From 15c280b8fce087f81ef22f658e7a0c6f9738845a Mon Sep 17 00:00:00 2001 From: CI Date: Tue, 3 Dec 2024 08:22:22 +0000 Subject: [PATCH] Build branch add-labels with version add-labels (3ee9ba7) Build pipeline: viash-hub.rnaseq.add-labels-xf9kj Source commit: https://github.com/viash-hub/rnaseq/commit/3ee9ba76ca2112681c41468800aab2fa38cdf453 Source message: Disable bbsplit --- src/workflows/prepare_genome/main.nf | 546 ++++++++--------- src/workflows/rnaseq/config.vsh.yaml | 7 +- src/workflows/rnaseq/main.nf | 3 +- .../bedtools_genomecov/.config.vsh.yaml | 4 +- .../bedtools_genomecov/bedtools_genomecov | 6 +- .../cat_additional_fasta/.config.vsh.yaml | 4 +- .../cat_additional_fasta/cat_additional_fasta | 6 +- target/executable/cat_fastq/.config.vsh.yaml | 4 +- target/executable/cat_fastq/cat_fastq | 6 +- target/executable/deseq2_qc/.config.vsh.yaml | 4 +- target/executable/deseq2_qc/deseq2_qc | 6 +- target/executable/dupradar/.config.vsh.yaml | 4 +- target/executable/dupradar/dupradar | 6 +- .../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 +- .../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 +- .../rsem_merge_counts/.config.vsh.yaml | 4 +- .../rsem_merge_counts/rsem_merge_counts | 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/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 +- .../.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 +- .../workflows/prepare_genome/prepare_genome | 546 ++++++++--------- .../.config.vsh.yaml | 4 +- .../quality_control/.config.vsh.yaml | 4 +- .../workflows/rnaseq/.config.vsh.yaml | 9 +- target/executable/workflows/rnaseq/rnaseq | 21 +- .../bedtools_genomecov/.config.vsh.yaml | 4 +- target/nextflow/bedtools_genomecov/main.nf | 4 +- .../cat_additional_fasta/.config.vsh.yaml | 4 +- target/nextflow/cat_additional_fasta/main.nf | 4 +- target/nextflow/cat_fastq/.config.vsh.yaml | 4 +- target/nextflow/cat_fastq/main.nf | 4 +- target/nextflow/deseq2_qc/.config.vsh.yaml | 4 +- target/nextflow/deseq2_qc/main.nf | 4 +- target/nextflow/dupradar/.config.vsh.yaml | 4 +- target/nextflow/dupradar/main.nf | 4 +- .../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 +- .../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 +- .../rsem_merge_counts/.config.vsh.yaml | 4 +- target/nextflow/rsem_merge_counts/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/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 +- .../.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 | 550 +++++++++--------- .../.config.vsh.yaml | 4 +- .../pseudo_alignment_and_quant/main.nf | 4 +- .../quality_control/.config.vsh.yaml | 4 +- .../workflows/quality_control/main.nf | 4 +- .../workflows/rnaseq/.config.vsh.yaml | 9 +- target/nextflow/workflows/rnaseq/main.nf | 17 +- .../workflows/rnaseq/nextflow_schema.json | 11 - 138 files changed, 1164 insertions(+), 1121 deletions(-) diff --git a/src/workflows/prepare_genome/main.nf b/src/workflows/prepare_genome/main.nf index 92ed037..ab07da9 100644 --- a/src/workflows/prepare_genome/main.nf +++ b/src/workflows/prepare_genome/main.nf @@ -1,288 +1,316 @@ workflow run_wf { - take: - input_ch + take: + input_ch - main: - output_ch = input_ch - - // Uncompress fasta - | gunzip.run ( - fromState: [ "input": "fasta" ], - toState: [ "fasta": "output" ], - key: "gunzip_fasta", - args: [ output: "reference_genome.fasta" ] - ) + main: + output_ch = input_ch - // uncompress gtf - | gunzip.run ( - runIf: {id, state -> state.gtf}, - fromState: [ "input": "gtf" ], - toState: [ "gtf": "output" ], - key: "gunzip_gtf", - args: [output: "gene_annotation.gtf"] - ) + // Uncompress fasta + | gunzip.run ( + fromState: [ "input": "fasta" ], + toState: [ "fasta": "output" ], + key: "gunzip_fasta", + args: [ output: "reference_genome.fasta" ], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) - // uncompress gff - | gunzip.run ( - runIf: {id, state -> !state.gtf && state.gff}, - fromState: [ "input": "gff" ], - toState: [ "gff": "output" ], - key: "gunzip_gff", - args: [output: "gene_annotation.gff"] - ) + // uncompress gtf + | gunzip.run ( + runIf: {id, state -> state.gtf}, + fromState: [ "input": "gtf" ], + toState: [ "gtf": "output" ], + key: "gunzip_gtf", + args: [output: "gene_annotation.gtf"], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) - // gff to gtf - | gffread.run ( - runIf: {id, state -> !state.gtf && state.gff}, - fromState: [ - "input": "gff", - "genome": "fasta" - ], - toState: [ "gtf": "outfile" ], - args: [ - outfile: "gene_annotation.gtf", - gtf_output: true, - keep_attrs: true, - keep_exon_attrs: true - ] - ) + // uncompress gff + | gunzip.run ( + runIf: {id, state -> !state.gtf && state.gff}, + fromState: [ "input": "gff" ], + toState: [ "gff": "output" ], + key: "gunzip_gff", + args: [output: "gene_annotation.gff"], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) - | gtf_filter.run( - runIf: {id, state -> state.gtf && state.filter_gtf}, - fromState: [ - "fasta": "fasta", - "gtf": "gtf" - ], - toState: [ "gtf": "filtered_gtf" ], - args: [filtered_gtf: "gene_annotation.gtf"] - ) + // gff to gtf + | gffread.run ( + runIf: {id, state -> !state.gtf && state.gff}, + fromState: [ + "input": "gff", + "genome": "fasta" + ], + toState: [ "gtf": "outfile" ], + args: [ + outfile: "gene_annotation.gtf", + gtf_output: true, + keep_attrs: true, + keep_exon_attrs: true + ], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) - // uncompress additional fasta - | gunzip.run ( - runIf: {id, state -> state.additional_fasta}, - fromState: [ "input": "additional_fasta" ], - toState: [ "additional_fasta": "output" ], - key: "gunzip_additional_fasta", - args: [output: "additional.fasta"] - ) + | gtf_filter.run( + runIf: {id, state -> state.gtf && state.filter_gtf}, + fromState: [ + "fasta": "fasta", + "gtf": "gtf" + ], + toState: [ "gtf": "filtered_gtf" ], + args: [filtered_gtf: "gene_annotation.gtf"], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) - // concatenate additional fasta - | cat_additional_fasta.run ( - runIf: {id, state -> state.additional_fasta}, - fromState: [ - "fasta": "fasta", - "gtf": "gtf", - "additional_fasta": "additional_fasta", - "biotype": "biotype" - ], - toState: [ - "fasta": "fasta_output", - "gtf": "gtf_output" - ], - args: [ - fasta_output: "genome_additional.fasta", - gtf_output: "genome_additional.gtf" - ] - ) + // uncompress additional fasta + | gunzip.run ( + runIf: {id, state -> state.additional_fasta}, + fromState: [ "input": "additional_fasta" ], + toState: [ "additional_fasta": "output" ], + key: "gunzip_additional_fasta", + args: [output: "additional.fasta"], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) - // uncompress bed file - | gunzip.run ( - runIf: {id, state -> state.gene_bed}, - fromState: [ "input": "gene_bed" ], - toState: [ "gene_bed": "output" ], - key: "gunzip_gene_bed", - args: [output: "genome_additional.bed"] - ) + // concatenate additional fasta + | cat_additional_fasta.run ( + runIf: {id, state -> state.additional_fasta}, + fromState: [ + "fasta": "fasta", + "gtf": "gtf", + "additional_fasta": "additional_fasta", + "biotype": "biotype" + ], + toState: [ + "fasta": "fasta_output", + "gtf": "gtf_output" + ], + args: [ + fasta_output: "genome_additional.fasta", + gtf_output: "genome_additional.gtf" + ], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) - // gtf to bed - | gtf2bed.run ( - runIf: { id, state -> !state.gene_bed}, - fromState: [ "gtf": "gtf" ], - toState: [ "gene_bed": "bed_output" ], - args: [bed_output: "genome_additional.bed"] - ) + // uncompress bed file + | gunzip.run ( + runIf: {id, state -> state.gene_bed}, + fromState: [ "input": "gene_bed" ], + toState: [ "gene_bed": "output" ], + key: "gunzip_gene_bed", + args: [output: "genome_additional.bed"], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) - // uncompress transcript fasta - | gunzip.run ( - runIf: {id, state -> state.transcript_fasta}, - fromState: [ "input": "transcript_fasta" ], - toState: [ "transcript_fasta": "output" ], - key: "transcript_fasta", - args: [output: "transcriptome.fasta"] - ) + // gtf to bed + | gtf2bed.run ( + runIf: { id, state -> !state.gene_bed}, + fromState: [ "gtf": "gtf" ], + toState: [ "gene_bed": "bed_output" ], + args: [bed_output: "genome_additional.bed"], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) - // preprocess transcripts fasta if gtf is in gencode format - | preprocess_transcripts_fasta.run ( - runIf: {id, state -> state.transcript_fasta && state.gencode}, - fromState: [ "transcript_fasta": "transcript_fasta" ], - toState: [ "transcript_fasta": "output" ], - args: [output: "transcriptome.fasta"] - ) + // uncompress transcript fasta + | gunzip.run ( + runIf: {id, state -> state.transcript_fasta}, + fromState: [ "input": "transcript_fasta" ], + toState: [ "transcript_fasta": "output" ], + key: "transcript_fasta", + args: [output: "transcriptome.fasta"], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) - // make transcript FASTA if not provided - | rsem_prepare_reference.run ( - runIf: {id, state -> !state.transcript_fasta}, - fromState: [ - "reference_fasta_files": "fasta", - "gtf": "gtf" - ], - toState: [ "make_transcript_fasta_output": "output" ], - key: "make_transcript_fasta", - args: [reference_name: "genome"] - ) - | map { id, state -> - def transcript_fasta = (!state.transcript_fasta) ? - state.make_transcript_fasta_output.listFiles().find{it.name == "genome.transcripts.fa"} : - state.transcript_fasta - [ id, state + [transcript_fasta: transcript_fasta] ] - } + // preprocess transcripts fasta if gtf is in gencode format + | preprocess_transcripts_fasta.run ( + runIf: {id, state -> state.transcript_fasta && state.gencode}, + fromState: [ "transcript_fasta": "transcript_fasta" ], + toState: [ "transcript_fasta": "output" ], + args: [output: "transcriptome.fasta"], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) - // chromosome size and fai index - | getchromsizes.run ( - fromState: [ "fasta": "fasta" ], - toState: [ - "fai": "fai", - "sizes": "sizes" - ], - key: "chromsizes", - args: [ - fai: "genome_additional.fasta.fai", - sizes: "genome_additional.fasta.sizes" - ] - ) - - // untar bbsplit index, if available - | untar.run ( - runIf: {id, state -> state.bbsplit_index}, - fromState: [ "input": "bbsplit_index" ], - toState: [ "bbsplit_index": "output" ], - key: "untar_bbsplit_index", - args: [output: "BBSplit_index"] - ) + // make transcript FASTA if not provided + | rsem_prepare_reference.run ( + runIf: {id, state -> !state.transcript_fasta}, + fromState: [ + "reference_fasta_files": "fasta", + "gtf": "gtf" + ], + toState: [ "make_transcript_fasta_output": "output" ], + key: "make_transcript_fasta", + args: [reference_name: "genome"], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) + | map { id, state -> + def transcript_fasta = (!state.transcript_fasta) ? + state.make_transcript_fasta_output.listFiles().find{it.name == "genome.transcripts.fa"} : + state.transcript_fasta + [ id, state + [transcript_fasta: transcript_fasta] ] + } - | map {id, state -> - def ref = [state.fasta] + state.bbsplit_fasta_list - [id, state + [bbsplit_ref: ref] ] + // chromosome size and fai index + | getchromsizes.run ( + fromState: [ "fasta": "fasta" ], + toState: [ + "fai": "fai", + "sizes": "sizes" + ], + key: "chromsizes", + args: [ + fai: "genome_additional.fasta.fai", + sizes: "genome_additional.fasta.sizes" + ], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) + + // untar bbsplit index, if available + | untar.run ( + runIf: {id, state -> state.bbsplit_index}, + fromState: [ "input": "bbsplit_index" ], + toState: [ "bbsplit_index": "output" ], + key: "untar_bbsplit_index", + directives: [ label: [ "lowmem", "midcpu" ] ] + ) + + | map { id, state -> + // Check if bbsplit_fasta_list is defined + if (state.bbsplit_fasta_list) { + def ref = [state.fasta] + state.bbsplit_fasta_list + } else { + def ref = [state.fasta] } + [id, state + [bbsplit_ref: ref] ] + } - // create bbsplit index, if not already availble - | bbmap_bbsplit.run ( - runIf: {id, state -> !state.skip_bbsplit && !state.bbsplit_index}, - fromState: ["ref": "bbsplit_ref"], - toState: [ "bbsplit_index": "index" ], - args: [ - only_build_index: true, - index: "BBSplit_index" - ], - key: "generate_bbsplit_index" - ) + | niceView() - // Uncompress STAR index or generate from scratch if required - | untar.run ( - runIf: {id, state -> state.star_index}, - fromState: [ "input": "star_index" ], - toState: [ "star_index": "output" ], - key: "untar_star_index", - args: [output: "STAR_index"] - ) - - // TODO: Add to viah-hub or adapt star_align_reads to enable the generateGenome runMode - | star_genome_generate.run ( - runIf: {id, state -> !state.star_index && !state.skip_alignment}, - fromState: [ - "genome_fasta_files": "fasta", - "sjdb_gtf_file": "gtf", - "sjdb_gtf_feature_exon": "star_sjdb_gtf_feature_exon" - ], - toState: [ "star_index": "index" ], - key: "generate_star_index", - args: [index: "STAR_index"] - ) + // create bbsplit index, if not already available + | bbmap_bbsplit.run ( + runIf: {id, state -> !state.skip_bbsplit && !state.bbsplit_index}, + fromState: ["ref": "bbsplit_ref"], + toState: [ "bbsplit_index": "index" ], + args: [ + only_build_index: true, + index: "BBSplit_index" + ], + key: "generate_bbsplit_index" + ) - // Uncompress RSEM index or generate from scratch if required - | untar.run ( - runIf: {id, state -> state.rsem_index}, - fromState: [ "input": "rsem_index" ], - toState: [ "rsem_index": "output" ], - key: "untar_rsem_index", - args: [output: "RSEM_index"] - ) + // Uncompress STAR index or generate from scratch if required + | untar.run ( + runIf: {id, state -> state.star_index}, + fromState: [ "input": "star_index" ], + toState: [ "star_index": "output" ], + key: "untar_star_index", + args: [output: "STAR_index"], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) - | rsem_prepare_reference.run ( - runIf: {id, state -> !state.rsem_index && state.aligner == 'star_rsem'}, - fromState: [ - "reference_fasta_files": "fasta", - "gtf": "gtf" - ], - toState: [ "rsem_index": "output" ], - key: "generate_rsem_index", - args: [reference_name: "genome"] - ) - - // TODO: Uncompress HISAT2 index or generate from scratch if required + // TODO: Add to viah-hub or adapt star_align_reads to enable the generateGenome runMode + | star_genome_generate.run ( + runIf: {id, state -> !state.star_index && !state.skip_alignment}, + fromState: [ + "genome_fasta_files": "fasta", + "sjdb_gtf_file": "gtf", + "sjdb_gtf_feature_exon": "star_sjdb_gtf_feature_exon" + ], + toState: [ "star_index": "index" ], + key: "generate_star_index", + args: [index: "STAR_index"], + directives: [ label: [ "highmem", "highcpu" ] ] + ) - // Uncompress Salmon index or generate from scratch if required - | untar.run ( - runIf: {id, state -> state.salmon_index}, - fromState: [ "input": "salmon_index" ], - toState: [ "salmon_index": "output" ], - key: "untar_salmon_index", - args: [output: "Salmon_index"] - ) + // Uncompress RSEM index or generate from scratch if required + | untar.run ( + runIf: {id, state -> state.rsem_index}, + fromState: [ "input": "rsem_index" ], + toState: [ "rsem_index": "output" ], + key: "untar_rsem_index", + args: [output: "RSEM_index"], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) - | salmon_index.run ( - runIf: {id, state -> (state.aligner == 'star_salmon' || state.pseudo_aligner == "salmon") && !state.salmon_index}, - fromState: [ - "genome": "fasta", - "transcripts": "transcript_fasta", - "kmer_len": "pseudo_aligner_kmer_size", - "gencode": "gencode" - ], - toState: [ "salmon_index": "index" ], - key: "generate_salmon_index", - args: [index: "Salmon_index"] - ) + | rsem_prepare_reference.run ( + runIf: {id, state -> !state.rsem_index && state.aligner == 'star_rsem'}, + fromState: [ + "reference_fasta_files": "fasta", + "gtf": "gtf" + ], + toState: [ "rsem_index": "output" ], + key: "generate_rsem_index", + args: [reference_name: "genome"], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) + + // TODO: Uncompress HISAT2 index or generate from scratch if required - // Uncompress Kallisto index or generate from scratch if required - | untar.run ( - runIf: {id, state -> state.kallisto_index}, - fromState: [ "input": "kallisto_index" ], - toState: [ "kallisto_index": "output" ], - key: "untar_kallisto_index", - args: [output: "Kallisto_index"] - ) + // Uncompress Salmon index or generate from scratch if required + | untar.run ( + runIf: {id, state -> state.salmon_index}, + fromState: [ "input": "salmon_index" ], + toState: [ "salmon_index": "output" ], + key: "untar_salmon_index", + args: [output: "Salmon_index"], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) - | kallisto_index.run( - runIf: {id, state -> state.pseudo_aligner == "kallisto" && !state.kallisto_index}, - fromState: [ - "input": "transcript_fasta", - "kmer_size": "pseudo_aligner_kmer_size" - ], - toState: [ "kallisto_index": "index" ], - key: "generate_kallisto_index", - args: [index: "Kallisto_index"] - ) + | salmon_index.run ( + runIf: {id, state -> (state.aligner == 'star_salmon' || state.pseudo_aligner == "salmon") && !state.salmon_index}, + fromState: [ + "genome": "fasta", + "transcripts": "transcript_fasta", + "kmer_len": "pseudo_aligner_kmer_size", + "gencode": "gencode" + ], + toState: [ "salmon_index": "index" ], + key: "generate_salmon_index", + args: [index: "Salmon_index"], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) - | map { id, state -> - def mod_state = state.findAll { key, value -> value instanceof java.nio.file.Path && value.exists() } - [ id, mod_state ] - } + // Uncompress Kallisto index or generate from scratch if required + | untar.run ( + runIf: {id, state -> state.kallisto_index}, + fromState: [ "input": "kallisto_index" ], + toState: [ "kallisto_index": "output" ], + key: "untar_kallisto_index", + args: [output: "Kallisto_index"], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) - | setState ( - "fasta_uncompressed": "fasta", - "gtf_uncompressed": "gtf", - "transcript_fasta_uncompressed": "transcript_fasta", - "gene_bed_uncompressed": "gene_bed", - "star_index_uncompressed": "star_index", - "salmon_index_uncompressed": "salmon_index", - "kallisto_index_uncompressed": "kallisto_index", - "bbsplit_index_uncompressed": "bbsplit_index", - "rsem_index_uncompressed": "rsem_index", - "chrom_sizes": "sizes", - "fai": "fai" - ) + | kallisto_index.run( + runIf: {id, state -> state.pseudo_aligner == "kallisto" && !state.kallisto_index}, + fromState: [ + "input": "transcript_fasta", + "kmer_size": "pseudo_aligner_kmer_size" + ], + toState: [ "kallisto_index": "index" ], + key: "generate_kallisto_index", + args: [index: "Kallisto_index"], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) - emit: - output_ch + | map { id, state -> + def mod_state = state.findAll { key, value -> value instanceof java.nio.file.Path && value.exists() } + [ id, mod_state ] + } + + | setState ( + "fasta_uncompressed": "fasta", + "gtf_uncompressed": "gtf", + "transcript_fasta_uncompressed": "transcript_fasta", + "gene_bed_uncompressed": "gene_bed", + "star_index_uncompressed": "star_index", + "salmon_index_uncompressed": "salmon_index", + "kallisto_index_uncompressed": "kallisto_index", + "bbsplit_index_uncompressed": "bbsplit_index", + "rsem_index_uncompressed": "rsem_index", + "chrom_sizes": "sizes", + "fai": "fai" + ) + + emit: + output_ch } diff --git a/src/workflows/rnaseq/config.vsh.yaml b/src/workflows/rnaseq/config.vsh.yaml index 798652c..136117a 100644 --- a/src/workflows/rnaseq/config.vsh.yaml +++ b/src/workflows/rnaseq/config.vsh.yaml @@ -218,9 +218,10 @@ argument_groups: type: boolean description: Skip the adapter trimming step. default: false - - name: "--skip_bbsplit" - type: boolean_true - description: Skip BBSplit for removal of non-reference genome reads. + # See: + # - name: "--skip_bbsplit" + # type: boolean_true + # description: Skip BBSplit for removal of non-reference genome reads. - name: "--skip_umi_extract" type: boolean description: Skip umi_tools extract step. diff --git a/src/workflows/rnaseq/main.nf b/src/workflows/rnaseq/main.nf index bd8eae4..164fbe9 100644 --- a/src/workflows/rnaseq/main.nf +++ b/src/workflows/rnaseq/main.nf @@ -39,7 +39,8 @@ workflow run_wf { // splicesites: list.collect { id, state -> state.splicesites }.unique()[0], // hisat2_index: list.collect { id, state -> state.hisat2_index }.unique()[0], bbsplit_index: list.collect { id, state -> state.bbsplit_index }.unique()[0], - skip_bbsplit: list.collect { id, state -> state.skip_bbsplit }.unique()[0], + // See: + skip_bbsplit: true, // list.collect { id, state -> state.skip_bbsplit }.unique()[0], skip_alignment: list.collect { id, state -> state.skip_alignment }.unique()[0], gencode: list.collect { id, state -> state.gencode }.unique()[0], biotype: list.collect { id, state -> state.biotype }.unique()[0], diff --git a/target/executable/bedtools_genomecov/.config.vsh.yaml b/target/executable/bedtools_genomecov/.config.vsh.yaml index 42a9e77..8de97e5 100644 --- a/target/executable/bedtools_genomecov/.config.vsh.yaml +++ b/target/executable/bedtools_genomecov/.config.vsh.yaml @@ -183,8 +183,8 @@ build_info: output: "target/executable/bedtools_genomecov" executable: "target/executable/bedtools_genomecov/bedtools_genomecov" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/bedtools_genomecov/bedtools_genomecov b/target/executable/bedtools_genomecov/bedtools_genomecov index 5ec528d..97dcfb5 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="2024-12-02T15:00:02Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="59cbb30eecf218c0572104f849ab542423f0e590" +LABEL org.opencontainers.image.created="2024-12-03T05:47:41Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="3ee9ba76ca2112681c41468800aab2fa38cdf453" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/cat_additional_fasta/.config.vsh.yaml b/target/executable/cat_additional_fasta/.config.vsh.yaml index 7227984..e0851a1 100644 --- a/target/executable/cat_additional_fasta/.config.vsh.yaml +++ b/target/executable/cat_additional_fasta/.config.vsh.yaml @@ -187,8 +187,8 @@ build_info: output: "target/executable/cat_additional_fasta" executable: "target/executable/cat_additional_fasta/cat_additional_fasta" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/cat_additional_fasta/cat_additional_fasta b/target/executable/cat_additional_fasta/cat_additional_fasta index c357af7..8c946ef 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="2024-12-02T15:00:01Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="59cbb30eecf218c0572104f849ab542423f0e590" +LABEL org.opencontainers.image.created="2024-12-03T05:47:40Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="3ee9ba76ca2112681c41468800aab2fa38cdf453" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/cat_fastq/.config.vsh.yaml b/target/executable/cat_fastq/.config.vsh.yaml index 4c665a2..c26a050 100644 --- a/target/executable/cat_fastq/.config.vsh.yaml +++ b/target/executable/cat_fastq/.config.vsh.yaml @@ -174,8 +174,8 @@ build_info: output: "target/executable/cat_fastq" executable: "target/executable/cat_fastq/cat_fastq" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/cat_fastq/cat_fastq b/target/executable/cat_fastq/cat_fastq index a9db260..948db25 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="2024-12-02T15:00:00Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="59cbb30eecf218c0572104f849ab542423f0e590" +LABEL org.opencontainers.image.created="2024-12-03T05:47:39Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="3ee9ba76ca2112681c41468800aab2fa38cdf453" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/deseq2_qc/.config.vsh.yaml b/target/executable/deseq2_qc/.config.vsh.yaml index f1e20e7..8e0ea6d 100644 --- a/target/executable/deseq2_qc/.config.vsh.yaml +++ b/target/executable/deseq2_qc/.config.vsh.yaml @@ -242,8 +242,8 @@ build_info: output: "target/executable/deseq2_qc" executable: "target/executable/deseq2_qc/deseq2_qc" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/deseq2_qc/deseq2_qc b/target/executable/deseq2_qc/deseq2_qc index a4bea97..a7f7339 100755 --- a/target/executable/deseq2_qc/deseq2_qc +++ b/target/executable/deseq2_qc/deseq2_qc @@ -506,9 +506,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag Rscript -e 'remotes::install_cran(c("optparse", "ggplot2", "RColorBrewer", "pheatmap", "stringr", "matrixStats"), repos = "https://cran.rstudio.com")' LABEL org.opencontainers.image.description="Companion container for running component deseq2_qc" -LABEL org.opencontainers.image.created="2024-12-02T15:00:00Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="59cbb30eecf218c0572104f849ab542423f0e590" +LABEL org.opencontainers.image.created="2024-12-03T05:47:40Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="3ee9ba76ca2112681c41468800aab2fa38cdf453" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/dupradar/.config.vsh.yaml b/target/executable/dupradar/.config.vsh.yaml index 875e0ae..d722776 100644 --- a/target/executable/dupradar/.config.vsh.yaml +++ b/target/executable/dupradar/.config.vsh.yaml @@ -271,8 +271,8 @@ build_info: output: "target/executable/dupradar" executable: "target/executable/dupradar/dupradar" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/dupradar/dupradar b/target/executable/dupradar/dupradar index c0363ba..90acc7c 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="2024-12-02T15:00:02Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="59cbb30eecf218c0572104f849ab542423f0e590" +LABEL org.opencontainers.image.created="2024-12-03T05:47:42Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="3ee9ba76ca2112681c41468800aab2fa38cdf453" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/getchromsizes/.config.vsh.yaml b/target/executable/getchromsizes/.config.vsh.yaml index 70e9a62..d52907b 100644 --- a/target/executable/getchromsizes/.config.vsh.yaml +++ b/target/executable/getchromsizes/.config.vsh.yaml @@ -172,8 +172,8 @@ build_info: output: "target/executable/getchromsizes" executable: "target/executable/getchromsizes/getchromsizes" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/getchromsizes/getchromsizes b/target/executable/getchromsizes/getchromsizes index 4f7aa6c..1f26a02 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="2024-12-02T15:00:01Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="59cbb30eecf218c0572104f849ab542423f0e590" +LABEL org.opencontainers.image.created="2024-12-03T05:47:40Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="3ee9ba76ca2112681c41468800aab2fa38cdf453" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/gtf2bed/.config.vsh.yaml b/target/executable/gtf2bed/.config.vsh.yaml index 49faaa7..55bcbcf 100644 --- a/target/executable/gtf2bed/.config.vsh.yaml +++ b/target/executable/gtf2bed/.config.vsh.yaml @@ -150,8 +150,8 @@ build_info: output: "target/executable/gtf2bed" executable: "target/executable/gtf2bed/gtf2bed" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/gtf2bed/gtf2bed b/target/executable/gtf2bed/gtf2bed index a8b5c7b..56f83df 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="2024-12-02T15:00:03Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="59cbb30eecf218c0572104f849ab542423f0e590" +LABEL org.opencontainers.image.created="2024-12-03T05:47:42Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="3ee9ba76ca2112681c41468800aab2fa38cdf453" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/gtf_filter/.config.vsh.yaml b/target/executable/gtf_filter/.config.vsh.yaml index 13592cf..d88a2e8 100644 --- a/target/executable/gtf_filter/.config.vsh.yaml +++ b/target/executable/gtf_filter/.config.vsh.yaml @@ -160,8 +160,8 @@ build_info: output: "target/executable/gtf_filter" executable: "target/executable/gtf_filter/gtf_filter" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/gtf_filter/gtf_filter b/target/executable/gtf_filter/gtf_filter index 01287cd..cd371f9 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="2024-12-02T15:00:01Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="59cbb30eecf218c0572104f849ab542423f0e590" +LABEL org.opencontainers.image.created="2024-12-03T05:47:41Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="3ee9ba76ca2112681c41468800aab2fa38cdf453" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/gunzip/.config.vsh.yaml b/target/executable/gunzip/.config.vsh.yaml index 58e4293..37f3d37 100644 --- a/target/executable/gunzip/.config.vsh.yaml +++ b/target/executable/gunzip/.config.vsh.yaml @@ -149,8 +149,8 @@ build_info: output: "target/executable/gunzip" executable: "target/executable/gunzip/gunzip" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/gunzip/gunzip b/target/executable/gunzip/gunzip index 01cf730..96c6a3d 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="2024-12-02T14:59:58Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="59cbb30eecf218c0572104f849ab542423f0e590" +LABEL org.opencontainers.image.created="2024-12-03T05:47:37Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="3ee9ba76ca2112681c41468800aab2fa38cdf453" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/multiqc_custom_biotype/.config.vsh.yaml b/target/executable/multiqc_custom_biotype/.config.vsh.yaml index b4e6370..0e89ef4 100644 --- a/target/executable/multiqc_custom_biotype/.config.vsh.yaml +++ b/target/executable/multiqc_custom_biotype/.config.vsh.yaml @@ -170,8 +170,8 @@ build_info: output: "target/executable/multiqc_custom_biotype" executable: "target/executable/multiqc_custom_biotype/multiqc_custom_biotype" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/multiqc_custom_biotype/multiqc_custom_biotype b/target/executable/multiqc_custom_biotype/multiqc_custom_biotype index d7207e4..70250cd 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="2024-12-02T15:00:00Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="59cbb30eecf218c0572104f849ab542423f0e590" +LABEL org.opencontainers.image.created="2024-12-03T05:47:40Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="3ee9ba76ca2112681c41468800aab2fa38cdf453" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/picard_markduplicates/.config.vsh.yaml b/target/executable/picard_markduplicates/.config.vsh.yaml index e5810da..3191387 100644 --- a/target/executable/picard_markduplicates/.config.vsh.yaml +++ b/target/executable/picard_markduplicates/.config.vsh.yaml @@ -212,8 +212,8 @@ build_info: output: "target/executable/picard_markduplicates" executable: "target/executable/picard_markduplicates/picard_markduplicates" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/picard_markduplicates/picard_markduplicates b/target/executable/picard_markduplicates/picard_markduplicates index 676ba63..7be011a 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="2024-12-02T14:59:58Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="59cbb30eecf218c0572104f849ab542423f0e590" +LABEL org.opencontainers.image.created="2024-12-03T05:47:37Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="3ee9ba76ca2112681c41468800aab2fa38cdf453" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/prepare_multiqc_input/.config.vsh.yaml b/target/executable/prepare_multiqc_input/.config.vsh.yaml index 011545b..41ce82a 100644 --- a/target/executable/prepare_multiqc_input/.config.vsh.yaml +++ b/target/executable/prepare_multiqc_input/.config.vsh.yaml @@ -417,8 +417,8 @@ build_info: output: "target/executable/prepare_multiqc_input" executable: "target/executable/prepare_multiqc_input/prepare_multiqc_input" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/prepare_multiqc_input/prepare_multiqc_input b/target/executable/prepare_multiqc_input/prepare_multiqc_input index 9c64375..1735be5 100755 --- a/target/executable/prepare_multiqc_input/prepare_multiqc_input +++ b/target/executable/prepare_multiqc_input/prepare_multiqc_input @@ -558,9 +558,9 @@ 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="2024-12-02T14:59:57Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="59cbb30eecf218c0572104f849ab542423f0e590" +LABEL org.opencontainers.image.created="2024-12-03T05:47:36Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="3ee9ba76ca2112681c41468800aab2fa38cdf453" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/preprocess_transcripts_fasta/.config.vsh.yaml b/target/executable/preprocess_transcripts_fasta/.config.vsh.yaml index 1f030e5..aa8afae 100644 --- a/target/executable/preprocess_transcripts_fasta/.config.vsh.yaml +++ b/target/executable/preprocess_transcripts_fasta/.config.vsh.yaml @@ -143,8 +143,8 @@ build_info: output: "target/executable/preprocess_transcripts_fasta" executable: "target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta b/target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta index 3da39d9..b1c9039 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="2024-12-02T14:59:59Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="59cbb30eecf218c0572104f849ab542423f0e590" +LABEL org.opencontainers.image.created="2024-12-03T05:47:38Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="3ee9ba76ca2112681c41468800aab2fa38cdf453" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/preseq_lcextrap/.config.vsh.yaml b/target/executable/preseq_lcextrap/.config.vsh.yaml index 10e4088..65e7496 100644 --- a/target/executable/preseq_lcextrap/.config.vsh.yaml +++ b/target/executable/preseq_lcextrap/.config.vsh.yaml @@ -196,8 +196,8 @@ build_info: output: "target/executable/preseq_lcextrap" executable: "target/executable/preseq_lcextrap/preseq_lcextrap" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/preseq_lcextrap/preseq_lcextrap b/target/executable/preseq_lcextrap/preseq_lcextrap index 6fadd9e..5783914 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="2024-12-02T14:59:58Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="59cbb30eecf218c0572104f849ab542423f0e590" +LABEL org.opencontainers.image.created="2024-12-03T05:47:37Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="3ee9ba76ca2112681c41468800aab2fa38cdf453" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/rsem_merge_counts/.config.vsh.yaml b/target/executable/rsem_merge_counts/.config.vsh.yaml index c748eaf..02c3b07 100644 --- a/target/executable/rsem_merge_counts/.config.vsh.yaml +++ b/target/executable/rsem_merge_counts/.config.vsh.yaml @@ -186,8 +186,8 @@ build_info: output: "target/executable/rsem_merge_counts" executable: "target/executable/rsem_merge_counts/rsem_merge_counts" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/rsem_merge_counts/rsem_merge_counts b/target/executable/rsem_merge_counts/rsem_merge_counts index 8070d4d..0706cec 100755 --- a/target/executable/rsem_merge_counts/rsem_merge_counts +++ b/target/executable/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_merge_counts" -LABEL org.opencontainers.image.created="2024-12-02T15:00:00Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="59cbb30eecf218c0572104f849ab542423f0e590" +LABEL org.opencontainers.image.created="2024-12-03T05:47:39Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="3ee9ba76ca2112681c41468800aab2fa38cdf453" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml b/target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml index e05db05..46a50d6 100644 --- a/target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml @@ -265,8 +265,8 @@ build_info: output: "target/executable/rseqc/rseqc_junctionannotation" executable: "target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation b/target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation index 66dddcb..3cabce9 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="2024-12-02T14:59:59Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="59cbb30eecf218c0572104f849ab542423f0e590" +LABEL org.opencontainers.image.created="2024-12-03T05:47:38Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="3ee9ba76ca2112681c41468800aab2fa38cdf453" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_junctionsaturation/.config.vsh.yaml b/target/executable/rseqc/rseqc_junctionsaturation/.config.vsh.yaml index 6778201..1c21eec 100644 --- a/target/executable/rseqc/rseqc_junctionsaturation/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_junctionsaturation/.config.vsh.yaml @@ -254,8 +254,8 @@ build_info: output: "target/executable/rseqc/rseqc_junctionsaturation" executable: "target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation b/target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation index 9d9bacf..c96af79 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="2024-12-02T15:00:00Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="59cbb30eecf218c0572104f849ab542423f0e590" +LABEL org.opencontainers.image.created="2024-12-03T05:47:39Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="3ee9ba76ca2112681c41468800aab2fa38cdf453" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_readdistribution/.config.vsh.yaml b/target/executable/rseqc/rseqc_readdistribution/.config.vsh.yaml index c137a3c..6cde56e 100644 --- a/target/executable/rseqc/rseqc_readdistribution/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_readdistribution/.config.vsh.yaml @@ -167,8 +167,8 @@ build_info: output: "target/executable/rseqc/rseqc_readdistribution" executable: "target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution b/target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution index d42d8ff..8f42a8d 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="2024-12-02T15:00:00Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="59cbb30eecf218c0572104f849ab542423f0e590" +LABEL org.opencontainers.image.created="2024-12-03T05:47:39Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="3ee9ba76ca2112681c41468800aab2fa38cdf453" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_readduplication/.config.vsh.yaml b/target/executable/rseqc/rseqc_readduplication/.config.vsh.yaml index e334ee9..d73ff5d 100644 --- a/target/executable/rseqc/rseqc_readduplication/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_readduplication/.config.vsh.yaml @@ -216,8 +216,8 @@ build_info: output: "target/executable/rseqc/rseqc_readduplication" executable: "target/executable/rseqc/rseqc_readduplication/rseqc_readduplication" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/rseqc/rseqc_readduplication/rseqc_readduplication b/target/executable/rseqc/rseqc_readduplication/rseqc_readduplication index 80f7e0b..2eb43f1 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="2024-12-02T14:59:59Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="59cbb30eecf218c0572104f849ab542423f0e590" +LABEL org.opencontainers.image.created="2024-12-03T05:47:38Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="3ee9ba76ca2112681c41468800aab2fa38cdf453" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_tin/.config.vsh.yaml b/target/executable/rseqc/rseqc_tin/.config.vsh.yaml index 85ccba4..38a0008 100644 --- a/target/executable/rseqc/rseqc_tin/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_tin/.config.vsh.yaml @@ -219,8 +219,8 @@ build_info: output: "target/executable/rseqc/rseqc_tin" executable: "target/executable/rseqc/rseqc_tin/rseqc_tin" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/rseqc/rseqc_tin/rseqc_tin b/target/executable/rseqc/rseqc_tin/rseqc_tin index 6bbd491..bb03524 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="2024-12-02T15:00:00Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="59cbb30eecf218c0572104f849ab542423f0e590" +LABEL org.opencontainers.image.created="2024-12-03T05:47:39Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="3ee9ba76ca2112681c41468800aab2fa38cdf453" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/sortmerna/.config.vsh.yaml b/target/executable/sortmerna/.config.vsh.yaml index 202af71..5c93adc 100644 --- a/target/executable/sortmerna/.config.vsh.yaml +++ b/target/executable/sortmerna/.config.vsh.yaml @@ -197,8 +197,8 @@ build_info: output: "target/executable/sortmerna" executable: "target/executable/sortmerna/sortmerna" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/sortmerna/sortmerna b/target/executable/sortmerna/sortmerna index 50c2088..f7a5203 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="2024-12-02T15:00:03Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="59cbb30eecf218c0572104f849ab542423f0e590" +LABEL org.opencontainers.image.created="2024-12-03T05:47:43Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="3ee9ba76ca2112681c41468800aab2fa38cdf453" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/stringtie/.config.vsh.yaml b/target/executable/stringtie/.config.vsh.yaml index b6a4e7c..71ef8a3 100644 --- a/target/executable/stringtie/.config.vsh.yaml +++ b/target/executable/stringtie/.config.vsh.yaml @@ -221,8 +221,8 @@ build_info: output: "target/executable/stringtie" executable: "target/executable/stringtie/stringtie" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/stringtie/stringtie b/target/executable/stringtie/stringtie index 590fb20..ba11ffa 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="2024-12-02T15:00:03Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="59cbb30eecf218c0572104f849ab542423f0e590" +LABEL org.opencontainers.image.created="2024-12-03T05:47:43Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="3ee9ba76ca2112681c41468800aab2fa38cdf453" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/summarizedexperiment/.config.vsh.yaml b/target/executable/summarizedexperiment/.config.vsh.yaml index eabb6e8..2a8ca91 100644 --- a/target/executable/summarizedexperiment/.config.vsh.yaml +++ b/target/executable/summarizedexperiment/.config.vsh.yaml @@ -204,8 +204,8 @@ build_info: output: "target/executable/summarizedexperiment" executable: "target/executable/summarizedexperiment/summarizedexperiment" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/summarizedexperiment/summarizedexperiment b/target/executable/summarizedexperiment/summarizedexperiment index 85b7605..a676fb1 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="2024-12-02T15:00:03Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="59cbb30eecf218c0572104f849ab542423f0e590" +LABEL org.opencontainers.image.created="2024-12-03T05:47:42Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="3ee9ba76ca2112681c41468800aab2fa38cdf453" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/tx2gene/.config.vsh.yaml b/target/executable/tx2gene/.config.vsh.yaml index acf38b6..4dd3a62 100644 --- a/target/executable/tx2gene/.config.vsh.yaml +++ b/target/executable/tx2gene/.config.vsh.yaml @@ -190,8 +190,8 @@ build_info: output: "target/executable/tx2gene" executable: "target/executable/tx2gene/tx2gene" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/tx2gene/tx2gene b/target/executable/tx2gene/tx2gene index 8ba2397..949d654 100755 --- a/target/executable/tx2gene/tx2gene +++ b/target/executable/tx2gene/tx2gene @@ -483,9 +483,9 @@ 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="2024-12-02T15:00:01Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="59cbb30eecf218c0572104f849ab542423f0e590" +LABEL org.opencontainers.image.created="2024-12-03T05:47:41Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="3ee9ba76ca2112681c41468800aab2fa38cdf453" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/tximport/.config.vsh.yaml b/target/executable/tximport/.config.vsh.yaml index 03b6595..e294453 100644 --- a/target/executable/tximport/.config.vsh.yaml +++ b/target/executable/tximport/.config.vsh.yaml @@ -256,8 +256,8 @@ build_info: output: "target/executable/tximport" executable: "target/executable/tximport/tximport" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/tximport/tximport b/target/executable/tximport/tximport index 7a46325..5c0d5d6 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="2024-12-02T15:00:02Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="59cbb30eecf218c0572104f849ab542423f0e590" +LABEL org.opencontainers.image.created="2024-12-03T05:47:41Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="3ee9ba76ca2112681c41468800aab2fa38cdf453" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/ucsc/bedclip/.config.vsh.yaml b/target/executable/ucsc/bedclip/.config.vsh.yaml index 16fe375..9159370 100644 --- a/target/executable/ucsc/bedclip/.config.vsh.yaml +++ b/target/executable/ucsc/bedclip/.config.vsh.yaml @@ -169,8 +169,8 @@ build_info: output: "target/executable/ucsc/bedclip" executable: "target/executable/ucsc/bedclip/bedclip" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/ucsc/bedclip/bedclip b/target/executable/ucsc/bedclip/bedclip index 22a0616..1ced724 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="2024-12-02T15:00:01Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="59cbb30eecf218c0572104f849ab542423f0e590" +LABEL org.opencontainers.image.created="2024-12-03T05:47:40Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="3ee9ba76ca2112681c41468800aab2fa38cdf453" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/ucsc/bedgraphtobigwig/.config.vsh.yaml b/target/executable/ucsc/bedgraphtobigwig/.config.vsh.yaml index 6529242..1bb135b 100644 --- a/target/executable/ucsc/bedgraphtobigwig/.config.vsh.yaml +++ b/target/executable/ucsc/bedgraphtobigwig/.config.vsh.yaml @@ -169,8 +169,8 @@ build_info: output: "target/executable/ucsc/bedgraphtobigwig" executable: "target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig b/target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig index 36b6c67..402a308 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="2024-12-02T15:00:01Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="59cbb30eecf218c0572104f849ab542423f0e590" +LABEL org.opencontainers.image.created="2024-12-03T05:47:40Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="3ee9ba76ca2112681c41468800aab2fa38cdf453" LABEL org.opencontainers.image.version="add-labels" 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 745fb74..0c1c3fb 100644 --- a/target/executable/workflows/genome_alignment_and_quant/.config.vsh.yaml +++ b/target/executable/workflows/genome_alignment_and_quant/.config.vsh.yaml @@ -595,8 +595,8 @@ 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: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@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 09c0b34..0654ad1 100644 --- a/target/executable/workflows/merge_quant_results/.config.vsh.yaml +++ b/target/executable/workflows/merge_quant_results/.config.vsh.yaml @@ -283,8 +283,8 @@ 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: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@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 09035c1..966c551 100644 --- a/target/executable/workflows/post_processing/.config.vsh.yaml +++ b/target/executable/workflows/post_processing/.config.vsh.yaml @@ -482,8 +482,8 @@ build_info: output: "target/executable/workflows/post_processing" executable: "target/executable/workflows/post_processing/post_processing" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@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 824b2fd..6cbe415 100644 --- a/target/executable/workflows/pre_processing/.config.vsh.yaml +++ b/target/executable/workflows/pre_processing/.config.vsh.yaml @@ -637,8 +637,8 @@ build_info: output: "target/executable/workflows/pre_processing" executable: "target/executable/workflows/pre_processing/pre_processing" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" dependencies: - "target/dependencies/vsh/vsh/biobox/main/nextflow/fastqc" - "target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_extract" diff --git a/target/executable/workflows/prepare_genome/.config.vsh.yaml b/target/executable/workflows/prepare_genome/.config.vsh.yaml index c8afb41..da7bec3 100644 --- a/target/executable/workflows/prepare_genome/.config.vsh.yaml +++ b/target/executable/workflows/prepare_genome/.config.vsh.yaml @@ -507,8 +507,8 @@ build_info: output: "target/executable/workflows/prepare_genome" executable: "target/executable/workflows/prepare_genome/prepare_genome" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/gunzip" - "target/dependencies/vsh/vsh/biobox/main/nextflow/gffread" diff --git a/target/executable/workflows/prepare_genome/prepare_genome b/target/executable/workflows/prepare_genome/prepare_genome index 303644a..54e0ab8 100755 --- a/target/executable/workflows/prepare_genome/prepare_genome +++ b/target/executable/workflows/prepare_genome/prepare_genome @@ -1171,291 +1171,319 @@ cat > "\$tempscript" << 'VIASHMAIN' //// VIASH END workflow run_wf { - take: - input_ch + take: + input_ch - main: - output_ch = input_ch - - // Uncompress fasta - | gunzip.run ( - fromState: [ "input": "fasta" ], - toState: [ "fasta": "output" ], - key: "gunzip_fasta", - args: [ output: "reference_genome.fasta" ] - ) + main: + output_ch = input_ch - // uncompress gtf - | gunzip.run ( - runIf: {id, state -> state.gtf}, - fromState: [ "input": "gtf" ], - toState: [ "gtf": "output" ], - key: "gunzip_gtf", - args: [output: "gene_annotation.gtf"] - ) + // Uncompress fasta + | gunzip.run ( + fromState: [ "input": "fasta" ], + toState: [ "fasta": "output" ], + key: "gunzip_fasta", + args: [ output: "reference_genome.fasta" ], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) - // uncompress gff - | gunzip.run ( - runIf: {id, state -> !state.gtf && state.gff}, - fromState: [ "input": "gff" ], - toState: [ "gff": "output" ], - key: "gunzip_gff", - args: [output: "gene_annotation.gff"] - ) + // uncompress gtf + | gunzip.run ( + runIf: {id, state -> state.gtf}, + fromState: [ "input": "gtf" ], + toState: [ "gtf": "output" ], + key: "gunzip_gtf", + args: [output: "gene_annotation.gtf"], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) - // gff to gtf - | gffread.run ( - runIf: {id, state -> !state.gtf && state.gff}, - fromState: [ - "input": "gff", - "genome": "fasta" - ], - toState: [ "gtf": "outfile" ], - args: [ - outfile: "gene_annotation.gtf", - gtf_output: true, - keep_attrs: true, - keep_exon_attrs: true - ] - ) + // uncompress gff + | gunzip.run ( + runIf: {id, state -> !state.gtf && state.gff}, + fromState: [ "input": "gff" ], + toState: [ "gff": "output" ], + key: "gunzip_gff", + args: [output: "gene_annotation.gff"], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) - | gtf_filter.run( - runIf: {id, state -> state.gtf && state.filter_gtf}, - fromState: [ - "fasta": "fasta", - "gtf": "gtf" - ], - toState: [ "gtf": "filtered_gtf" ], - args: [filtered_gtf: "gene_annotation.gtf"] - ) + // gff to gtf + | gffread.run ( + runIf: {id, state -> !state.gtf && state.gff}, + fromState: [ + "input": "gff", + "genome": "fasta" + ], + toState: [ "gtf": "outfile" ], + args: [ + outfile: "gene_annotation.gtf", + gtf_output: true, + keep_attrs: true, + keep_exon_attrs: true + ], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) - // uncompress additional fasta - | gunzip.run ( - runIf: {id, state -> state.additional_fasta}, - fromState: [ "input": "additional_fasta" ], - toState: [ "additional_fasta": "output" ], - key: "gunzip_additional_fasta", - args: [output: "additional.fasta"] - ) + | gtf_filter.run( + runIf: {id, state -> state.gtf && state.filter_gtf}, + fromState: [ + "fasta": "fasta", + "gtf": "gtf" + ], + toState: [ "gtf": "filtered_gtf" ], + args: [filtered_gtf: "gene_annotation.gtf"], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) - // concatenate additional fasta - | cat_additional_fasta.run ( - runIf: {id, state -> state.additional_fasta}, - fromState: [ - "fasta": "fasta", - "gtf": "gtf", - "additional_fasta": "additional_fasta", - "biotype": "biotype" - ], - toState: [ - "fasta": "fasta_output", - "gtf": "gtf_output" - ], - args: [ - fasta_output: "genome_additional.fasta", - gtf_output: "genome_additional.gtf" - ] - ) + // uncompress additional fasta + | gunzip.run ( + runIf: {id, state -> state.additional_fasta}, + fromState: [ "input": "additional_fasta" ], + toState: [ "additional_fasta": "output" ], + key: "gunzip_additional_fasta", + args: [output: "additional.fasta"], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) - // uncompress bed file - | gunzip.run ( - runIf: {id, state -> state.gene_bed}, - fromState: [ "input": "gene_bed" ], - toState: [ "gene_bed": "output" ], - key: "gunzip_gene_bed", - args: [output: "genome_additional.bed"] - ) + // concatenate additional fasta + | cat_additional_fasta.run ( + runIf: {id, state -> state.additional_fasta}, + fromState: [ + "fasta": "fasta", + "gtf": "gtf", + "additional_fasta": "additional_fasta", + "biotype": "biotype" + ], + toState: [ + "fasta": "fasta_output", + "gtf": "gtf_output" + ], + args: [ + fasta_output: "genome_additional.fasta", + gtf_output: "genome_additional.gtf" + ], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) - // gtf to bed - | gtf2bed.run ( - runIf: { id, state -> !state.gene_bed}, - fromState: [ "gtf": "gtf" ], - toState: [ "gene_bed": "bed_output" ], - args: [bed_output: "genome_additional.bed"] - ) + // uncompress bed file + | gunzip.run ( + runIf: {id, state -> state.gene_bed}, + fromState: [ "input": "gene_bed" ], + toState: [ "gene_bed": "output" ], + key: "gunzip_gene_bed", + args: [output: "genome_additional.bed"], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) - // uncompress transcript fasta - | gunzip.run ( - runIf: {id, state -> state.transcript_fasta}, - fromState: [ "input": "transcript_fasta" ], - toState: [ "transcript_fasta": "output" ], - key: "transcript_fasta", - args: [output: "transcriptome.fasta"] - ) + // gtf to bed + | gtf2bed.run ( + runIf: { id, state -> !state.gene_bed}, + fromState: [ "gtf": "gtf" ], + toState: [ "gene_bed": "bed_output" ], + args: [bed_output: "genome_additional.bed"], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) - // preprocess transcripts fasta if gtf is in gencode format - | preprocess_transcripts_fasta.run ( - runIf: {id, state -> state.transcript_fasta && state.gencode}, - fromState: [ "transcript_fasta": "transcript_fasta" ], - toState: [ "transcript_fasta": "output" ], - args: [output: "transcriptome.fasta"] - ) + // uncompress transcript fasta + | gunzip.run ( + runIf: {id, state -> state.transcript_fasta}, + fromState: [ "input": "transcript_fasta" ], + toState: [ "transcript_fasta": "output" ], + key: "transcript_fasta", + args: [output: "transcriptome.fasta"], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) - // make transcript FASTA if not provided - | rsem_prepare_reference.run ( - runIf: {id, state -> !state.transcript_fasta}, - fromState: [ - "reference_fasta_files": "fasta", - "gtf": "gtf" - ], - toState: [ "make_transcript_fasta_output": "output" ], - key: "make_transcript_fasta", - args: [reference_name: "genome"] - ) - | map { id, state -> - def transcript_fasta = (!state.transcript_fasta) ? - state.make_transcript_fasta_output.listFiles().find{it.name == "genome.transcripts.fa"} : - state.transcript_fasta - [ id, state + [transcript_fasta: transcript_fasta] ] - } + // preprocess transcripts fasta if gtf is in gencode format + | preprocess_transcripts_fasta.run ( + runIf: {id, state -> state.transcript_fasta && state.gencode}, + fromState: [ "transcript_fasta": "transcript_fasta" ], + toState: [ "transcript_fasta": "output" ], + args: [output: "transcriptome.fasta"], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) - // chromosome size and fai index - | getchromsizes.run ( - fromState: [ "fasta": "fasta" ], - toState: [ - "fai": "fai", - "sizes": "sizes" - ], - key: "chromsizes", - args: [ - fai: "genome_additional.fasta.fai", - sizes: "genome_additional.fasta.sizes" - ] - ) - - // untar bbsplit index, if available - | untar.run ( - runIf: {id, state -> state.bbsplit_index}, - fromState: [ "input": "bbsplit_index" ], - toState: [ "bbsplit_index": "output" ], - key: "untar_bbsplit_index", - args: [output: "BBSplit_index"] - ) + // make transcript FASTA if not provided + | rsem_prepare_reference.run ( + runIf: {id, state -> !state.transcript_fasta}, + fromState: [ + "reference_fasta_files": "fasta", + "gtf": "gtf" + ], + toState: [ "make_transcript_fasta_output": "output" ], + key: "make_transcript_fasta", + args: [reference_name: "genome"], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) + | map { id, state -> + def transcript_fasta = (!state.transcript_fasta) ? + state.make_transcript_fasta_output.listFiles().find{it.name == "genome.transcripts.fa"} : + state.transcript_fasta + [ id, state + [transcript_fasta: transcript_fasta] ] + } - | map {id, state -> - def ref = [state.fasta] + state.bbsplit_fasta_list - [id, state + [bbsplit_ref: ref] ] + // chromosome size and fai index + | getchromsizes.run ( + fromState: [ "fasta": "fasta" ], + toState: [ + "fai": "fai", + "sizes": "sizes" + ], + key: "chromsizes", + args: [ + fai: "genome_additional.fasta.fai", + sizes: "genome_additional.fasta.sizes" + ], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) + + // untar bbsplit index, if available + | untar.run ( + runIf: {id, state -> state.bbsplit_index}, + fromState: [ "input": "bbsplit_index" ], + toState: [ "bbsplit_index": "output" ], + key: "untar_bbsplit_index", + directives: [ label: [ "lowmem", "midcpu" ] ] + ) + + | map { id, state -> + // Check if bbsplit_fasta_list is defined + if (state.bbsplit_fasta_list) { + def ref = [state.fasta] + state.bbsplit_fasta_list + } else { + def ref = [state.fasta] } + [id, state + [bbsplit_ref: ref] ] + } - // create bbsplit index, if not already availble - | bbmap_bbsplit.run ( - runIf: {id, state -> !state.skip_bbsplit && !state.bbsplit_index}, - fromState: ["ref": "bbsplit_ref"], - toState: [ "bbsplit_index": "index" ], - args: [ - only_build_index: true, - index: "BBSplit_index" - ], - key: "generate_bbsplit_index" - ) + | niceView() - // Uncompress STAR index or generate from scratch if required - | untar.run ( - runIf: {id, state -> state.star_index}, - fromState: [ "input": "star_index" ], - toState: [ "star_index": "output" ], - key: "untar_star_index", - args: [output: "STAR_index"] - ) - - // TODO: Add to viah-hub or adapt star_align_reads to enable the generateGenome runMode - | star_genome_generate.run ( - runIf: {id, state -> !state.star_index && !state.skip_alignment}, - fromState: [ - "genome_fasta_files": "fasta", - "sjdb_gtf_file": "gtf", - "sjdb_gtf_feature_exon": "star_sjdb_gtf_feature_exon" - ], - toState: [ "star_index": "index" ], - key: "generate_star_index", - args: [index: "STAR_index"] - ) + // create bbsplit index, if not already available + | bbmap_bbsplit.run ( + runIf: {id, state -> !state.skip_bbsplit && !state.bbsplit_index}, + fromState: ["ref": "bbsplit_ref"], + toState: [ "bbsplit_index": "index" ], + args: [ + only_build_index: true, + index: "BBSplit_index" + ], + key: "generate_bbsplit_index" + ) - // Uncompress RSEM index or generate from scratch if required - | untar.run ( - runIf: {id, state -> state.rsem_index}, - fromState: [ "input": "rsem_index" ], - toState: [ "rsem_index": "output" ], - key: "untar_rsem_index", - args: [output: "RSEM_index"] - ) + // Uncompress STAR index or generate from scratch if required + | untar.run ( + runIf: {id, state -> state.star_index}, + fromState: [ "input": "star_index" ], + toState: [ "star_index": "output" ], + key: "untar_star_index", + args: [output: "STAR_index"], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) - | rsem_prepare_reference.run ( - runIf: {id, state -> !state.rsem_index && state.aligner == 'star_rsem'}, - fromState: [ - "reference_fasta_files": "fasta", - "gtf": "gtf" - ], - toState: [ "rsem_index": "output" ], - key: "generate_rsem_index", - args: [reference_name: "genome"] - ) - - // TODO: Uncompress HISAT2 index or generate from scratch if required + // TODO: Add to viah-hub or adapt star_align_reads to enable the generateGenome runMode + | star_genome_generate.run ( + runIf: {id, state -> !state.star_index && !state.skip_alignment}, + fromState: [ + "genome_fasta_files": "fasta", + "sjdb_gtf_file": "gtf", + "sjdb_gtf_feature_exon": "star_sjdb_gtf_feature_exon" + ], + toState: [ "star_index": "index" ], + key: "generate_star_index", + args: [index: "STAR_index"], + directives: [ label: [ "highmem", "highcpu" ] ] + ) - // Uncompress Salmon index or generate from scratch if required - | untar.run ( - runIf: {id, state -> state.salmon_index}, - fromState: [ "input": "salmon_index" ], - toState: [ "salmon_index": "output" ], - key: "untar_salmon_index", - args: [output: "Salmon_index"] - ) + // Uncompress RSEM index or generate from scratch if required + | untar.run ( + runIf: {id, state -> state.rsem_index}, + fromState: [ "input": "rsem_index" ], + toState: [ "rsem_index": "output" ], + key: "untar_rsem_index", + args: [output: "RSEM_index"], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) - | salmon_index.run ( - runIf: {id, state -> (state.aligner == 'star_salmon' || state.pseudo_aligner == "salmon") && !state.salmon_index}, - fromState: [ - "genome": "fasta", - "transcripts": "transcript_fasta", - "kmer_len": "pseudo_aligner_kmer_size", - "gencode": "gencode" - ], - toState: [ "salmon_index": "index" ], - key: "generate_salmon_index", - args: [index: "Salmon_index"] - ) + | rsem_prepare_reference.run ( + runIf: {id, state -> !state.rsem_index && state.aligner == 'star_rsem'}, + fromState: [ + "reference_fasta_files": "fasta", + "gtf": "gtf" + ], + toState: [ "rsem_index": "output" ], + key: "generate_rsem_index", + args: [reference_name: "genome"], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) + + // TODO: Uncompress HISAT2 index or generate from scratch if required - // Uncompress Kallisto index or generate from scratch if required - | untar.run ( - runIf: {id, state -> state.kallisto_index}, - fromState: [ "input": "kallisto_index" ], - toState: [ "kallisto_index": "output" ], - key: "untar_kallisto_index", - args: [output: "Kallisto_index"] - ) + // Uncompress Salmon index or generate from scratch if required + | untar.run ( + runIf: {id, state -> state.salmon_index}, + fromState: [ "input": "salmon_index" ], + toState: [ "salmon_index": "output" ], + key: "untar_salmon_index", + args: [output: "Salmon_index"], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) - | kallisto_index.run( - runIf: {id, state -> state.pseudo_aligner == "kallisto" && !state.kallisto_index}, - fromState: [ - "input": "transcript_fasta", - "kmer_size": "pseudo_aligner_kmer_size" - ], - toState: [ "kallisto_index": "index" ], - key: "generate_kallisto_index", - args: [index: "Kallisto_index"] - ) + | salmon_index.run ( + runIf: {id, state -> (state.aligner == 'star_salmon' || state.pseudo_aligner == "salmon") && !state.salmon_index}, + fromState: [ + "genome": "fasta", + "transcripts": "transcript_fasta", + "kmer_len": "pseudo_aligner_kmer_size", + "gencode": "gencode" + ], + toState: [ "salmon_index": "index" ], + key: "generate_salmon_index", + args: [index: "Salmon_index"], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) - | map { id, state -> - def mod_state = state.findAll { key, value -> value instanceof java.nio.file.Path && value.exists() } - [ id, mod_state ] - } + // Uncompress Kallisto index or generate from scratch if required + | untar.run ( + runIf: {id, state -> state.kallisto_index}, + fromState: [ "input": "kallisto_index" ], + toState: [ "kallisto_index": "output" ], + key: "untar_kallisto_index", + args: [output: "Kallisto_index"], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) - | setState ( - "fasta_uncompressed": "fasta", - "gtf_uncompressed": "gtf", - "transcript_fasta_uncompressed": "transcript_fasta", - "gene_bed_uncompressed": "gene_bed", - "star_index_uncompressed": "star_index", - "salmon_index_uncompressed": "salmon_index", - "kallisto_index_uncompressed": "kallisto_index", - "bbsplit_index_uncompressed": "bbsplit_index", - "rsem_index_uncompressed": "rsem_index", - "chrom_sizes": "sizes", - "fai": "fai" - ) + | kallisto_index.run( + runIf: {id, state -> state.pseudo_aligner == "kallisto" && !state.kallisto_index}, + fromState: [ + "input": "transcript_fasta", + "kmer_size": "pseudo_aligner_kmer_size" + ], + toState: [ "kallisto_index": "index" ], + key: "generate_kallisto_index", + args: [index: "Kallisto_index"], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) - emit: - output_ch + | map { id, state -> + def mod_state = state.findAll { key, value -> value instanceof java.nio.file.Path && value.exists() } + [ id, mod_state ] + } + + | setState ( + "fasta_uncompressed": "fasta", + "gtf_uncompressed": "gtf", + "transcript_fasta_uncompressed": "transcript_fasta", + "gene_bed_uncompressed": "gene_bed", + "star_index_uncompressed": "star_index", + "salmon_index_uncompressed": "salmon_index", + "kallisto_index_uncompressed": "kallisto_index", + "bbsplit_index_uncompressed": "bbsplit_index", + "rsem_index_uncompressed": "rsem_index", + "chrom_sizes": "sizes", + "fai": "fai" + ) + + emit: + output_ch } VIASHMAIN nextflow run . -main-script "\$tempscript" & 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 86554e9..2c7f43c 100644 --- a/target/executable/workflows/pseudo_alignment_and_quant/.config.vsh.yaml +++ b/target/executable/workflows/pseudo_alignment_and_quant/.config.vsh.yaml @@ -290,8 +290,8 @@ 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: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" dependencies: - "target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant" - "target/dependencies/vsh/vsh/biobox/main/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 8b035e2..25281a3 100644 --- a/target/executable/workflows/quality_control/.config.vsh.yaml +++ b/target/executable/workflows/quality_control/.config.vsh.yaml @@ -1561,8 +1561,8 @@ build_info: output: "target/executable/workflows/quality_control" executable: "target/executable/workflows/quality_control/quality_control" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" dependencies: - "target/dependencies/vsh/vsh/biobox/main/nextflow/rseqc/rseqc_bamstat" - "target/dependencies/vsh/vsh/biobox/main/nextflow/rseqc/rseqc_inferexperiment" diff --git a/target/executable/workflows/rnaseq/.config.vsh.yaml b/target/executable/workflows/rnaseq/.config.vsh.yaml index 4efa46e..ca6c7aa 100644 --- a/target/executable/workflows/rnaseq/.config.vsh.yaml +++ b/target/executable/workflows/rnaseq/.config.vsh.yaml @@ -521,11 +521,6 @@ argument_groups: direction: "input" multiple: false multiple_sep: ";" - - type: "boolean_true" - name: "--skip_bbsplit" - description: "Skip BBSplit for removal of non-reference genome reads." - info: null - direction: "input" - type: "boolean" name: "--skip_umi_extract" description: "Skip umi_tools extract step." @@ -2064,8 +2059,8 @@ build_info: output: "target/executable/workflows/rnaseq" executable: "target/executable/workflows/rnaseq/rnaseq" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@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 ecc206e..81a4145 100755 --- a/target/executable/workflows/rnaseq/rnaseq +++ b/target/executable/workflows/rnaseq/rnaseq @@ -441,10 +441,6 @@ function ViashHelp { echo " default: false" echo " Skip the adapter trimming step." echo "" - echo " --skip_bbsplit" - echo " type: boolean_true" - echo " Skip BBSplit for removal of non-reference genome reads." - echo "" echo " --skip_umi_extract" echo " type: boolean" echo " default: false" @@ -1583,11 +1579,6 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_SKIP_TRIMMING=$(ViashRemoveFlags "$1") shift 1 ;; - --skip_bbsplit) - [ -n "$VIASH_PAR_SKIP_BBSPLIT" ] && ViashError Bad arguments for option \'--skip_bbsplit\': \'$VIASH_PAR_SKIP_BBSPLIT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_SKIP_BBSPLIT=true - shift 1 - ;; --skip_umi_extract) [ -n "$VIASH_PAR_SKIP_UMI_EXTRACT" ] && ViashError Bad arguments for option \'--skip_umi_extract\': \'$VIASH_PAR_SKIP_UMI_EXTRACT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 VIASH_PAR_SKIP_UMI_EXTRACT="$2" @@ -3175,9 +3166,6 @@ fi if [ -z ${VIASH_PAR_SKIP_TRIMMING+x} ]; then VIASH_PAR_SKIP_TRIMMING="false" fi -if [ -z ${VIASH_PAR_SKIP_BBSPLIT+x} ]; then - VIASH_PAR_SKIP_BBSPLIT="false" -fi if [ -z ${VIASH_PAR_SKIP_UMI_EXTRACT+x} ]; then VIASH_PAR_SKIP_UMI_EXTRACT="false" fi @@ -3749,12 +3737,6 @@ if [[ -n "$VIASH_PAR_SKIP_TRIMMING" ]]; then exit 1 fi fi -if [[ -n "$VIASH_PAR_SKIP_BBSPLIT" ]]; then - if ! [[ "$VIASH_PAR_SKIP_BBSPLIT" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then - ViashError '--skip_bbsplit' has to be a boolean_true. Use "--help" to get more information on the parameters. - exit 1 - fi -fi if [[ -n "$VIASH_PAR_SKIP_UMI_EXTRACT" ]]; then if ! [[ "$VIASH_PAR_SKIP_UMI_EXTRACT" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then ViashError '--skip_umi_extract' has to be a boolean. Use "--help" to get more information on the parameters. @@ -4415,7 +4397,8 @@ workflow run_wf { // splicesites: list.collect { id, state -> state.splicesites }.unique()[0], // hisat2_index: list.collect { id, state -> state.hisat2_index }.unique()[0], bbsplit_index: list.collect { id, state -> state.bbsplit_index }.unique()[0], - skip_bbsplit: list.collect { id, state -> state.skip_bbsplit }.unique()[0], + // See: + skip_bbsplit: true, // list.collect { id, state -> state.skip_bbsplit }.unique()[0], skip_alignment: list.collect { id, state -> state.skip_alignment }.unique()[0], gencode: list.collect { id, state -> state.gencode }.unique()[0], biotype: list.collect { id, state -> state.biotype }.unique()[0], diff --git a/target/nextflow/bedtools_genomecov/.config.vsh.yaml b/target/nextflow/bedtools_genomecov/.config.vsh.yaml index 21d08a8..c591971 100644 --- a/target/nextflow/bedtools_genomecov/.config.vsh.yaml +++ b/target/nextflow/bedtools_genomecov/.config.vsh.yaml @@ -183,8 +183,8 @@ build_info: output: "target/nextflow/bedtools_genomecov" executable: "target/nextflow/bedtools_genomecov/main.nf" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/bedtools_genomecov/main.nf b/target/nextflow/bedtools_genomecov/main.nf index 45a8c81..1b0a19a 100644 --- a/target/nextflow/bedtools_genomecov/main.nf +++ b/target/nextflow/bedtools_genomecov/main.nf @@ -3039,8 +3039,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/bedtools_genomecov", "viash_version" : "0.9.0", - "git_commit" : "59cbb30eecf218c0572104f849ab542423f0e590", - "git_remote" : "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + "git_commit" : "3ee9ba76ca2112681c41468800aab2fa38cdf453", + "git_remote" : "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@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 91cf19f..5b1de79 100644 --- a/target/nextflow/cat_additional_fasta/.config.vsh.yaml +++ b/target/nextflow/cat_additional_fasta/.config.vsh.yaml @@ -187,8 +187,8 @@ build_info: output: "target/nextflow/cat_additional_fasta" executable: "target/nextflow/cat_additional_fasta/main.nf" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/cat_additional_fasta/main.nf b/target/nextflow/cat_additional_fasta/main.nf index b7ac3d4..191a5bd 100644 --- a/target/nextflow/cat_additional_fasta/main.nf +++ b/target/nextflow/cat_additional_fasta/main.nf @@ -3040,8 +3040,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/cat_additional_fasta", "viash_version" : "0.9.0", - "git_commit" : "59cbb30eecf218c0572104f849ab542423f0e590", - "git_remote" : "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + "git_commit" : "3ee9ba76ca2112681c41468800aab2fa38cdf453", + "git_remote" : "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@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 e905bcf..ee7e4d1 100644 --- a/target/nextflow/cat_fastq/.config.vsh.yaml +++ b/target/nextflow/cat_fastq/.config.vsh.yaml @@ -174,8 +174,8 @@ build_info: output: "target/nextflow/cat_fastq" executable: "target/nextflow/cat_fastq/main.nf" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/cat_fastq/main.nf b/target/nextflow/cat_fastq/main.nf index 3179c18..be66b5c 100644 --- a/target/nextflow/cat_fastq/main.nf +++ b/target/nextflow/cat_fastq/main.nf @@ -3031,8 +3031,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/cat_fastq", "viash_version" : "0.9.0", - "git_commit" : "59cbb30eecf218c0572104f849ab542423f0e590", - "git_remote" : "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + "git_commit" : "3ee9ba76ca2112681c41468800aab2fa38cdf453", + "git_remote" : "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@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 3806a77..cb03e5e 100644 --- a/target/nextflow/deseq2_qc/.config.vsh.yaml +++ b/target/nextflow/deseq2_qc/.config.vsh.yaml @@ -242,8 +242,8 @@ build_info: output: "target/nextflow/deseq2_qc" executable: "target/nextflow/deseq2_qc/main.nf" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/deseq2_qc/main.nf b/target/nextflow/deseq2_qc/main.nf index a1afe9c..ea3d47c 100644 --- a/target/nextflow/deseq2_qc/main.nf +++ b/target/nextflow/deseq2_qc/main.nf @@ -3112,8 +3112,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/deseq2_qc", "viash_version" : "0.9.0", - "git_commit" : "59cbb30eecf218c0572104f849ab542423f0e590", - "git_remote" : "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + "git_commit" : "3ee9ba76ca2112681c41468800aab2fa38cdf453", + "git_remote" : "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@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 9715068..9fe3a69 100644 --- a/target/nextflow/dupradar/.config.vsh.yaml +++ b/target/nextflow/dupradar/.config.vsh.yaml @@ -271,8 +271,8 @@ build_info: output: "target/nextflow/dupradar" executable: "target/nextflow/dupradar/main.nf" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/dupradar/main.nf b/target/nextflow/dupradar/main.nf index 6af612e..807e381 100644 --- a/target/nextflow/dupradar/main.nf +++ b/target/nextflow/dupradar/main.nf @@ -3144,8 +3144,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/dupradar", "viash_version" : "0.9.0", - "git_commit" : "59cbb30eecf218c0572104f849ab542423f0e590", - "git_remote" : "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + "git_commit" : "3ee9ba76ca2112681c41468800aab2fa38cdf453", + "git_remote" : "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@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 7701622..7b2542e 100644 --- a/target/nextflow/getchromsizes/.config.vsh.yaml +++ b/target/nextflow/getchromsizes/.config.vsh.yaml @@ -172,8 +172,8 @@ build_info: output: "target/nextflow/getchromsizes" executable: "target/nextflow/getchromsizes/main.nf" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/getchromsizes/main.nf b/target/nextflow/getchromsizes/main.nf index dfd085d..97fada6 100644 --- a/target/nextflow/getchromsizes/main.nf +++ b/target/nextflow/getchromsizes/main.nf @@ -3021,8 +3021,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/getchromsizes", "viash_version" : "0.9.0", - "git_commit" : "59cbb30eecf218c0572104f849ab542423f0e590", - "git_remote" : "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + "git_commit" : "3ee9ba76ca2112681c41468800aab2fa38cdf453", + "git_remote" : "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@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 e894067..d6a3012 100644 --- a/target/nextflow/gtf2bed/.config.vsh.yaml +++ b/target/nextflow/gtf2bed/.config.vsh.yaml @@ -150,8 +150,8 @@ build_info: output: "target/nextflow/gtf2bed" executable: "target/nextflow/gtf2bed/main.nf" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/gtf2bed/main.nf b/target/nextflow/gtf2bed/main.nf index 5666987..42eaa9e 100644 --- a/target/nextflow/gtf2bed/main.nf +++ b/target/nextflow/gtf2bed/main.nf @@ -3003,8 +3003,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/gtf2bed", "viash_version" : "0.9.0", - "git_commit" : "59cbb30eecf218c0572104f849ab542423f0e590", - "git_remote" : "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + "git_commit" : "3ee9ba76ca2112681c41468800aab2fa38cdf453", + "git_remote" : "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@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 2786815..ed54c0d 100644 --- a/target/nextflow/gtf_filter/.config.vsh.yaml +++ b/target/nextflow/gtf_filter/.config.vsh.yaml @@ -160,8 +160,8 @@ build_info: output: "target/nextflow/gtf_filter" executable: "target/nextflow/gtf_filter/main.nf" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/gtf_filter/main.nf b/target/nextflow/gtf_filter/main.nf index bc6e023..be6a70c 100644 --- a/target/nextflow/gtf_filter/main.nf +++ b/target/nextflow/gtf_filter/main.nf @@ -3011,8 +3011,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/gtf_filter", "viash_version" : "0.9.0", - "git_commit" : "59cbb30eecf218c0572104f849ab542423f0e590", - "git_remote" : "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + "git_commit" : "3ee9ba76ca2112681c41468800aab2fa38cdf453", + "git_remote" : "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@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 90fdeed..c145c2d 100644 --- a/target/nextflow/gunzip/.config.vsh.yaml +++ b/target/nextflow/gunzip/.config.vsh.yaml @@ -149,8 +149,8 @@ build_info: output: "target/nextflow/gunzip" executable: "target/nextflow/gunzip/main.nf" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/gunzip/main.nf b/target/nextflow/gunzip/main.nf index 038f3b2..13f8039 100644 --- a/target/nextflow/gunzip/main.nf +++ b/target/nextflow/gunzip/main.nf @@ -3000,8 +3000,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/gunzip", "viash_version" : "0.9.0", - "git_commit" : "59cbb30eecf218c0572104f849ab542423f0e590", - "git_remote" : "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + "git_commit" : "3ee9ba76ca2112681c41468800aab2fa38cdf453", + "git_remote" : "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@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 f66d92c..fa9b516 100644 --- a/target/nextflow/multiqc_custom_biotype/.config.vsh.yaml +++ b/target/nextflow/multiqc_custom_biotype/.config.vsh.yaml @@ -170,8 +170,8 @@ build_info: output: "target/nextflow/multiqc_custom_biotype" executable: "target/nextflow/multiqc_custom_biotype/main.nf" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/multiqc_custom_biotype/main.nf b/target/nextflow/multiqc_custom_biotype/main.nf index 79c7e51..25e7a5e 100644 --- a/target/nextflow/multiqc_custom_biotype/main.nf +++ b/target/nextflow/multiqc_custom_biotype/main.nf @@ -3020,8 +3020,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/multiqc_custom_biotype", "viash_version" : "0.9.0", - "git_commit" : "59cbb30eecf218c0572104f849ab542423f0e590", - "git_remote" : "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + "git_commit" : "3ee9ba76ca2112681c41468800aab2fa38cdf453", + "git_remote" : "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@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 77e9f44..b827321 100644 --- a/target/nextflow/picard_markduplicates/.config.vsh.yaml +++ b/target/nextflow/picard_markduplicates/.config.vsh.yaml @@ -212,8 +212,8 @@ build_info: output: "target/nextflow/picard_markduplicates" executable: "target/nextflow/picard_markduplicates/main.nf" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/picard_markduplicates/main.nf b/target/nextflow/picard_markduplicates/main.nf index 8ff4800..642f6b3 100644 --- a/target/nextflow/picard_markduplicates/main.nf +++ b/target/nextflow/picard_markduplicates/main.nf @@ -3071,8 +3071,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/picard_markduplicates", "viash_version" : "0.9.0", - "git_commit" : "59cbb30eecf218c0572104f849ab542423f0e590", - "git_remote" : "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + "git_commit" : "3ee9ba76ca2112681c41468800aab2fa38cdf453", + "git_remote" : "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@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 7d3dfdb..3d46e82 100644 --- a/target/nextflow/prepare_multiqc_input/.config.vsh.yaml +++ b/target/nextflow/prepare_multiqc_input/.config.vsh.yaml @@ -417,8 +417,8 @@ build_info: output: "target/nextflow/prepare_multiqc_input" executable: "target/nextflow/prepare_multiqc_input/main.nf" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/prepare_multiqc_input/main.nf b/target/nextflow/prepare_multiqc_input/main.nf index fb5e18f..db46e79 100644 --- a/target/nextflow/prepare_multiqc_input/main.nf +++ b/target/nextflow/prepare_multiqc_input/main.nf @@ -3290,8 +3290,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/prepare_multiqc_input", "viash_version" : "0.9.0", - "git_commit" : "59cbb30eecf218c0572104f849ab542423f0e590", - "git_remote" : "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + "git_commit" : "3ee9ba76ca2112681c41468800aab2fa38cdf453", + "git_remote" : "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@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 3b9ea91..be070ee 100644 --- a/target/nextflow/preprocess_transcripts_fasta/.config.vsh.yaml +++ b/target/nextflow/preprocess_transcripts_fasta/.config.vsh.yaml @@ -143,8 +143,8 @@ build_info: output: "target/nextflow/preprocess_transcripts_fasta" executable: "target/nextflow/preprocess_transcripts_fasta/main.nf" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/preprocess_transcripts_fasta/main.nf b/target/nextflow/preprocess_transcripts_fasta/main.nf index f03f93b..fae03ac 100644 --- a/target/nextflow/preprocess_transcripts_fasta/main.nf +++ b/target/nextflow/preprocess_transcripts_fasta/main.nf @@ -2990,8 +2990,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/preprocess_transcripts_fasta", "viash_version" : "0.9.0", - "git_commit" : "59cbb30eecf218c0572104f849ab542423f0e590", - "git_remote" : "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + "git_commit" : "3ee9ba76ca2112681c41468800aab2fa38cdf453", + "git_remote" : "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@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 752e3ba..5e68df2 100644 --- a/target/nextflow/preseq_lcextrap/.config.vsh.yaml +++ b/target/nextflow/preseq_lcextrap/.config.vsh.yaml @@ -196,8 +196,8 @@ build_info: output: "target/nextflow/preseq_lcextrap" executable: "target/nextflow/preseq_lcextrap/main.nf" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/preseq_lcextrap/main.nf b/target/nextflow/preseq_lcextrap/main.nf index 41fcb91..cf0451d 100644 --- a/target/nextflow/preseq_lcextrap/main.nf +++ b/target/nextflow/preseq_lcextrap/main.nf @@ -3043,8 +3043,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/preseq_lcextrap", "viash_version" : "0.9.0", - "git_commit" : "59cbb30eecf218c0572104f849ab542423f0e590", - "git_remote" : "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + "git_commit" : "3ee9ba76ca2112681c41468800aab2fa38cdf453", + "git_remote" : "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/rsem_merge_counts/.config.vsh.yaml b/target/nextflow/rsem_merge_counts/.config.vsh.yaml index 601f7c0..c0f2d26 100644 --- a/target/nextflow/rsem_merge_counts/.config.vsh.yaml +++ b/target/nextflow/rsem_merge_counts/.config.vsh.yaml @@ -186,8 +186,8 @@ build_info: output: "target/nextflow/rsem_merge_counts" executable: "target/nextflow/rsem_merge_counts/main.nf" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/rsem_merge_counts/main.nf b/target/nextflow/rsem_merge_counts/main.nf index e1532c5..4cb92d9 100644 --- a/target/nextflow/rsem_merge_counts/main.nf +++ b/target/nextflow/rsem_merge_counts/main.nf @@ -3035,8 +3035,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rsem_merge_counts", "viash_version" : "0.9.0", - "git_commit" : "59cbb30eecf218c0572104f849ab542423f0e590", - "git_remote" : "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + "git_commit" : "3ee9ba76ca2112681c41468800aab2fa38cdf453", + "git_remote" : "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@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 78f6b5e..8824a26 100644 --- a/target/nextflow/rseqc/rseqc_junctionannotation/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_junctionannotation/.config.vsh.yaml @@ -265,8 +265,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_junctionannotation" executable: "target/nextflow/rseqc/rseqc_junctionannotation/main.nf" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/rseqc/rseqc_junctionannotation/main.nf b/target/nextflow/rseqc/rseqc_junctionannotation/main.nf index 714f841..69ac6ff 100644 --- a/target/nextflow/rseqc/rseqc_junctionannotation/main.nf +++ b/target/nextflow/rseqc/rseqc_junctionannotation/main.nf @@ -3136,8 +3136,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_junctionannotation", "viash_version" : "0.9.0", - "git_commit" : "59cbb30eecf218c0572104f849ab542423f0e590", - "git_remote" : "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + "git_commit" : "3ee9ba76ca2112681c41468800aab2fa38cdf453", + "git_remote" : "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@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 96677c6..649c686 100644 --- a/target/nextflow/rseqc/rseqc_junctionsaturation/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_junctionsaturation/.config.vsh.yaml @@ -254,8 +254,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_junctionsaturation" executable: "target/nextflow/rseqc/rseqc_junctionsaturation/main.nf" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/rseqc/rseqc_junctionsaturation/main.nf b/target/nextflow/rseqc/rseqc_junctionsaturation/main.nf index 85e9779..7aeba9a 100644 --- a/target/nextflow/rseqc/rseqc_junctionsaturation/main.nf +++ b/target/nextflow/rseqc/rseqc_junctionsaturation/main.nf @@ -3121,8 +3121,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_junctionsaturation", "viash_version" : "0.9.0", - "git_commit" : "59cbb30eecf218c0572104f849ab542423f0e590", - "git_remote" : "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + "git_commit" : "3ee9ba76ca2112681c41468800aab2fa38cdf453", + "git_remote" : "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@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 55763a7..4b8e770 100644 --- a/target/nextflow/rseqc/rseqc_readdistribution/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_readdistribution/.config.vsh.yaml @@ -167,8 +167,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_readdistribution" executable: "target/nextflow/rseqc/rseqc_readdistribution/main.nf" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/rseqc/rseqc_readdistribution/main.nf b/target/nextflow/rseqc/rseqc_readdistribution/main.nf index b2330c7..a604214 100644 --- a/target/nextflow/rseqc/rseqc_readdistribution/main.nf +++ b/target/nextflow/rseqc/rseqc_readdistribution/main.nf @@ -3025,8 +3025,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_readdistribution", "viash_version" : "0.9.0", - "git_commit" : "59cbb30eecf218c0572104f849ab542423f0e590", - "git_remote" : "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + "git_commit" : "3ee9ba76ca2112681c41468800aab2fa38cdf453", + "git_remote" : "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@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 aa9b17f..b701e73 100644 --- a/target/nextflow/rseqc/rseqc_readduplication/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_readduplication/.config.vsh.yaml @@ -216,8 +216,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_readduplication" executable: "target/nextflow/rseqc/rseqc_readduplication/main.nf" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/rseqc/rseqc_readduplication/main.nf b/target/nextflow/rseqc/rseqc_readduplication/main.nf index 1e32f3c..06c71ee 100644 --- a/target/nextflow/rseqc/rseqc_readduplication/main.nf +++ b/target/nextflow/rseqc/rseqc_readduplication/main.nf @@ -3079,8 +3079,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_readduplication", "viash_version" : "0.9.0", - "git_commit" : "59cbb30eecf218c0572104f849ab542423f0e590", - "git_remote" : "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + "git_commit" : "3ee9ba76ca2112681c41468800aab2fa38cdf453", + "git_remote" : "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@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 d28787a..cda9627 100644 --- a/target/nextflow/rseqc/rseqc_tin/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_tin/.config.vsh.yaml @@ -219,8 +219,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_tin" executable: "target/nextflow/rseqc/rseqc_tin/main.nf" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/rseqc/rseqc_tin/main.nf b/target/nextflow/rseqc/rseqc_tin/main.nf index 5dff8f2..d78f5d4 100644 --- a/target/nextflow/rseqc/rseqc_tin/main.nf +++ b/target/nextflow/rseqc/rseqc_tin/main.nf @@ -3084,8 +3084,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_tin", "viash_version" : "0.9.0", - "git_commit" : "59cbb30eecf218c0572104f849ab542423f0e590", - "git_remote" : "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + "git_commit" : "3ee9ba76ca2112681c41468800aab2fa38cdf453", + "git_remote" : "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@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 06e7892..c55f4df 100644 --- a/target/nextflow/sortmerna/.config.vsh.yaml +++ b/target/nextflow/sortmerna/.config.vsh.yaml @@ -197,8 +197,8 @@ build_info: output: "target/nextflow/sortmerna" executable: "target/nextflow/sortmerna/main.nf" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/sortmerna/main.nf b/target/nextflow/sortmerna/main.nf index 53e797c..3bb6590 100644 --- a/target/nextflow/sortmerna/main.nf +++ b/target/nextflow/sortmerna/main.nf @@ -3050,8 +3050,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/sortmerna", "viash_version" : "0.9.0", - "git_commit" : "59cbb30eecf218c0572104f849ab542423f0e590", - "git_remote" : "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + "git_commit" : "3ee9ba76ca2112681c41468800aab2fa38cdf453", + "git_remote" : "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@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 0459026..2af8994 100644 --- a/target/nextflow/stringtie/.config.vsh.yaml +++ b/target/nextflow/stringtie/.config.vsh.yaml @@ -221,8 +221,8 @@ build_info: output: "target/nextflow/stringtie" executable: "target/nextflow/stringtie/main.nf" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/stringtie/main.nf b/target/nextflow/stringtie/main.nf index 95aa287..231b56b 100644 --- a/target/nextflow/stringtie/main.nf +++ b/target/nextflow/stringtie/main.nf @@ -3081,8 +3081,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/stringtie", "viash_version" : "0.9.0", - "git_commit" : "59cbb30eecf218c0572104f849ab542423f0e590", - "git_remote" : "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + "git_commit" : "3ee9ba76ca2112681c41468800aab2fa38cdf453", + "git_remote" : "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@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 442d6bf..d21baad 100644 --- a/target/nextflow/summarizedexperiment/.config.vsh.yaml +++ b/target/nextflow/summarizedexperiment/.config.vsh.yaml @@ -204,8 +204,8 @@ build_info: output: "target/nextflow/summarizedexperiment" executable: "target/nextflow/summarizedexperiment/main.nf" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/summarizedexperiment/main.nf b/target/nextflow/summarizedexperiment/main.nf index a9d9edf..0e12261 100644 --- a/target/nextflow/summarizedexperiment/main.nf +++ b/target/nextflow/summarizedexperiment/main.nf @@ -3062,8 +3062,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/summarizedexperiment", "viash_version" : "0.9.0", - "git_commit" : "59cbb30eecf218c0572104f849ab542423f0e590", - "git_remote" : "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + "git_commit" : "3ee9ba76ca2112681c41468800aab2fa38cdf453", + "git_remote" : "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@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 f1e4d58..21c4871 100644 --- a/target/nextflow/tx2gene/.config.vsh.yaml +++ b/target/nextflow/tx2gene/.config.vsh.yaml @@ -190,8 +190,8 @@ build_info: output: "target/nextflow/tx2gene" executable: "target/nextflow/tx2gene/main.nf" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/tx2gene/main.nf b/target/nextflow/tx2gene/main.nf index 1dde9d6..97f78e3 100644 --- a/target/nextflow/tx2gene/main.nf +++ b/target/nextflow/tx2gene/main.nf @@ -3051,8 +3051,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/tx2gene", "viash_version" : "0.9.0", - "git_commit" : "59cbb30eecf218c0572104f849ab542423f0e590", - "git_remote" : "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + "git_commit" : "3ee9ba76ca2112681c41468800aab2fa38cdf453", + "git_remote" : "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@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 e8a8a2f..24a6cf2 100644 --- a/target/nextflow/tximport/.config.vsh.yaml +++ b/target/nextflow/tximport/.config.vsh.yaml @@ -256,8 +256,8 @@ build_info: output: "target/nextflow/tximport" executable: "target/nextflow/tximport/main.nf" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/tximport/main.nf b/target/nextflow/tximport/main.nf index c2954bb..272f757 100644 --- a/target/nextflow/tximport/main.nf +++ b/target/nextflow/tximport/main.nf @@ -3129,8 +3129,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/tximport", "viash_version" : "0.9.0", - "git_commit" : "59cbb30eecf218c0572104f849ab542423f0e590", - "git_remote" : "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + "git_commit" : "3ee9ba76ca2112681c41468800aab2fa38cdf453", + "git_remote" : "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@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 529a1e5..3516b0e 100644 --- a/target/nextflow/ucsc/bedclip/.config.vsh.yaml +++ b/target/nextflow/ucsc/bedclip/.config.vsh.yaml @@ -169,8 +169,8 @@ build_info: output: "target/nextflow/ucsc/bedclip" executable: "target/nextflow/ucsc/bedclip/main.nf" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/ucsc/bedclip/main.nf b/target/nextflow/ucsc/bedclip/main.nf index 1bbbaa1..679c843 100644 --- a/target/nextflow/ucsc/bedclip/main.nf +++ b/target/nextflow/ucsc/bedclip/main.nf @@ -3026,8 +3026,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/ucsc/bedclip", "viash_version" : "0.9.0", - "git_commit" : "59cbb30eecf218c0572104f849ab542423f0e590", - "git_remote" : "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + "git_commit" : "3ee9ba76ca2112681c41468800aab2fa38cdf453", + "git_remote" : "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@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 e8280ef..f156589 100644 --- a/target/nextflow/ucsc/bedgraphtobigwig/.config.vsh.yaml +++ b/target/nextflow/ucsc/bedgraphtobigwig/.config.vsh.yaml @@ -169,8 +169,8 @@ build_info: output: "target/nextflow/ucsc/bedgraphtobigwig" executable: "target/nextflow/ucsc/bedgraphtobigwig/main.nf" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/ucsc/bedgraphtobigwig/main.nf b/target/nextflow/ucsc/bedgraphtobigwig/main.nf index 056efde..b83a8fe 100644 --- a/target/nextflow/ucsc/bedgraphtobigwig/main.nf +++ b/target/nextflow/ucsc/bedgraphtobigwig/main.nf @@ -3026,8 +3026,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/ucsc/bedgraphtobigwig", "viash_version" : "0.9.0", - "git_commit" : "59cbb30eecf218c0572104f849ab542423f0e590", - "git_remote" : "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + "git_commit" : "3ee9ba76ca2112681c41468800aab2fa38cdf453", + "git_remote" : "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@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 32cbab7..b3c2768 100644 --- a/target/nextflow/workflows/genome_alignment_and_quant/.config.vsh.yaml +++ b/target/nextflow/workflows/genome_alignment_and_quant/.config.vsh.yaml @@ -595,8 +595,8 @@ 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: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@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 55b5987..0d09d8e 100644 --- a/target/nextflow/workflows/genome_alignment_and_quant/main.nf +++ b/target/nextflow/workflows/genome_alignment_and_quant/main.nf @@ -3524,8 +3524,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/genome_alignment_and_quant", "viash_version" : "0.9.0", - "git_commit" : "59cbb30eecf218c0572104f849ab542423f0e590", - "git_remote" : "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + "git_commit" : "3ee9ba76ca2112681c41468800aab2fa38cdf453", + "git_remote" : "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@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 57d3720..136a17b 100644 --- a/target/nextflow/workflows/merge_quant_results/.config.vsh.yaml +++ b/target/nextflow/workflows/merge_quant_results/.config.vsh.yaml @@ -283,8 +283,8 @@ 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: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@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 85d4b6e..79e8791 100644 --- a/target/nextflow/workflows/merge_quant_results/main.nf +++ b/target/nextflow/workflows/merge_quant_results/main.nf @@ -3157,8 +3157,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/merge_quant_results", "viash_version" : "0.9.0", - "git_commit" : "59cbb30eecf218c0572104f849ab542423f0e590", - "git_remote" : "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + "git_commit" : "3ee9ba76ca2112681c41468800aab2fa38cdf453", + "git_remote" : "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@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 10f84ff..7a4db4b 100644 --- a/target/nextflow/workflows/post_processing/.config.vsh.yaml +++ b/target/nextflow/workflows/post_processing/.config.vsh.yaml @@ -482,8 +482,8 @@ build_info: output: "target/nextflow/workflows/post_processing" executable: "target/nextflow/workflows/post_processing/main.nf" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@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 249d1ea..3a4de4f 100644 --- a/target/nextflow/workflows/post_processing/main.nf +++ b/target/nextflow/workflows/post_processing/main.nf @@ -3395,8 +3395,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/post_processing", "viash_version" : "0.9.0", - "git_commit" : "59cbb30eecf218c0572104f849ab542423f0e590", - "git_remote" : "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + "git_commit" : "3ee9ba76ca2112681c41468800aab2fa38cdf453", + "git_remote" : "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@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 1a0c1f5..06e4d44 100644 --- a/target/nextflow/workflows/pre_processing/.config.vsh.yaml +++ b/target/nextflow/workflows/pre_processing/.config.vsh.yaml @@ -637,8 +637,8 @@ build_info: output: "target/nextflow/workflows/pre_processing" executable: "target/nextflow/workflows/pre_processing/main.nf" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" dependencies: - "target/dependencies/vsh/vsh/biobox/main/nextflow/fastqc" - "target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_extract" diff --git a/target/nextflow/workflows/pre_processing/main.nf b/target/nextflow/workflows/pre_processing/main.nf index cc9dd29..d5d2da6 100644 --- a/target/nextflow/workflows/pre_processing/main.nf +++ b/target/nextflow/workflows/pre_processing/main.nf @@ -3584,8 +3584,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/pre_processing", "viash_version" : "0.9.0", - "git_commit" : "59cbb30eecf218c0572104f849ab542423f0e590", - "git_remote" : "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + "git_commit" : "3ee9ba76ca2112681c41468800aab2fa38cdf453", + "git_remote" : "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@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 a3b4f60..da24e86 100644 --- a/target/nextflow/workflows/prepare_genome/.config.vsh.yaml +++ b/target/nextflow/workflows/prepare_genome/.config.vsh.yaml @@ -507,8 +507,8 @@ build_info: output: "target/nextflow/workflows/prepare_genome" executable: "target/nextflow/workflows/prepare_genome/main.nf" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@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 275837e..e63dbd1 100644 --- a/target/nextflow/workflows/prepare_genome/main.nf +++ b/target/nextflow/workflows/prepare_genome/main.nf @@ -3425,8 +3425,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/prepare_genome", "viash_version" : "0.9.0", - "git_commit" : "59cbb30eecf218c0572104f849ab542423f0e590", - "git_remote" : "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + "git_commit" : "3ee9ba76ca2112681c41468800aab2fa38cdf453", + "git_remote" : "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", @@ -3487,291 +3487,319 @@ include { kallisto_index } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/ma // user-provided Nextflow code workflow run_wf { - take: - input_ch + take: + input_ch - main: - output_ch = input_ch - - // Uncompress fasta - | gunzip.run ( - fromState: [ "input": "fasta" ], - toState: [ "fasta": "output" ], - key: "gunzip_fasta", - args: [ output: "reference_genome.fasta" ] - ) + main: + output_ch = input_ch - // uncompress gtf - | gunzip.run ( - runIf: {id, state -> state.gtf}, - fromState: [ "input": "gtf" ], - toState: [ "gtf": "output" ], - key: "gunzip_gtf", - args: [output: "gene_annotation.gtf"] - ) + // Uncompress fasta + | gunzip.run ( + fromState: [ "input": "fasta" ], + toState: [ "fasta": "output" ], + key: "gunzip_fasta", + args: [ output: "reference_genome.fasta" ], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) - // uncompress gff - | gunzip.run ( - runIf: {id, state -> !state.gtf && state.gff}, - fromState: [ "input": "gff" ], - toState: [ "gff": "output" ], - key: "gunzip_gff", - args: [output: "gene_annotation.gff"] - ) + // uncompress gtf + | gunzip.run ( + runIf: {id, state -> state.gtf}, + fromState: [ "input": "gtf" ], + toState: [ "gtf": "output" ], + key: "gunzip_gtf", + args: [output: "gene_annotation.gtf"], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) - // gff to gtf - | gffread.run ( - runIf: {id, state -> !state.gtf && state.gff}, - fromState: [ - "input": "gff", - "genome": "fasta" - ], - toState: [ "gtf": "outfile" ], - args: [ - outfile: "gene_annotation.gtf", - gtf_output: true, - keep_attrs: true, - keep_exon_attrs: true - ] - ) + // uncompress gff + | gunzip.run ( + runIf: {id, state -> !state.gtf && state.gff}, + fromState: [ "input": "gff" ], + toState: [ "gff": "output" ], + key: "gunzip_gff", + args: [output: "gene_annotation.gff"], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) - | gtf_filter.run( - runIf: {id, state -> state.gtf && state.filter_gtf}, - fromState: [ - "fasta": "fasta", - "gtf": "gtf" - ], - toState: [ "gtf": "filtered_gtf" ], - args: [filtered_gtf: "gene_annotation.gtf"] - ) + // gff to gtf + | gffread.run ( + runIf: {id, state -> !state.gtf && state.gff}, + fromState: [ + "input": "gff", + "genome": "fasta" + ], + toState: [ "gtf": "outfile" ], + args: [ + outfile: "gene_annotation.gtf", + gtf_output: true, + keep_attrs: true, + keep_exon_attrs: true + ], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) - // uncompress additional fasta - | gunzip.run ( - runIf: {id, state -> state.additional_fasta}, - fromState: [ "input": "additional_fasta" ], - toState: [ "additional_fasta": "output" ], - key: "gunzip_additional_fasta", - args: [output: "additional.fasta"] - ) + | gtf_filter.run( + runIf: {id, state -> state.gtf && state.filter_gtf}, + fromState: [ + "fasta": "fasta", + "gtf": "gtf" + ], + toState: [ "gtf": "filtered_gtf" ], + args: [filtered_gtf: "gene_annotation.gtf"], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) - // concatenate additional fasta - | cat_additional_fasta.run ( - runIf: {id, state -> state.additional_fasta}, - fromState: [ - "fasta": "fasta", - "gtf": "gtf", - "additional_fasta": "additional_fasta", - "biotype": "biotype" - ], - toState: [ - "fasta": "fasta_output", - "gtf": "gtf_output" - ], - args: [ - fasta_output: "genome_additional.fasta", - gtf_output: "genome_additional.gtf" - ] - ) + // uncompress additional fasta + | gunzip.run ( + runIf: {id, state -> state.additional_fasta}, + fromState: [ "input": "additional_fasta" ], + toState: [ "additional_fasta": "output" ], + key: "gunzip_additional_fasta", + args: [output: "additional.fasta"], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) - // uncompress bed file - | gunzip.run ( - runIf: {id, state -> state.gene_bed}, - fromState: [ "input": "gene_bed" ], - toState: [ "gene_bed": "output" ], - key: "gunzip_gene_bed", - args: [output: "genome_additional.bed"] - ) + // concatenate additional fasta + | cat_additional_fasta.run ( + runIf: {id, state -> state.additional_fasta}, + fromState: [ + "fasta": "fasta", + "gtf": "gtf", + "additional_fasta": "additional_fasta", + "biotype": "biotype" + ], + toState: [ + "fasta": "fasta_output", + "gtf": "gtf_output" + ], + args: [ + fasta_output: "genome_additional.fasta", + gtf_output: "genome_additional.gtf" + ], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) - // gtf to bed - | gtf2bed.run ( - runIf: { id, state -> !state.gene_bed}, - fromState: [ "gtf": "gtf" ], - toState: [ "gene_bed": "bed_output" ], - args: [bed_output: "genome_additional.bed"] - ) + // uncompress bed file + | gunzip.run ( + runIf: {id, state -> state.gene_bed}, + fromState: [ "input": "gene_bed" ], + toState: [ "gene_bed": "output" ], + key: "gunzip_gene_bed", + args: [output: "genome_additional.bed"], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) - // uncompress transcript fasta - | gunzip.run ( - runIf: {id, state -> state.transcript_fasta}, - fromState: [ "input": "transcript_fasta" ], - toState: [ "transcript_fasta": "output" ], - key: "transcript_fasta", - args: [output: "transcriptome.fasta"] - ) + // gtf to bed + | gtf2bed.run ( + runIf: { id, state -> !state.gene_bed}, + fromState: [ "gtf": "gtf" ], + toState: [ "gene_bed": "bed_output" ], + args: [bed_output: "genome_additional.bed"], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) - // preprocess transcripts fasta if gtf is in gencode format - | preprocess_transcripts_fasta.run ( - runIf: {id, state -> state.transcript_fasta && state.gencode}, - fromState: [ "transcript_fasta": "transcript_fasta" ], - toState: [ "transcript_fasta": "output" ], - args: [output: "transcriptome.fasta"] - ) + // uncompress transcript fasta + | gunzip.run ( + runIf: {id, state -> state.transcript_fasta}, + fromState: [ "input": "transcript_fasta" ], + toState: [ "transcript_fasta": "output" ], + key: "transcript_fasta", + args: [output: "transcriptome.fasta"], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) - // make transcript FASTA if not provided - | rsem_prepare_reference.run ( - runIf: {id, state -> !state.transcript_fasta}, - fromState: [ - "reference_fasta_files": "fasta", - "gtf": "gtf" - ], - toState: [ "make_transcript_fasta_output": "output" ], - key: "make_transcript_fasta", - args: [reference_name: "genome"] - ) - | map { id, state -> - def transcript_fasta = (!state.transcript_fasta) ? - state.make_transcript_fasta_output.listFiles().find{it.name == "genome.transcripts.fa"} : - state.transcript_fasta - [ id, state + [transcript_fasta: transcript_fasta] ] - } + // preprocess transcripts fasta if gtf is in gencode format + | preprocess_transcripts_fasta.run ( + runIf: {id, state -> state.transcript_fasta && state.gencode}, + fromState: [ "transcript_fasta": "transcript_fasta" ], + toState: [ "transcript_fasta": "output" ], + args: [output: "transcriptome.fasta"], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) - // chromosome size and fai index - | getchromsizes.run ( - fromState: [ "fasta": "fasta" ], - toState: [ - "fai": "fai", - "sizes": "sizes" - ], - key: "chromsizes", - args: [ - fai: "genome_additional.fasta.fai", - sizes: "genome_additional.fasta.sizes" - ] - ) - - // untar bbsplit index, if available - | untar.run ( - runIf: {id, state -> state.bbsplit_index}, - fromState: [ "input": "bbsplit_index" ], - toState: [ "bbsplit_index": "output" ], - key: "untar_bbsplit_index", - args: [output: "BBSplit_index"] - ) + // make transcript FASTA if not provided + | rsem_prepare_reference.run ( + runIf: {id, state -> !state.transcript_fasta}, + fromState: [ + "reference_fasta_files": "fasta", + "gtf": "gtf" + ], + toState: [ "make_transcript_fasta_output": "output" ], + key: "make_transcript_fasta", + args: [reference_name: "genome"], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) + | map { id, state -> + def transcript_fasta = (!state.transcript_fasta) ? + state.make_transcript_fasta_output.listFiles().find{it.name == "genome.transcripts.fa"} : + state.transcript_fasta + [ id, state + [transcript_fasta: transcript_fasta] ] + } - | map {id, state -> - def ref = [state.fasta] + state.bbsplit_fasta_list - [id, state + [bbsplit_ref: ref] ] + // chromosome size and fai index + | getchromsizes.run ( + fromState: [ "fasta": "fasta" ], + toState: [ + "fai": "fai", + "sizes": "sizes" + ], + key: "chromsizes", + args: [ + fai: "genome_additional.fasta.fai", + sizes: "genome_additional.fasta.sizes" + ], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) + + // untar bbsplit index, if available + | untar.run ( + runIf: {id, state -> state.bbsplit_index}, + fromState: [ "input": "bbsplit_index" ], + toState: [ "bbsplit_index": "output" ], + key: "untar_bbsplit_index", + directives: [ label: [ "lowmem", "midcpu" ] ] + ) + + | map { id, state -> + // Check if bbsplit_fasta_list is defined + if (state.bbsplit_fasta_list) { + def ref = [state.fasta] + state.bbsplit_fasta_list + } else { + def ref = [state.fasta] } + [id, state + [bbsplit_ref: ref] ] + } - // create bbsplit index, if not already availble - | bbmap_bbsplit.run ( - runIf: {id, state -> !state.skip_bbsplit && !state.bbsplit_index}, - fromState: ["ref": "bbsplit_ref"], - toState: [ "bbsplit_index": "index" ], - args: [ - only_build_index: true, - index: "BBSplit_index" - ], - key: "generate_bbsplit_index" - ) + | niceView() - // Uncompress STAR index or generate from scratch if required - | untar.run ( - runIf: {id, state -> state.star_index}, - fromState: [ "input": "star_index" ], - toState: [ "star_index": "output" ], - key: "untar_star_index", - args: [output: "STAR_index"] - ) - - // TODO: Add to viah-hub or adapt star_align_reads to enable the generateGenome runMode - | star_genome_generate.run ( - runIf: {id, state -> !state.star_index && !state.skip_alignment}, - fromState: [ - "genome_fasta_files": "fasta", - "sjdb_gtf_file": "gtf", - "sjdb_gtf_feature_exon": "star_sjdb_gtf_feature_exon" - ], - toState: [ "star_index": "index" ], - key: "generate_star_index", - args: [index: "STAR_index"] - ) + // create bbsplit index, if not already available + | bbmap_bbsplit.run ( + runIf: {id, state -> !state.skip_bbsplit && !state.bbsplit_index}, + fromState: ["ref": "bbsplit_ref"], + toState: [ "bbsplit_index": "index" ], + args: [ + only_build_index: true, + index: "BBSplit_index" + ], + key: "generate_bbsplit_index" + ) - // Uncompress RSEM index or generate from scratch if required - | untar.run ( - runIf: {id, state -> state.rsem_index}, - fromState: [ "input": "rsem_index" ], - toState: [ "rsem_index": "output" ], - key: "untar_rsem_index", - args: [output: "RSEM_index"] - ) + // Uncompress STAR index or generate from scratch if required + | untar.run ( + runIf: {id, state -> state.star_index}, + fromState: [ "input": "star_index" ], + toState: [ "star_index": "output" ], + key: "untar_star_index", + args: [output: "STAR_index"], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) - | rsem_prepare_reference.run ( - runIf: {id, state -> !state.rsem_index && state.aligner == 'star_rsem'}, - fromState: [ - "reference_fasta_files": "fasta", - "gtf": "gtf" - ], - toState: [ "rsem_index": "output" ], - key: "generate_rsem_index", - args: [reference_name: "genome"] - ) - - // TODO: Uncompress HISAT2 index or generate from scratch if required + // TODO: Add to viah-hub or adapt star_align_reads to enable the generateGenome runMode + | star_genome_generate.run ( + runIf: {id, state -> !state.star_index && !state.skip_alignment}, + fromState: [ + "genome_fasta_files": "fasta", + "sjdb_gtf_file": "gtf", + "sjdb_gtf_feature_exon": "star_sjdb_gtf_feature_exon" + ], + toState: [ "star_index": "index" ], + key: "generate_star_index", + args: [index: "STAR_index"], + directives: [ label: [ "highmem", "highcpu" ] ] + ) - // Uncompress Salmon index or generate from scratch if required - | untar.run ( - runIf: {id, state -> state.salmon_index}, - fromState: [ "input": "salmon_index" ], - toState: [ "salmon_index": "output" ], - key: "untar_salmon_index", - args: [output: "Salmon_index"] - ) + // Uncompress RSEM index or generate from scratch if required + | untar.run ( + runIf: {id, state -> state.rsem_index}, + fromState: [ "input": "rsem_index" ], + toState: [ "rsem_index": "output" ], + key: "untar_rsem_index", + args: [output: "RSEM_index"], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) - | salmon_index.run ( - runIf: {id, state -> (state.aligner == 'star_salmon' || state.pseudo_aligner == "salmon") && !state.salmon_index}, - fromState: [ - "genome": "fasta", - "transcripts": "transcript_fasta", - "kmer_len": "pseudo_aligner_kmer_size", - "gencode": "gencode" - ], - toState: [ "salmon_index": "index" ], - key: "generate_salmon_index", - args: [index: "Salmon_index"] - ) + | rsem_prepare_reference.run ( + runIf: {id, state -> !state.rsem_index && state.aligner == 'star_rsem'}, + fromState: [ + "reference_fasta_files": "fasta", + "gtf": "gtf" + ], + toState: [ "rsem_index": "output" ], + key: "generate_rsem_index", + args: [reference_name: "genome"], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) + + // TODO: Uncompress HISAT2 index or generate from scratch if required - // Uncompress Kallisto index or generate from scratch if required - | untar.run ( - runIf: {id, state -> state.kallisto_index}, - fromState: [ "input": "kallisto_index" ], - toState: [ "kallisto_index": "output" ], - key: "untar_kallisto_index", - args: [output: "Kallisto_index"] - ) + // Uncompress Salmon index or generate from scratch if required + | untar.run ( + runIf: {id, state -> state.salmon_index}, + fromState: [ "input": "salmon_index" ], + toState: [ "salmon_index": "output" ], + key: "untar_salmon_index", + args: [output: "Salmon_index"], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) - | kallisto_index.run( - runIf: {id, state -> state.pseudo_aligner == "kallisto" && !state.kallisto_index}, - fromState: [ - "input": "transcript_fasta", - "kmer_size": "pseudo_aligner_kmer_size" - ], - toState: [ "kallisto_index": "index" ], - key: "generate_kallisto_index", - args: [index: "Kallisto_index"] - ) + | salmon_index.run ( + runIf: {id, state -> (state.aligner == 'star_salmon' || state.pseudo_aligner == "salmon") && !state.salmon_index}, + fromState: [ + "genome": "fasta", + "transcripts": "transcript_fasta", + "kmer_len": "pseudo_aligner_kmer_size", + "gencode": "gencode" + ], + toState: [ "salmon_index": "index" ], + key: "generate_salmon_index", + args: [index: "Salmon_index"], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) - | map { id, state -> - def mod_state = state.findAll { key, value -> value instanceof java.nio.file.Path && value.exists() } - [ id, mod_state ] - } + // Uncompress Kallisto index or generate from scratch if required + | untar.run ( + runIf: {id, state -> state.kallisto_index}, + fromState: [ "input": "kallisto_index" ], + toState: [ "kallisto_index": "output" ], + key: "untar_kallisto_index", + args: [output: "Kallisto_index"], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) - | setState ( - "fasta_uncompressed": "fasta", - "gtf_uncompressed": "gtf", - "transcript_fasta_uncompressed": "transcript_fasta", - "gene_bed_uncompressed": "gene_bed", - "star_index_uncompressed": "star_index", - "salmon_index_uncompressed": "salmon_index", - "kallisto_index_uncompressed": "kallisto_index", - "bbsplit_index_uncompressed": "bbsplit_index", - "rsem_index_uncompressed": "rsem_index", - "chrom_sizes": "sizes", - "fai": "fai" - ) + | kallisto_index.run( + runIf: {id, state -> state.pseudo_aligner == "kallisto" && !state.kallisto_index}, + fromState: [ + "input": "transcript_fasta", + "kmer_size": "pseudo_aligner_kmer_size" + ], + toState: [ "kallisto_index": "index" ], + key: "generate_kallisto_index", + args: [index: "Kallisto_index"], + directives: [ label: [ "lowmem", "midcpu" ] ] + ) - emit: - output_ch + | map { id, state -> + def mod_state = state.findAll { key, value -> value instanceof java.nio.file.Path && value.exists() } + [ id, mod_state ] + } + + | setState ( + "fasta_uncompressed": "fasta", + "gtf_uncompressed": "gtf", + "transcript_fasta_uncompressed": "transcript_fasta", + "gene_bed_uncompressed": "gene_bed", + "star_index_uncompressed": "star_index", + "salmon_index_uncompressed": "salmon_index", + "kallisto_index_uncompressed": "kallisto_index", + "bbsplit_index_uncompressed": "bbsplit_index", + "rsem_index_uncompressed": "rsem_index", + "chrom_sizes": "sizes", + "fai": "fai" + ) + + emit: + output_ch } // inner workflow hook 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 56ab807..94dcb19 100644 --- a/target/nextflow/workflows/pseudo_alignment_and_quant/.config.vsh.yaml +++ b/target/nextflow/workflows/pseudo_alignment_and_quant/.config.vsh.yaml @@ -290,8 +290,8 @@ 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: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" dependencies: - "target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant" - "target/dependencies/vsh/vsh/biobox/main/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 9fe795f..5d65298 100644 --- a/target/nextflow/workflows/pseudo_alignment_and_quant/main.nf +++ b/target/nextflow/workflows/pseudo_alignment_and_quant/main.nf @@ -3153,8 +3153,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/pseudo_alignment_and_quant", "viash_version" : "0.9.0", - "git_commit" : "59cbb30eecf218c0572104f849ab542423f0e590", - "git_remote" : "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + "git_commit" : "3ee9ba76ca2112681c41468800aab2fa38cdf453", + "git_remote" : "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@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 89b6603..6aff192 100644 --- a/target/nextflow/workflows/quality_control/.config.vsh.yaml +++ b/target/nextflow/workflows/quality_control/.config.vsh.yaml @@ -1561,8 +1561,8 @@ build_info: output: "target/nextflow/workflows/quality_control" executable: "target/nextflow/workflows/quality_control/main.nf" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" dependencies: - "target/dependencies/vsh/vsh/biobox/main/nextflow/rseqc/rseqc_bamstat" - "target/dependencies/vsh/vsh/biobox/main/nextflow/rseqc/rseqc_inferexperiment" diff --git a/target/nextflow/workflows/quality_control/main.nf b/target/nextflow/workflows/quality_control/main.nf index d02a768..fe8f7b1 100644 --- a/target/nextflow/workflows/quality_control/main.nf +++ b/target/nextflow/workflows/quality_control/main.nf @@ -4636,8 +4636,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/quality_control", "viash_version" : "0.9.0", - "git_commit" : "59cbb30eecf218c0572104f849ab542423f0e590", - "git_remote" : "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + "git_commit" : "3ee9ba76ca2112681c41468800aab2fa38cdf453", + "git_remote" : "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/workflows/rnaseq/.config.vsh.yaml b/target/nextflow/workflows/rnaseq/.config.vsh.yaml index 13b902d..a9b9f7b 100644 --- a/target/nextflow/workflows/rnaseq/.config.vsh.yaml +++ b/target/nextflow/workflows/rnaseq/.config.vsh.yaml @@ -521,11 +521,6 @@ argument_groups: direction: "input" multiple: false multiple_sep: ";" - - type: "boolean_true" - name: "--skip_bbsplit" - description: "Skip BBSplit for removal of non-reference genome reads." - info: null - direction: "input" - type: "boolean" name: "--skip_umi_extract" description: "Skip umi_tools extract step." @@ -2064,8 +2059,8 @@ build_info: output: "target/nextflow/workflows/rnaseq" executable: "target/nextflow/workflows/rnaseq/main.nf" viash_version: "0.9.0" - git_commit: "59cbb30eecf218c0572104f849ab542423f0e590" - git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453" + git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@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 796e6c3..7de48b8 100644 --- a/target/nextflow/workflows/rnaseq/main.nf +++ b/target/nextflow/workflows/rnaseq/main.nf @@ -3397,12 +3397,6 @@ meta = [ "multiple" : false, "multiple_sep" : ";" }, - { - "type" : "boolean_true", - "name" : "--skip_bbsplit", - "description" : "Skip BBSplit for removal of non-reference genome reads.", - "direction" : "input" - }, { "type" : "boolean", "name" : "--skip_umi_extract", @@ -4901,14 +4895,14 @@ meta = [ "default" : [ "deseq2_qc" ], -''' + ''' "must_exist" : true, + "must_exist" : true, "create_parent" : true, "required" : false, "direction" : "output", "multiple" : false, "multiple_sep" : ";" }, - { + {''' + ''' "type" : "file", "name" : "--deseq2_output_pseudo", "default" : [ @@ -5231,8 +5225,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/rnaseq", "viash_version" : "0.9.0", - "git_commit" : "59cbb30eecf218c0572104f849ab542423f0e590", - "git_remote" : "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq" + "git_commit" : "3ee9ba76ca2112681c41468800aab2fa38cdf453", + "git_remote" : "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", @@ -5326,7 +5320,8 @@ workflow run_wf { // splicesites: list.collect { id, state -> state.splicesites }.unique()[0], // hisat2_index: list.collect { id, state -> state.hisat2_index }.unique()[0], bbsplit_index: list.collect { id, state -> state.bbsplit_index }.unique()[0], - skip_bbsplit: list.collect { id, state -> state.skip_bbsplit }.unique()[0], + // See: + skip_bbsplit: true, // list.collect { id, state -> state.skip_bbsplit }.unique()[0], skip_alignment: list.collect { id, state -> state.skip_alignment }.unique()[0], gencode: list.collect { id, state -> state.gencode }.unique()[0], biotype: list.collect { id, state -> state.biotype }.unique()[0], diff --git a/target/nextflow/workflows/rnaseq/nextflow_schema.json b/target/nextflow/workflows/rnaseq/nextflow_schema.json index 2ca773a..8197f72 100644 --- a/target/nextflow/workflows/rnaseq/nextflow_schema.json +++ b/target/nextflow/workflows/rnaseq/nextflow_schema.json @@ -626,17 +626,6 @@ } - , - "skip_bbsplit": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Skip BBSplit for removal of non-reference genome reads", - "help_text": "Type: `boolean_true`, default: `false`. Skip BBSplit for removal of non-reference genome reads." - , - "default":false - } - - , "skip_umi_extract": { "type":