && !state.skip_align }, fromState: [ "paired": "paired", "input": "genome_bam", @@ -4755,7 +4775,7 @@ workflow run_wf { ) | rseqc_bamstat.run ( - runIf: { id, state -> "bam_stat" in state.rseqc_modules }, + runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "bam_stat" in state.rseqc_modules && !state.skip_align }, fromState: [ "input": "genome_bam", "map_qual": "map_qual" @@ -4763,7 +4783,7 @@ workflow run_wf { toState: [ "bamstat_output": "output" ] ) | rseqc_inferexperiment.run( - runIf: { id, state -> "infer_experiment" in state.rseqc_modules }, + runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "infer_experiment" in state.rseqc_modules && !state.skip_align }, fromState: [ "input": "genome_bam", "refgene": "gene_bed", @@ -4779,7 +4799,7 @@ workflow run_wf { [ id, state + [ inferred_strand: inferred_strand, passed_strand_check: passed_strand_check ] ] } | rseqc_innerdistance.run( - runIf: { id, state -> state.paired && "inner_distance" in state.rseqc_modules }, + runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && state.paired && "inner_distance" in state.rseqc_modules && !state.skip_align }, key: "inner_distance", fromState: [ "input": "genome_bam", @@ -4799,7 +4819,7 @@ workflow run_wf { ] ) | rseqc_junctionannotation.run( - runIf: { id, state -> "junction_annotation" in state.rseqc_modules }, + runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "junction_annotation" in state.rseqc_modules && !state.skip_align }, fromState: [ "input": "genome_bam", "refgene": "gene_bed", @@ -4817,7 +4837,7 @@ workflow run_wf { ] ) | rseqc_junctionsaturation.run( - runIf: { id, state -> "junction_saturation" in state.rseqc_modules }, + runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "junction_saturation" in state.rseqc_modules && !state.skip_align }, fromState: [ "input": "genome_bam", "refgene": "gene_bed", @@ -4834,7 +4854,7 @@ workflow run_wf { ] ) | rseqc_readdistribution.run( - runIf: { id, state -> "read_distribution" in state.rseqc_modules }, + runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "read_distribution" in state.rseqc_modules && !state.skip_align }, fromState: [ "input": "genome_bam", "refgene": "gene_bed", @@ -4842,7 +4862,7 @@ workflow run_wf { toState: [ "read_distribution_output": "output" ] ) | rseqc_readduplication.run( - runIf: { id, state -> "read_duplication" in state.rseqc_modules }, + runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "read_duplication" in state.rseqc_modules && !state.skip_align }, fromState: [ "input": "genome_bam", "read_count_upper_limit": "read_count_upper_limit", @@ -4856,7 +4876,7 @@ workflow run_wf { ] ) | rseqc_tin.run( - runIf: { id, state -> "tin" in state.rseqc_modules }, + runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "tin" in state.rseqc_modules && !state.skip_align }, fromState: [ "bam_input": "genome_bam", "bai_input": "genome_bam_index", @@ -4872,6 +4892,7 @@ workflow run_wf { ) | dupradar.run( + runIf: { id, state -> !state.skip_qc && !state.skip_dupradar && !state.skip_align }, fromState: [ "id": "id", "input": "genome_bam", @@ -4891,6 +4912,7 @@ workflow run_wf { ) | qualimap.run( + runIf: { id, state -> !state.skip_qc && !state.skip_qualimap && !state.skip_align }, fromState: [ "input": "genome_bam", "gtf": "gtf", @@ -4911,7 +4933,7 @@ workflow run_wf { | toSortedList | map { list -> - def ids = list.collect { id, state -> state.id } + def ids = list.collect { id, state -> id } def strandedness = list.collect { id, state -> state.strandedness } def num_trimmed_reads = list.collect { id, state -> state.num_trimmed_reads } def passed_trimmed_reads = list.collect { id, state -> state.passed_trimmed_reads } @@ -5217,7 +5239,7 @@ workflow run_wf { | deseq2_qc.run ( runIf: { id, state -> !state.skip_qc && !state.skip_deseq2_qc && !state.skip_pseudo_align }, fromState: [ - "counts": "counts", + "counts": "pseudo_counts_gene_length_scaled", "vst": "deseq2_vst", "label": "pseudo_aligner" ], @@ -5229,7 +5251,7 @@ workflow run_wf { ], key: "deseq2_qc_pseuso_align_quant" ) - + | niceView() // Get list of samples that failed trimming, mapping, and strand check for MultiQC report | map { id, state -> def fail_trimming_header = ["Sample", "Reads after trimming"] @@ -5252,7 +5274,7 @@ workflow run_wf { fail_mapping_multiqc += tsv_data.join('\n') } if (!state.passed_strand_check[i]) { - tsv_data = ([ids[i], state.strandedness[i]] + state.inferred_strand[i]).join('\t') + tsv_data = ([state.ids[i], state.strandedness[i]] + state.inferred_strand[i]).join('\t') fail_strand_multiqc += tsv_data.join('\n') } } @@ -5272,6 +5294,7 @@ workflow run_wf { } | prepare_multiqc_input.run( + runIf: { id, state -> !state.skip_qc && !state.skip_multiqc }, fromState: [ "fail_trimming_multiqc": "fail_trimming_multiqc", "fail_mapping_multiqc": "fail_mapping_multiqc", @@ -5312,6 +5335,7 @@ workflow run_wf { ) | multiqc.run ( + runIf: { id, state -> !state.skip_qc && !state.skip_multiqc }, fromState: [ "title": "multiqc_title", "input": "multiqc_input", diff --git a/target/nextflow/workflows/quality_control/nextflow_schema.json b/target/nextflow/workflows/quality_control/nextflow_schema.json index 7af1a16..92ad21f 100644 --- a/target/nextflow/workflows/quality_control/nextflow_schema.json +++ b/target/nextflow/workflows/quality_control/nextflow_schema.json @@ -238,6 +238,50 @@ } + , + "skip_dupradar": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. ", + "help_text": "Type: `boolean_true`, default: `false`. " + , + "default": "False" + } + + + , + "skip_qualimap": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. ", + "help_text": "Type: `boolean_true`, default: `false`. " + , + "default": "False" + } + + + , + "skip_rseqc": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. ", + "help_text": "Type: `boolean_true`, default: `false`. " + , + "default": "False" + } + + + , + "skip_multiqc": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. ", + "help_text": "Type: `boolean_true`, default: `false`. " + , + "default": "False" + } + + , "skip_preseq": { "type": diff --git a/target/nextflow/workflows/rnaseq/.config.vsh.yaml b/target/nextflow/workflows/rnaseq/.config.vsh.yaml index 92b40d2..1d2db70 100644 --- a/target/nextflow/workflows/rnaseq/.config.vsh.yaml +++ b/target/nextflow/workflows/rnaseq/.config.vsh.yaml @@ -607,17 +607,22 @@ argument_groups: info: null direction: "input" - type: "boolean_true" - name: "skip_dupradar" + name: "--skip_dupradar" description: "Skip dupRadar." info: null direction: "input" - type: "boolean_true" - name: "skip_rseqc" + name: "--skip_qualimap" + description: "Skip Qualimap." + info: null + direction: "input" + - type: "boolean_true" + name: "--skip_rseqc" description: "Skip RSeQC." info: null direction: "input" - type: "boolean_true" - name: "skip_multiqc" + name: "--skip_multiqc" description: "Skip MultiQC." info: null direction: "input" @@ -2077,8 +2082,8 @@ build_info: output: "target/nextflow/workflows/rnaseq" executable: "target/nextflow/workflows/rnaseq/main.nf" viash_version: "0.9.0" - git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7" - git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a" + git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@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 e0c7fc4..62caa0a 100644 --- a/target/nextflow/workflows/rnaseq/main.nf +++ b/target/nextflow/workflows/rnaseq/main.nf @@ -3492,19 +3492,25 @@ meta = [ }, { "type" : "boolean_true", - "name" : "skip_dupradar", + "name" : "--skip_dupradar", "description" : "Skip dupRadar.", "direction" : "input" }, { "type" : "boolean_true", - "name" : "skip_rseqc", + "name" : "--skip_qualimap", + "description" : "Skip Qualimap.", + "direction" : "input" + }, + { + "type" : "boolean_true", + "name" : "--skip_rseqc", "description" : "Skip RSeQC.", "direction" : "input" }, { "type" : "boolean_true", - "name" : "skip_multiqc", + "name" : "--skip_multiqc", "description" : "Skip MultiQC.", "direction" : "input" } @@ -4879,12 +4885,12 @@ meta = [ "required" : false, "direction" : "output", "multiple" : false, - "multiple_sep" : ";" + ''' + ''' "multiple_sep" : ";" }, { "type" : "file", "name" : "--dupradar_output_expression_histogram", - "description" : "path to outpu''' + '''t file (pdf) of distribution of RPK values per gene histogram", + "description" : "path to output file (pdf) of distribution of RPK values per gene histogram", "default" : [ "dupradar/histogram/$id.expression_hist.pdf" ], @@ -5236,8 +5242,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/rnaseq", "viash_version" : "0.9.0", - "git_commit" : "05d48ac2f802e6510893b0966727b56adf2d5bf7", - "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq" + "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a", + "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", @@ -5533,7 +5539,7 @@ workflow run_wf { // Filter channels to get samples that passed STAR minimum mapping percentage | map { id, state -> - def percent_mapped = getStarPercentMapped(state.star_multiqc) + def percent_mapped = (!state.skip_alignment) ? getStarPercentMapped(state.star_multiqc) : 0.0 def passed_mapping = (percent_mapped >= state.min_mapped_reads) ? true : false [ id, state + [percent_mapped: percent_mapped, passed_mapping: passed_mapping] ] } @@ -5628,6 +5634,11 @@ workflow run_wf { "strandedness": "strandedness", "skip_align": "skip_alignment", "skip_pseudo_align": "skip_pseudo_alignment", + "skip_dupradar": "skip_dupradar", + "skip_qualimap": "skip_qualimap", + "skip_rseqc": "skip_rseqc", + "skip_multiqc": "skip_multiqc", + "skip_preseq": "skip_preseq", "gtf": "gtf", "num_trimmed_reads": "num_trimmed_reads", "passed_trimmed_reads": "passed_trimmed_reads", diff --git a/target/nextflow/workflows/rnaseq/nextflow_schema.json b/target/nextflow/workflows/rnaseq/nextflow_schema.json index 34bdcc9..ae7190a 100644 --- a/target/nextflow/workflows/rnaseq/nextflow_schema.json +++ b/target/nextflow/workflows/rnaseq/nextflow_schema.json @@ -768,6 +768,17 @@ } + , + "skip_qualimap": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Skip Qualimap", + "help_text": "Type: `boolean_true`, default: `false`. Skip Qualimap." + , + "default": "False" + } + + , "skip_rseqc": { "type":