From b127f32213d658ea9c332ff5406bab5a903c345c Mon Sep 17 00:00:00 2001 From: CI Date: Mon, 30 Sep 2024 08:25:15 +0000 Subject: [PATCH] Build branch multiple_fixes with version multiple_fixes (f3645db) Build pipeline: viash-hub.rnaseq.multiple-fixes-dvnvc Source commit: https://github.com/viash-hub/rnaseq/commit/f3645db764dda85eb0fbd0439e7ca872b46a0dcb Source message: update config --- assets/multiqc_config.yml | 12 +- src/prepare_multiqc_input/script.sh | 8 +- .../config.vsh.yaml | 3 + .../genome_alignment_and_quant/main.nf | 6 + src/workflows/post_processing/config.vsh.yaml | 12 +- src/workflows/pre_processing/config.vsh.yaml | 4 +- src/workflows/pre_processing/main.nf | 2 +- .../config.vsh.yaml | 1 - .../pseudo_alignment_and_quant/main.nf | 7 +- src/workflows/quality_control/config.vsh.yaml | 12 +- src/workflows/quality_control/main.nf | 291 +++++++++----- src/workflows/rnaseq/config.vsh.yaml | 8 +- src/workflows/rnaseq/main.nf | 29 +- .../executable/bbmap_bbsplit/.config.vsh.yaml | 4 +- target/executable/bbmap_bbsplit/bbmap_bbsplit | 6 +- .../bedtools_genomecov/.config.vsh.yaml | 4 +- .../bedtools_genomecov/bedtools_genomecov | 6 +- .../cat_additional_fasta/.config.vsh.yaml | 4 +- .../cat_additional_fasta/cat_additional_fasta | 6 +- target/executable/cat_fastq/.config.vsh.yaml | 4 +- target/executable/cat_fastq/cat_fastq | 6 +- target/executable/deseq2_qc/.config.vsh.yaml | 4 +- target/executable/deseq2_qc/deseq2_qc | 6 +- target/executable/dupradar/.config.vsh.yaml | 4 +- target/executable/dupradar/dupradar | 6 +- target/executable/fastqc/.config.vsh.yaml | 4 +- target/executable/fastqc/fastqc | 6 +- .../executable/fq_subsample/.config.vsh.yaml | 4 +- target/executable/fq_subsample/fq_subsample | 6 +- .../executable/getchromsizes/.config.vsh.yaml | 4 +- target/executable/getchromsizes/getchromsizes | 6 +- target/executable/gtf2bed/.config.vsh.yaml | 4 +- target/executable/gtf2bed/gtf2bed | 6 +- target/executable/gtf_filter/.config.vsh.yaml | 4 +- target/executable/gtf_filter/gtf_filter | 6 +- target/executable/gunzip/.config.vsh.yaml | 4 +- target/executable/gunzip/gunzip | 6 +- .../kallisto/kallisto_index/.config.vsh.yaml | 4 +- .../kallisto/kallisto_index/kallisto_index | 6 +- .../kallisto/kallisto_quant/.config.vsh.yaml | 4 +- .../kallisto/kallisto_quant/kallisto_quant | 6 +- .../multiqc_custom_biotype/.config.vsh.yaml | 4 +- .../multiqc_custom_biotype | 6 +- .../picard_markduplicates/.config.vsh.yaml | 4 +- .../picard_markduplicates | 6 +- .../prepare_multiqc_input/.config.vsh.yaml | 4 +- .../prepare_multiqc_input | 14 +- .../.config.vsh.yaml | 4 +- .../preprocess_transcripts_fasta | 6 +- .../preseq_lcextrap/.config.vsh.yaml | 4 +- .../preseq_lcextrap/preseq_lcextrap | 6 +- target/executable/qualimap/.config.vsh.yaml | 4 +- target/executable/qualimap/qualimap | 6 +- .../.config.vsh.yaml | 4 +- .../rsem_calculate_expression | 6 +- .../rsem/rsem_merge_counts/.config.vsh.yaml | 4 +- .../rsem/rsem_merge_counts/rsem_merge_counts | 6 +- .../rseqc/rseqc_bamstat/.config.vsh.yaml | 4 +- .../rseqc/rseqc_bamstat/rseqc_bamstat | 6 +- .../rseqc_inferexperiment/.config.vsh.yaml | 4 +- .../rseqc_inferexperiment | 6 +- .../rseqc_innerdistance/.config.vsh.yaml | 4 +- .../rseqc_innerdistance/rseqc_innerdistance | 6 +- .../rseqc_junctionannotation/.config.vsh.yaml | 4 +- .../rseqc_junctionannotation | 6 +- .../rseqc_junctionsaturation/.config.vsh.yaml | 4 +- .../rseqc_junctionsaturation | 6 +- .../rseqc_readdistribution/.config.vsh.yaml | 4 +- .../rseqc_readdistribution | 6 +- .../rseqc_readduplication/.config.vsh.yaml | 4 +- .../rseqc_readduplication | 6 +- .../rseqc/rseqc_tin/.config.vsh.yaml | 4 +- target/executable/rseqc/rseqc_tin/rseqc_tin | 6 +- target/executable/sortmerna/.config.vsh.yaml | 4 +- target/executable/sortmerna/sortmerna | 6 +- target/executable/stringtie/.config.vsh.yaml | 4 +- target/executable/stringtie/stringtie | 6 +- .../summarizedexperiment/.config.vsh.yaml | 4 +- .../summarizedexperiment/summarizedexperiment | 6 +- target/executable/trimgalore/.config.vsh.yaml | 4 +- target/executable/trimgalore/trimgalore | 4 +- target/executable/tx2gene/.config.vsh.yaml | 4 +- target/executable/tx2gene/tx2gene | 6 +- target/executable/tximport/.config.vsh.yaml | 4 +- target/executable/tximport/tximport | 6 +- .../executable/ucsc/bedclip/.config.vsh.yaml | 4 +- target/executable/ucsc/bedclip/bedclip | 6 +- .../ucsc/bedgraphtobigwig/.config.vsh.yaml | 4 +- .../ucsc/bedgraphtobigwig/bedgraphtobigwig | 6 +- .../umitools/umitools_dedup/.config.vsh.yaml | 4 +- .../umitools/umitools_dedup/umitools_dedup | 6 +- .../umitools_extract/.config.vsh.yaml | 4 +- .../umitools_extract/umitools_extract | 6 +- .../umitools_prepareforquant/.config.vsh.yaml | 4 +- .../umitools_prepareforquant | 6 +- .../.config.vsh.yaml | 13 +- .../genome_alignment_and_quant | 27 ++ .../merge_quant_results/.config.vsh.yaml | 4 +- .../post_processing/.config.vsh.yaml | 16 +- .../workflows/post_processing/post_processing | 24 +- .../workflows/pre_processing/.config.vsh.yaml | 8 +- .../workflows/pre_processing/pre_processing | 10 +- .../workflows/prepare_genome/.config.vsh.yaml | 4 +- .../.config.vsh.yaml | 6 +- .../pseudo_alignment_and_quant | 11 +- .../quality_control/.config.vsh.yaml | 41 +- .../workflows/quality_control/quality_control | 361 +++++++++++------- .../workflows/rnaseq/.config.vsh.yaml | 17 +- target/executable/workflows/rnaseq/rnaseq | 58 ++- .../nextflow/bbmap_bbsplit/.config.vsh.yaml | 4 +- target/nextflow/bbmap_bbsplit/main.nf | 4 +- .../bedtools_genomecov/.config.vsh.yaml | 4 +- target/nextflow/bedtools_genomecov/main.nf | 4 +- .../cat_additional_fasta/.config.vsh.yaml | 4 +- target/nextflow/cat_additional_fasta/main.nf | 4 +- target/nextflow/cat_fastq/.config.vsh.yaml | 4 +- target/nextflow/cat_fastq/main.nf | 4 +- target/nextflow/deseq2_qc/.config.vsh.yaml | 4 +- target/nextflow/deseq2_qc/main.nf | 4 +- target/nextflow/dupradar/.config.vsh.yaml | 4 +- target/nextflow/dupradar/main.nf | 4 +- target/nextflow/fastqc/.config.vsh.yaml | 4 +- target/nextflow/fastqc/main.nf | 4 +- target/nextflow/fq_subsample/.config.vsh.yaml | 4 +- target/nextflow/fq_subsample/main.nf | 4 +- .../nextflow/getchromsizes/.config.vsh.yaml | 4 +- target/nextflow/getchromsizes/main.nf | 4 +- target/nextflow/gtf2bed/.config.vsh.yaml | 4 +- target/nextflow/gtf2bed/main.nf | 4 +- target/nextflow/gtf_filter/.config.vsh.yaml | 4 +- target/nextflow/gtf_filter/main.nf | 4 +- target/nextflow/gunzip/.config.vsh.yaml | 4 +- target/nextflow/gunzip/main.nf | 4 +- .../kallisto/kallisto_index/.config.vsh.yaml | 4 +- .../nextflow/kallisto/kallisto_index/main.nf | 4 +- .../kallisto/kallisto_quant/.config.vsh.yaml | 4 +- .../nextflow/kallisto/kallisto_quant/main.nf | 4 +- .../multiqc_custom_biotype/.config.vsh.yaml | 4 +- .../nextflow/multiqc_custom_biotype/main.nf | 4 +- .../picard_markduplicates/.config.vsh.yaml | 4 +- target/nextflow/picard_markduplicates/main.nf | 4 +- .../prepare_multiqc_input/.config.vsh.yaml | 4 +- target/nextflow/prepare_multiqc_input/main.nf | 12 +- .../.config.vsh.yaml | 4 +- .../preprocess_transcripts_fasta/main.nf | 4 +- .../nextflow/preseq_lcextrap/.config.vsh.yaml | 4 +- target/nextflow/preseq_lcextrap/main.nf | 4 +- target/nextflow/qualimap/.config.vsh.yaml | 4 +- target/nextflow/qualimap/main.nf | 4 +- .../.config.vsh.yaml | 4 +- .../rsem/rsem_calculate_expression/main.nf | 4 +- .../rsem/rsem_merge_counts/.config.vsh.yaml | 4 +- .../nextflow/rsem/rsem_merge_counts/main.nf | 4 +- .../rseqc/rseqc_bamstat/.config.vsh.yaml | 4 +- target/nextflow/rseqc/rseqc_bamstat/main.nf | 4 +- .../rseqc_inferexperiment/.config.vsh.yaml | 4 +- .../rseqc/rseqc_inferexperiment/main.nf | 4 +- .../rseqc_innerdistance/.config.vsh.yaml | 4 +- .../rseqc/rseqc_innerdistance/main.nf | 4 +- .../rseqc_junctionannotation/.config.vsh.yaml | 4 +- .../rseqc/rseqc_junctionannotation/main.nf | 4 +- .../rseqc_junctionsaturation/.config.vsh.yaml | 4 +- .../rseqc/rseqc_junctionsaturation/main.nf | 4 +- .../rseqc_readdistribution/.config.vsh.yaml | 4 +- .../rseqc/rseqc_readdistribution/main.nf | 4 +- .../rseqc_readduplication/.config.vsh.yaml | 4 +- .../rseqc/rseqc_readduplication/main.nf | 4 +- .../nextflow/rseqc/rseqc_tin/.config.vsh.yaml | 4 +- target/nextflow/rseqc/rseqc_tin/main.nf | 4 +- target/nextflow/sortmerna/.config.vsh.yaml | 4 +- target/nextflow/sortmerna/main.nf | 4 +- target/nextflow/stringtie/.config.vsh.yaml | 4 +- target/nextflow/stringtie/main.nf | 4 +- .../summarizedexperiment/.config.vsh.yaml | 4 +- target/nextflow/summarizedexperiment/main.nf | 4 +- target/nextflow/trimgalore/.config.vsh.yaml | 4 +- target/nextflow/trimgalore/main.nf | 4 +- target/nextflow/tx2gene/.config.vsh.yaml | 4 +- target/nextflow/tx2gene/main.nf | 4 +- target/nextflow/tximport/.config.vsh.yaml | 4 +- target/nextflow/tximport/main.nf | 4 +- target/nextflow/ucsc/bedclip/.config.vsh.yaml | 4 +- target/nextflow/ucsc/bedclip/main.nf | 4 +- .../ucsc/bedgraphtobigwig/.config.vsh.yaml | 4 +- target/nextflow/ucsc/bedgraphtobigwig/main.nf | 4 +- .../umitools/umitools_dedup/.config.vsh.yaml | 4 +- .../nextflow/umitools/umitools_dedup/main.nf | 4 +- .../umitools_extract/.config.vsh.yaml | 4 +- .../umitools/umitools_extract/main.nf | 4 +- .../umitools_prepareforquant/.config.vsh.yaml | 4 +- .../nextflow/umitools_prepareforquant/main.nf | 4 +- .../.config.vsh.yaml | 13 +- .../genome_alignment_and_quant/main.nf | 20 +- .../nextflow_schema.json | 11 + .../merge_quant_results/.config.vsh.yaml | 4 +- .../workflows/merge_quant_results/main.nf | 4 +- .../post_processing/.config.vsh.yaml | 16 +- .../workflows/post_processing/main.nf | 16 +- .../post_processing/nextflow_schema.json | 6 +- .../workflows/pre_processing/.config.vsh.yaml | 8 +- .../nextflow/workflows/pre_processing/main.nf | 10 +- .../workflows/prepare_genome/.config.vsh.yaml | 4 +- .../nextflow/workflows/prepare_genome/main.nf | 4 +- .../.config.vsh.yaml | 6 +- .../pseudo_alignment_and_quant/main.nf | 14 +- .../nextflow_schema.json | 6 +- .../quality_control/.config.vsh.yaml | 41 +- .../workflows/quality_control/main.nf | 334 ++++++++++------ .../quality_control/nextflow_schema.json | 41 +- .../workflows/rnaseq/.config.vsh.yaml | 17 +- target/nextflow/workflows/rnaseq/main.nf | 52 ++- .../workflows/rnaseq/nextflow_schema.json | 11 + 212 files changed, 1377 insertions(+), 1008 deletions(-) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index d8871b3..e37f756 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -64,12 +64,12 @@ table_columns_visible: fastqc: percent_duplicates: False -fn_clean_extn: +extra_fn_clean_extn: - ".mapping_quality" - - ".MarkDuplicates_flagstat" - - ".MarkDuplicates_stats" - - ".genome_sorted" - - ".MarkDuplicates" + - ".MarkDuplicates_flagstat.output.flagstat" + - ".MarkDuplicates_idxstats.output.idxstats" + - ".MarkDuplicates_stats.output.txt" + - ".genome_sorted_MarkDuplicates.output.bam" - ".genome_sorted_MarkDuplicates" - ".read_1" - ".read_2" @@ -112,7 +112,7 @@ custom_data: # See https://multiqc.info/docs/#optimise-file-search-patterns for details sp: - fastqc: + fastqc/zip: fn: "*.fastqc.zip" cutadapt: diff --git a/src/prepare_multiqc_input/script.sh b/src/prepare_multiqc_input/script.sh index f5a9322..daa63e2 100644 --- a/src/prepare_multiqc_input/script.sh +++ b/src/prepare_multiqc_input/script.sh @@ -22,8 +22,9 @@ IFS="," read -ra star_multiqc <<< $par_star_multiqc && for file in "${star_multi IFS="," read -ra rsem_multiqc <<< $par_rsem_multiqc && for file in "${rsem_multiqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done -# TODO: Fetch Salmon meta info -# IFS="," read -ra salmon_multiqc <<< $par_salmon_multiqc && for file in "${salmon_multiqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done +IFS="," read -ra salmon_multiqc <<< $par_salmon_multiqc && for file in "${salmon_multiqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done + +IFS="," read -ra pseudo_multiqc <<< $par_pseudo_multiqc && for file in "${pseudo_multiqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done IFS="," read -ra samtools_stats <<< $par_samtools_stats && for file in "${samtools_stats[@]}"; do [ -e "$file" ] && cp -r "$file" $par_output/; done @@ -33,9 +34,6 @@ IFS="," read -ra samtools_idxstats <<< $par_samtools_idxstats && for file in "${ IFS="," read -ra markduplicates_multiqc <<< $par_markduplicates_multiqc && for file in "${markduplicates_multiqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done -IFS="," read -ra pseudo_multiqc <<< $par_pseudo_multiqc && for file in "${pseudo_multiqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done - - IFS="," read -ra featurecounts_multiqc <<< $par_featurecounts_multiqc && for file in "${featurecounts_multiqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done IFS="," read -ra featurecounts_rrna_multiqc <<< $par_featurecounts_rrna_multiqc && for file in "${featurecounts_rrna_multiqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done diff --git a/src/workflows/genome_alignment_and_quant/config.vsh.yaml b/src/workflows/genome_alignment_and_quant/config.vsh.yaml index aeafc2a..7816d39 100644 --- a/src/workflows/genome_alignment_and_quant/config.vsh.yaml +++ b/src/workflows/genome_alignment_and_quant/config.vsh.yaml @@ -145,6 +145,9 @@ argument_groups: type: file direction: output default: $id.quant.sf + - name: "--salmon_multiqc" + type: file + direction: output - name: "--rsem_counts_gene" type: file description: Expression counts on gene level diff --git a/src/workflows/genome_alignment_and_quant/main.nf b/src/workflows/genome_alignment_and_quant/main.nf index 7acf8c4..9ba3aee 100644 --- a/src/workflows/genome_alignment_and_quant/main.nf +++ b/src/workflows/genome_alignment_and_quant/main.nf @@ -280,6 +280,11 @@ workflow run_wf { ] ) + | map { id, state -> + def mod_state = (state.aligner == 'star_salmon') ? state + [salmon_multiqc: state.quant_out_dir] : state + [ id, mod_state ] + } + | niceView() | rsem_calculate_expression.run ( runIf: { id, state -> state.aligner == 'star_rsem' }, fromState: [ @@ -357,6 +362,7 @@ workflow run_wf { [ "star_alignment": "star_alignment", "star_multiqc": "star_multiqc", "rsem_multiqc": "rsem_multiqc", + "salmon_multiqc": "salmon_multiqc", "genome_bam_sorted": "genome_bam_sorted", "genome_bam_index": "genome_bam_index", "genome_bam_stats": "genome_bam_stats", diff --git a/src/workflows/post_processing/config.vsh.yaml b/src/workflows/post_processing/config.vsh.yaml index fa6fe56..b91e0a0 100644 --- a/src/workflows/post_processing/config.vsh.yaml +++ b/src/workflows/post_processing/config.vsh.yaml @@ -79,27 +79,27 @@ argument_groups: - name: "--processed_genome_bam" type: file direction: output - default: $id.markdup.sorted.bam + default: $id..genome.bam - name: "--genome_bam_index" type: file direction: output - default: $id.markdup.sorted.bam + default: $id.genome.bam.bai - name: "--genome_bam_stats" type: file direction: output - default: $id.markdup.sorted.bam.stats + default: $id.genome.stats - name: "--genome_bam_flagstat" type: file direction: output - default: $id.markdup.sorted.bam.flagstat + default: $id.genome.flagstat - name: "--genome_bam_idxstats" type: file direction: output - default: $id.markdup.sorted.bam.idxstats + default: $id.genome.idxstats - name: "--markduplicates_metrics" type: file direction: output - default: $id.markdup.sorted.MarkDuplicates.metrics.txt + default: $id.MarkDuplicates.metrics.txt - name: "--stringtie_transcript_gtf" type: file direction: output diff --git a/src/workflows/pre_processing/config.vsh.yaml b/src/workflows/pre_processing/config.vsh.yaml index f3e8686..b26fde6 100644 --- a/src/workflows/pre_processing/config.vsh.yaml +++ b/src/workflows/pre_processing/config.vsh.yaml @@ -162,14 +162,14 @@ argument_groups: required: false must_exist: false description: Path to output directory - default: $id.$key.read_1.fastq + default: $id.read_1.fastq - name: "--qc_output2" type: file direction: output required: false must_exist: false description: Path to output directory - default: $id.$key.read_2.fastq + default: $id.read_2.fastq - name: "--fastqc_html_1" type: file direction: output diff --git a/src/workflows/pre_processing/main.nf b/src/workflows/pre_processing/main.nf index 6717451..6e54b3f 100644 --- a/src/workflows/pre_processing/main.nf +++ b/src/workflows/pre_processing/main.nf @@ -75,7 +75,7 @@ workflow run_wf { "trim_html_1": "trimmed_fastqc_html_1", "trim_html_2": "trimmed_fastqc_html_2" ], - args: [gzip: true] + args: [gzip: true, fastqc: true] ) // Trim reads using fastp diff --git a/src/workflows/pseudo_alignment_and_quant/config.vsh.yaml b/src/workflows/pseudo_alignment_and_quant/config.vsh.yaml index 989a0d3..976bc06 100644 --- a/src/workflows/pseudo_alignment_and_quant/config.vsh.yaml +++ b/src/workflows/pseudo_alignment_and_quant/config.vsh.yaml @@ -59,7 +59,6 @@ argument_groups: - name: "--pseudo_multiqc" type: file direction: output - default: $id.quant.log - name: "--quant_out_dir" type: file direction: output diff --git a/src/workflows/pseudo_alignment_and_quant/main.nf b/src/workflows/pseudo_alignment_and_quant/main.nf index e407dd9..e275962 100644 --- a/src/workflows/pseudo_alignment_and_quant/main.nf +++ b/src/workflows/pseudo_alignment_and_quant/main.nf @@ -46,11 +46,16 @@ workflow run_wf { lib_type: state.lib_type ] }, toState: [ - "quant_outs_dir": "output", + "quant_out_dir": "output", "salmon_quant_results_file": "quant_results" ] ) + | map { id, state -> + def mod_state = (state.pseudo_aligner == 'salmon') ? state + [pseudo_multiqc: state.quant_out_dir] : state + [ id, mod_state ] + } + | kallisto_quant.run ( runIf: { id, state -> state.pseudo_aligner == 'kallisto'}, fromState: [ diff --git a/src/workflows/quality_control/config.vsh.yaml b/src/workflows/quality_control/config.vsh.yaml index 8453844..63ccddb 100644 --- a/src/workflows/quality_control/config.vsh.yaml +++ b/src/workflows/quality_control/config.vsh.yaml @@ -264,11 +264,6 @@ argument_groups: type: string - name: "--multiqc_methods_description" type: file - - name: "--mqc_yml" - type: file - description: Software versions - - name: "--workflow_summary" - type: file - name: "--passed_trimmed_reads" type: boolean - name: "--num_trimmed_reads" @@ -303,8 +298,8 @@ argument_groups: must_exist: false # - name: "--hisat2_multiqc" # type: file - # - name: "--rsem_multiqc" - # type: file + - name: "--rsem_multiqc" + type: file - name: "--genome_bam_stats" type: file must_exist: false @@ -548,9 +543,6 @@ argument_groups: type: file direction: output default: multiqc_plots - - name: "--multiqc_versions" - type: file - direction: output # Biotype QC - name: "--featurecounts" diff --git a/src/workflows/quality_control/main.nf b/src/workflows/quality_control/main.nf index f7350da..d74e758 100644 --- a/src/workflows/quality_control/main.nf +++ b/src/workflows/quality_control/main.nf @@ -55,7 +55,7 @@ workflow run_wf { "input": "genome_bam", "extra_preseq_args": "extra_preseq_args" ], - toState: [ "preseq_output": "output" ], + toState: [ "preseq_output": "output" ] ) | rseqc_bamstat.run ( @@ -214,11 +214,49 @@ workflow run_wf { merged_ch = qc_ch | toSortedList - - // TODO: Get Salmon meta info | map { list -> def ids = list.collect { id, state -> state.id } def strandedness = list.collect { id, state -> state.strandedness } + def num_trimmed_reads = list.collect { id, state -> state.num_trimmed_reads } + def passed_trimmed_reads = list.collect { id, state -> state.passed_trimmed_reads } + def passed_mapping = list.collect { id, state -> state.passed_mapping } + def percent_mapped = list.collect { id, state -> state.percent_mapped } + def inferred_strand = list.collect { id, state -> state.inferred_strand } + def passed_strand_check = list.collect { id, state -> state.passed_strand_check } + def gtf = list.collect { id, state -> state.gtf }.unique()[0] + def gtf_extra_attributes = list.collect { id, state -> state.gtf_extra_attributes }.unique()[0] + def gtf_group_features = list.collect { id, state -> state.gtf_group_features }.unique()[0] + def pca_header_multiqc = list.collect { id, state -> state.pca_header_multiqc }.unique()[0] + def clustering_header_multiqc = list.collect { id, state -> state.clustering_header_multiqc }.unique()[0] + def aligner = list.collect { id, state -> state.aligner }.unique()[0] + def pseudo_aligner = list.collect { id, state -> state.pseudo_aligner }.unique()[0] + def deseq2_vst = list.collect { id, state -> state.deseq2_vst }.unique()[0] + def extra_deseq2_args = list.collect { id, state -> state.extra_deseq2_args }.unique()[0] + def extra_deseq2_args2 = list.collect { id, state -> state.extra_deseq2_args2 }.unique()[0] + def skip_deseq2_qc = list.collect { id, state -> state.skip_deseq2_qc }.unique()[0] + def skip_qc = list.collect { id, state -> state.skip_qc }.unique()[0] + def skip_align = list.collect { id, state -> state.skip_align }.unique()[0] + def skip_pseudo_align = list.collect { id, state -> state.skip_pseudo_align }.unique()[0] + def quant_results = list.collect { id, state -> + (state.quant_results_file instanceof java.nio.file.Path && state.quant_results_file.exists()) ? + state.quant_results_file : + null } + def rsem_counts_gene = list.collect { id, state -> + (state.rsem_counts_gene instanceof java.nio.file.Path && state.rsem_counts_gene.exists()) ? + state.rsem_counts_gene : + null } + def rsem_counts_transcripts = list.collect { id, state -> + (state.rsem_counts_transcripts instanceof java.nio.file.Path && state.rsem_counts_transcripts.exists()) ? + state.rsem_counts_transcripts : + null } + def pseudo_salmon_quant_results = list.collect { id, state -> + (state.pseudo_salmon_quant_results_file instanceof java.nio.file.Path && state.pseudo_salmon_quant_results_file.exists()) ? + state.pseudo_salmon_quant_results_file : + null } + def pseudo_kallisto_quant_results = list.collect { id, state -> + (state.pseudo_kallisto_quant_results_file instanceof java.nio.file.Path && state.pseudo_kallisto_quant_results_file.exists()) ? + state.pseudo_kallisto_quant_results_file : + null } def fastqc_zip_1 = list.collect { id, state -> (state.fastqc_zip_1 instanceof java.nio.file.Path && state.fastqc_zip_1.exists()) ? state.fastqc_zip_1 : @@ -243,34 +281,14 @@ workflow run_wf { (state.trim_log_2 instanceof java.nio.file.Path && state.trim_log_2.exists()) ? state.trim_log_2 : null } - def sortmerna_log = list.collect { id, state -> - (state.sortmerna_log instanceof java.nio.file.Path && state.sortmerna_log.exists()) ? - state.sortmerna_log : + def sortmerna_multiqc = list.collect { id, state -> + (state.sortmerna_multiqc instanceof java.nio.file.Path && state.sortmerna_multiqc.exists()) ? + state.sortmerna_multiqc : null } def star_multiqc = list.collect { id, state -> (state.star_multiqc instanceof java.nio.file.Path && state.star_multiqc.exists()) ? state.star_multiqc : null } - def quant_results = list.collect { id, state -> - (state.quant_results_file instanceof java.nio.file.Path && state.quant_results_file.exists()) ? - state.quant_results_file : - null } - def rsem_counts_gene = list.collect { id, state -> - (state.rsem_counts_gene instanceof java.nio.file.Path && state.rsem_counts_gene.exists()) ? - state.rsem_counts_gene : - null } - def rsem_counts_transcripts = list.collect { id, state -> - (state.rsem_counts_transcripts instanceof java.nio.file.Path && state.rsem_counts_transcripts.exists()) ? - state.rsem_counts_transcripts : - null } - def pseudo_salmon_quant_results = list.collect { id, state -> - (state.pseudo_salmon_quant_results_file instanceof java.nio.file.Path && state.pseudo_salmon_quant_results_file.exists()) ? - state.pseudo_salmon_quant_results_file : - null } - def pseudo_kallisto_quant_results = list.collect { id, state -> - (state.pseudo_kallisto_quant_results_file instanceof java.nio.file.Path && state.pseudo_kallisto_quant_results_file.exists()) ? - state.pseudo_kallisto_quant_results_file : - null } def genome_bam_stats = list.collect { id, state -> (state.genome_bam_stats instanceof java.nio.file.Path && state.genome_bam_stats.exists()) ? state.genome_bam_stats : @@ -287,6 +305,14 @@ workflow run_wf { (state.markduplicates_multiqc instanceof java.nio.file.Path && state.markduplicates_multiqc.exists()) ? state.markduplicates_multiqc : null } + def salmon_multiqc = list.collect { id, state -> + (state.salmon_multiqc instanceof java.nio.file.Path && state.salmon_multiqc.exists()) ? + state.salmon_multiqc : + null } + def rsem_multiqc = list.collect { id, state -> + (state.rsem_multiqc instanceof java.nio.file.Path && state.rsem_multiqc.exists()) ? + state.rsem_multiqc : + null } def pseudo_multiqc = list.collect { id, state -> (state.pseudo_multiqc instanceof java.nio.file.Path && state.pseudo_multiqc.exists()) ? state.pseudo_multiqc : @@ -347,55 +373,18 @@ workflow run_wf { (state.tin_output_summary instanceof java.nio.file.Path && state.tin_output_summary.exists()) ? state.tin_output_summary : null } - def num_trimmed_reads = list.collect { id, state -> state.num_trimmed_reads } - def passed_trimmed_reads = list.collect { id, state -> state.passed_trimmed_reads } - def passed_mapping = list.collect { id, state -> state.passed_mapping } - def percent_mapped = list.collect { id, state -> state.percent_mapped } - def inferred_strand = list.collect { id, state -> state.inferred_strand } - def passed_strand_check = list.collect { id, state -> state.passed_strand_check } - def gtf = list.collect { id, state -> state.gtf }.unique()[0] - def gtf_extra_attributes = list.collect { id, state -> state.gtf_extra_attributes }.unique()[0] - def gtf_group_features = list.collect { id, state -> state.gtf_group_features }.unique()[0] - def pca_header_multiqc = list.collect { id, state -> state.pca_header_multiqc }.unique()[0] - def clustering_header_multiqc = list.collect { id, state -> state.clustering_header_multiqc }.unique()[0] - def aligner = list.collect { id, state -> state.aligner }.unique()[0] - def pseudo_aligner = list.collect { id, state -> state.pseudo_aligner }.unique()[0] - def deseq2_vst = list.collect { id, state -> state.deseq2_vst }.unique()[0] - def extra_deseq2_args = list.collect { id, state -> state.extra_deseq2_args }.unique()[0] - def extra_deseq2_args2 = list.collect { id, state -> state.extra_deseq2_args2 }.unique()[0] - def skip_deseq2_qc = list.collect { id, state -> state.skip_deseq2_qc }.unique()[0] def multiqc_custom_config = list.collect { id, state -> state.multiqc_custom_config }.unique()[0] - def skip_qc = list.collect { id, state -> state.skip_qc }.unique()[0] - def skip_align = list.collect { id, state -> state.skip_align }.unique()[0] - def skip_pseudo_align = list.collect { id, state -> state.skip_pseudo_align }.unique()[0] ["merged", [ ids: ids, strandedness: strandedness, - fastqc_zip: fastqc_zip_1 + fastqc_zip_2, - trim_zip: trim_zip_1 + trim_zip_2, - trim_log: trim_log_1 + trim_log_2, - sortmerna_log: sortmerna_log, - star_multiqc: star_multiqc, - salmon_multiqc: quant_results, - genome_bam_stats: genome_bam_stats, - genome_bam_flagstat: genome_bam_flagstat, - genome_bam_idxstats: genome_bam_idxstats, - markduplicates_multiqc: markduplicates_multiqc, - pseudo_multiqc: pseudo_multiqc, - featurecounts_multiqc: featurecounts_multiqc, - featurecounts_rrna_multiqc: featurecounts_rrna_multiqc, - preseq_output: preseq_output, - qualimap_output_dir: qualimap_output_dir, - dupradar_output_dup_intercept_mqc: dupradar_output_dup_intercept_mqc, - dupradar_output_duprate_exp_denscurve_mqc: dupradar_output_duprate_exp_denscurve_mqc, - bamstat_output: bamstat_output, - inner_dist_output_freq: inner_dist_output_freq, - inferexperiment_multiqc: inferexperiment_multiqc, - junction_annotation_output_log: junction_annotation_output_log, - junction_saturation_output_plot_r: junction_saturation_output_plot_r, - read_distribution_output: read_distribution_output, - read_duplication_output_duplication_rate_mapping: read_duplication_output_duplication_rate_mapping, - tin_output_summary: tin_output_summary, + num_trimmed_reads: num_trimmed_reads, + passed_trimmed_reads: passed_trimmed_reads, + passed_mapping: passed_mapping, + percent_mapped: percent_mapped, + inferred_strand: inferred_strand, + passed_strand_check: passed_strand_check, + skip_align: skip_align, + skip_pseudo_align: skip_pseudo_align, quant_results: quant_results, rsem_counts_gene: rsem_counts_gene, rsem_counts_transcripts: rsem_counts_transcripts, @@ -412,21 +401,143 @@ workflow run_wf { extra_deseq2_args: extra_deseq2_args, extra_deseq2_args2: extra_deseq2_args2, skip_deseq2_qc: skip_deseq2_qc, - num_trimmed_reads: num_trimmed_reads, - passed_trimmed_reads: passed_trimmed_reads, - passed_mapping: passed_mapping, - percent_mapped: percent_mapped, - inferred_strand: inferred_strand, - passed_strand_check: passed_strand_check, - multiqc_custom_config: multiqc_custom_config, - skip_align: skip_align, - skip_pseudo_align: skip_pseudo_align + fastqc_zip: fastqc_zip_1 + fastqc_zip_2, + trim_zip: trim_zip_1 + trim_zip_2, + trim_log: trim_log_1 + trim_log_2, + sortmerna_multiqc: sortmerna_multiqc, + star_multiqc: star_multiqc, + genome_bam_stats: genome_bam_stats, + genome_bam_flagstat: genome_bam_flagstat, + genome_bam_idxstats: genome_bam_idxstats, + markduplicates_multiqc: markduplicates_multiqc, + salmon_multiqc: salmon_multiqc, + rsem_multiqc: rsem_multiqc, + pseudo_multiqc: pseudo_multiqc, + featurecounts_multiqc: featurecounts_multiqc, + featurecounts_rrna_multiqc: featurecounts_rrna_multiqc, + preseq_output: preseq_output, + qualimap_output_dir: qualimap_output_dir, + dupradar_output_dup_intercept_mqc: dupradar_output_dup_intercept_mqc, + dupradar_output_duprate_exp_denscurve_mqc: dupradar_output_duprate_exp_denscurve_mqc, + bamstat_output: bamstat_output, + inner_dist_output_freq: inner_dist_output_freq, + inferexperiment_multiqc: inferexperiment_multiqc, + junction_annotation_output_log: junction_annotation_output_log, + junction_saturation_output_plot_r: junction_saturation_output_plot_r, + read_distribution_output: read_distribution_output, + read_duplication_output_duplication_rate_mapping: read_duplication_output_duplication_rate_mapping, + tin_output_summary: tin_output_summary, + multiqc_custom_config: multiqc_custom_config ] ] } - + + // | map { list -> + // def ids = list.collect { id, state -> state.id } + // def strandedness = list.collect { id, state -> state.strandedness } + // def num_trimmed_reads = list.collect { id, state -> state.num_trimmed_reads } + // def passed_trimmed_reads = list.collect { id, state -> state.passed_trimmed_reads } + // def passed_mapping = list.collect { id, state -> state.passed_mapping } + // def percent_mapped = list.collect { id, state -> state.percent_mapped } + // def inferred_strand = list.collect { id, state -> state.inferred_strand } + // def passed_strand_check = list.collect { id, state -> state.passed_strand_check } + // def gtf = list.collect { id, state -> state.gtf }.unique()[0] + // def gtf_extra_attributes = list.collect { id, state -> state.gtf_extra_attributes }.unique()[0] + // def gtf_group_features = list.collect { id, state -> state.gtf_group_features }.unique()[0] + // def pca_header_multiqc = list.collect { id, state -> state.pca_header_multiqc }.unique()[0] + // def clustering_header_multiqc = list.collect { id, state -> state.clustering_header_multiqc }.unique()[0] + // def aligner = list.collect { id, state -> state.aligner }.unique()[0] + // def pseudo_aligner = list.collect { id, state -> state.pseudo_aligner }.unique()[0] + // def deseq2_vst = list.collect { id, state -> state.deseq2_vst }.unique()[0] + // def extra_deseq2_args = list.collect { id, state -> state.extra_deseq2_args }.unique()[0] + // def extra_deseq2_args2 = list.collect { id, state -> state.extra_deseq2_args2 }.unique()[0] + // def skip_deseq2_qc = list.collect { id, state -> state.skip_deseq2_qc }.unique()[0] + // def skip_qc = list.collect { id, state -> state.skip_qc }.unique()[0] + // def skip_align = list.collect { id, state -> state.skip_align }.unique()[0] + // def skip_pseudo_align = list.collect { id, state -> state.skip_pseudo_align }.unique()[0] + // def quant_results = list.collect { id, state -> + // (state.quant_results_file instanceof java.nio.file.Path && state.quant_results_file.exists()) ? + // state.quant_results_file : + // null } + // def rsem_counts_gene = list.collect { id, state -> + // (state.rsem_counts_gene instanceof java.nio.file.Path && state.rsem_counts_gene.exists()) ? + // state.rsem_counts_gene : + // null } + // def rsem_counts_transcripts = list.collect { id, state -> + // (state.rsem_counts_transcripts instanceof java.nio.file.Path && state.rsem_counts_transcripts.exists()) ? + // state.rsem_counts_transcripts : + // null } + // def pseudo_salmon_quant_results = list.collect { id, state -> + // (state.pseudo_salmon_quant_results_file instanceof java.nio.file.Path && state.pseudo_salmon_quant_results_file.exists()) ? + // state.pseudo_salmon_quant_results_file : + // null } + // def pseudo_kallisto_quant_results = list.collect { id, state -> + // (state.pseudo_kallisto_quant_results_file instanceof java.nio.file.Path && state.pseudo_kallisto_quant_results_file.exists()) ? + // state.pseudo_kallisto_quant_results_file : + // null } + // def fastqc_zip_1_dirs = list.collect{it[1].fastqc_zip_1.getParent()} + // def fastqc_zip_2_dirs = list.collect{it[1].fastqc_zip_2.getParent()} + // def trim_zip_1_dirs = list.collect{it[1].trim_zip_1.getParent()} + // def trim_zip_2_dirs = list.collect{it[1].trim_zip_2.getParent()} + // def trim_log_1_dirs = list.collect{it[1].trim_log_1.getParent()} + // def trim_log_2_dirs = list.collect{it[1].trim_log_2.getParent()} + // def sortmerna_multiqc_dirs = list.collect{it[1].sortmerna_multiqc.getParent()} + // def star_multiqc_dirs = list.collect{it[1].star_multiqc.getParent()} + // def genome_bam_stats_dirs = list.collect{it[1].genome_bam_stats.getParent()} + // def genome_bam_flagstat_dirs = list.collect{it[1].genome_bam_flagstat.getParent()} + // def genome_bam_idxstats_dirs = list.collect{it[1].genome_bam_idxstats} + // def markduplicates_multiqc_dirs = list.collect{it[1].markduplicates_multiqc.getParent()} + // def salmon_multiqc_dirs = list.collect{it[1].salmon_multiqc} + // def rsem_multiqc_dirs = list.collect{it[1].rsem_multiqc.getParent()} + // def pseudo_multiqc_dirs = list.collect{it[1].pseudo_multiqc.getParent()} + // def featurecounts_multiqc_dirs = list.collect{it[1].featurecounts_multiqc.getParent()} + // def featurecounts_rrna_multiqc_dirs = list.collect{it[1].featurecounts_rrna_multiqc.getParent()} + // def preseq_output_dirs = list.collect{it[1].preseq_output.getParent()} + // def qualimap_output_dirs = list.collect{it[1].qualimap_output_dir} + // def dupradar_output_dup_intercept_mqc_dirs = list.collect{it[1].dupradar_output_dup_intercept_mqc.getParent()} + // def dupradar_output_duprate_exp_denscurve_mqc_dirs = list.collect{it[1].dupradar_output_duprate_exp_denscurve_mqc.getParent()} + // def bamstat_output_dirs = list.collect{it[1].bamstat_output.getParent()} + // def strandedness_output_dirs = list.collect{it[1].strandedness_output.getParent()} + // def inner_dist_output_freq_dirs = list.collect{it[1].inner_dist_output_freq.getParent()} + // def junction_annotation_output_log_dirs = list.collect{it[1].junction_annotation_output_log.getParent()} + // def junction_saturation_output_plot_r_dirs = list.collect{it[1].junction_saturation_output_plot_r.getParent()} + // def read_distribution_output_dirs = list.collect{it[1].read_distribution_output.getParent()} + // def read_duplication_output_duplication_rate_mapping_dirs = list.collect{it[1].read_duplication_output_duplication_rate_mapping.getParent()} + // def tin_output_summary_dirs = list.collect{it[1].tin_output_summary.getParent()} + // def multiqc_custom_config_dirs = list.collect{it[1].multiqc_custom_config.getParent()} + // ["merged", [ + // ids: ids, + // strandedness: strandedness, + // num_trimmed_reads: num_trimmed_reads, + // passed_trimmed_reads: passed_trimmed_reads, + // passed_mapping: passed_mapping, + // percent_mapped: percent_mapped, + // inferred_strand: inferred_strand, + // passed_strand_check: passed_strand_check, + // skip_align: skip_align, + // skip_pseudo_align: skip_pseudo_align, + // quant_results: quant_results, + // rsem_counts_gene: rsem_counts_gene, + // rsem_counts_transcripts: rsem_counts_transcripts, + // pseudo_salmon_quant_results: pseudo_salmon_quant_results, + // pseudo_kallisto_quant_results: pseudo_kallisto_quant_results, + // gtf: gtf, + // gtf_extra_attributes: gtf_extra_attributes, + // gtf_group_features: gtf_group_features, + // pca_header_multiqc: pca_header_multiqc, + // clustering_header_multiqc: clustering_header_multiqc, + // aligner: aligner, + // pseudo_aligner: pseudo_aligner, + // deseq2_vst: deseq2_vst, + // extra_deseq2_args: extra_deseq2_args, + // extra_deseq2_args2: extra_deseq2_args2, + // skip_deseq2_qc: skip_deseq2_qc, + // multiqc_input: fastqc_zip_1_dirs + fastqc_zip_2_dirs + trim_zip_1_dirs + trim_zip_2_dirs + trim_log_1_dirs + trim_log_2_dirs + sortmerna_multiqc_dirs + star_multiqc_dirs + genome_bam_stats_dirs + genome_bam_flagstat_dirs + genome_bam_idxstats_dirs + markduplicates_multiqc_dirs + salmon_multiqc_dirs + rsem_multiqc_dirs + pseudo_multiqc_dirs + featurecounts_multiqc_dirs + featurecounts_rrna_multiqc_dirs + preseq_output_dirs + qualimap_output_dirs + dupradar_output_dup_intercept_mqc_dirs + dupradar_output_duprate_exp_denscurve_mqc_dirs + bamstat_output_dirs + strandedness_output_dirs + inner_dist_output_freq_dirs + junction_annotation_output_log_dirs + junction_saturation_output_plot_r_dirs + read_distribution_output_dirs + read_duplication_output_duplication_rate_mapping_dirs + tin_output_summary_dirs + multiqc_custom_config_dirs + // ] ] + // } + // Merge quantification results of alignment | merge_quant_results.run ( - runIf: { id, state -> (!state.skip_align && state.aligner == 'star_salmon') || !skip_pseudo_align }, + runIf: { id, state -> !state.skip_align && state.aligner == 'star_salmon' }, fromState: [ "salmon_quant_results": "quant_results", "gtf": "gtf", @@ -445,7 +556,7 @@ workflow run_wf { "lengths_transcript": "lengths_transcript", "quant_merged_summarizedexperiment": "quant_merged_summarizedexperiment" ], - key: "merge_qunat_results" + key: "merge_quant_results" ) | rsem_merge_counts.run ( @@ -575,14 +686,15 @@ workflow run_wf { "fastqc_raw_multiqc": "fastqc_zip", "fastqc_trim_multiqc": "trim_zip", "trim_log_multiqc": "trim_log", - "sortmerna_multiqc": "sortmerna_log", + "sortmerna_multiqc": "sortmerna_multiqc", "star_multiqc": "star_multiqc", "salmon_multiqc": "salmon_multiqc", + "rsem_multiqc": "rsem_multiqc", + "pseudo_multiqc": "pseudo_multiqc", "samtools_stats": "genome_bam_stats", "samtools_flagstat": "genome_bam_flagstat", "samtools_idxstats": "genome_bam_idxstats", - "markduplicates_multiqc": "markduplicates_multiqc", - "pseudo_multiqc": "pseudo_multiqc", + "markduplicates_multiqc": "markduplicates_multiqc", "featurecounts_multiqc": "featurecounts_multiqc", "featurecounts_rrna_multiqc": "featurecounts_rrna_multiqc", "aligner_pca_multiqc": "deseq2_pca_multiqc", @@ -614,7 +726,7 @@ workflow run_wf { toState: [ "multiqc_report": "output_report", "multiqc_data": "output_data", - "multiqc_plots": "output_plots", + "multiqc_plots": "output_plots" ] ) @@ -716,8 +828,7 @@ workflow run_wf { "deseq2_output_pseudo": "deseq2_output_pseudo", "multiqc_report": "multiqc_report", "multiqc_data": "multiqc_data", - "multiqc_plots": "multiqc_plots", - "multiqc_versions": "multiqc_versions" + "multiqc_plots": "multiqc_plots" ] ) @@ -777,3 +888,5 @@ def getInferexperimentStrandedness(inferexperiment_file, cutoff=30) { return [ strandedness, sense, antisense, undetermined ] } + + diff --git a/src/workflows/rnaseq/config.vsh.yaml b/src/workflows/rnaseq/config.vsh.yaml index 3898c1b..151cb77 100644 --- a/src/workflows/rnaseq/config.vsh.yaml +++ b/src/workflows/rnaseq/config.vsh.yaml @@ -536,11 +536,15 @@ argument_groups: direction: output default: samtools_stats/$id.transcriptome.idxstats - # Salmon + # Transcript quantification - name: "--salmon_quant_results" type: file direction: output - default: Salmon/$id + default: STAR_Salmon/$id + - name: "--pseudo_quant_results" + type: file + direction: output + default: Pseudo_align_quant/$id # RSEM - name: "--rsem_counts_gene" diff --git a/src/workflows/rnaseq/main.nf b/src/workflows/rnaseq/main.nf index 14283b5..8a22197 100644 --- a/src/workflows/rnaseq/main.nf +++ b/src/workflows/rnaseq/main.nf @@ -219,6 +219,8 @@ workflow run_wf { toState: [ "star_alignment": "star_alignment", "star_multiqc": "star_multiqc", + "rsem_multiqc": "rsem_multiqc", + "salmon_multiqc": "salmon_multiqc", "genome_bam_sorted": "genome_bam_sorted", "genome_bam_index": "genome_bam_index", "genome_bam_stats": "genome_bam_stats", @@ -244,7 +246,7 @@ workflow run_wf { def passed_mapping = (percent_mapped >= state.min_mapped_reads) ? true : false [ id, state + [percent_mapped: percent_mapped, passed_mapping: passed_mapping] ] } - + // Pseudo-alignment and quantification | pseudo_alignment_and_quant.run ( runIf: { id, state -> !state.skip_pseudo_alignment && state.passed_trimmed_reads }, @@ -336,18 +338,23 @@ workflow run_wf { "skip_align": "skip_alignment", "skip_pseudo_align": "skip_pseudo_alignment", "gtf": "gtf", + "num_trimmed_reads": "num_trimmed_reads", + "passed_trimmed_reads": "passed_trimmed_reads", + "passed_mapping": "passed_mapping", + "percent_mapped": "percent_mapped", "genome_bam": "genome_bam_sorted", "genome_bam_index": "genome_bam_index", - "quant_out_dir": "quant_out_dir", + "salmon_multiqc": "salmon_multiqc", "quant_results_file": "quant_results_file", + "rsem_multiqc": "rsem_multiqc", "rsem_counts_gene": "rsem_counts_gene", "rsem_counts_transcripts": "rsem_counts_transcripts", + "pseudo_multiqc": "pseudo_multiqc", "pseudo_quant_out_dir": "pseudo_quant_out_dir", "pseudo_salmon_quant_results_file": "pseudo_salmon_quant_results_file", "pseudo_kallisto_quant_results_file": "pseudo_kallisto_quant_results_file", "aligner": "aligner", "pseudo_aligner": "pseudo_aligner", - "pseudo_multiqc": "pseudo_multiqc", "gene_bed": "gene_bed", "extra_preseq_args": "extra_preseq_args", "extra_featurecounts_args": "extra_featurecounts_args", @@ -375,11 +382,7 @@ workflow run_wf { "genome_bam_flagstat": "genome_bam_flagstat", "genome_bam_idxstats": "genome_bam_idxstats", "markduplicates_multiqc": "markduplicates_metrics", - "rseqc_modules": "rseqc_modules", - "num_trimmed_reads": "num_trimmed_reads", - "passed_trimmed_reads": "passed_trimmed_reads", - "passed_mapping": "passed_mapping", - "percent_mapped": "percent_mapped" + "rseqc_modules": "rseqc_modules" ], toState: [ "preseq_output": "preseq_output", @@ -425,7 +428,7 @@ workflow run_wf { "counts_gene_scaled": "counts_gene_scaled", "tpm_transcript": "tpm_transcript", "counts_transcript": "counts_transcript", - "salmon_merged_summarizedexperiment": "salmon_merged_summarizedexperiment", + "qunat_merged_summarizedexperiment": "quant_merged_summarizedexperiment", "deseq2_output": "deseq2_output", "multiqc_report": "multiqc_report", "multiqc_data": "multiqc_data", @@ -472,7 +475,8 @@ workflow run_wf { "transcriptome_bam_stats": "transcriptome_bam_stats", "transcriptome_bam_flagstat": "transcriptome_bam_flagstat", "transcriptome_bam_idxstats": "transcriptome_bam_idxstats", - "salmon_quant_results": "salmon_quant_results", + "salmon_quant_results": "quant_out_dir", + "pseudo_quant_results": "pseudo_quant_out_dir", "stringtie_transcript_gtf": "stringtie_transcript_gtf", "stringtie_coverage_gtf": "stringtie_coverage_gtf", "stringtie_abundance": "stringtie_abundance", @@ -538,8 +542,7 @@ workflow run_wf { "deseq2_output_pseudo": "deseq2_output_pseudo", "multiqc_report": "multiqc_report", "multiqc_data": "multiqc_data", - "multiqc_plots": "multiqc_plots", - "multiqc_versions": "multiqc_versions" + "multiqc_plots": "multiqc_plots" ] ) @@ -618,7 +621,7 @@ def getFastpReadsAfterFiltering(json_file) { } // -// Function that parses and returns the alignment rate from the STAR log output +// Function that parses and returns the alignment rate from the STAR log outputs // def getStarPercentMapped(align_log) { def percent_aligned = 0 diff --git a/target/executable/bbmap_bbsplit/.config.vsh.yaml b/target/executable/bbmap_bbsplit/.config.vsh.yaml index e0b6ed0..fb51071 100644 --- a/target/executable/bbmap_bbsplit/.config.vsh.yaml +++ b/target/executable/bbmap_bbsplit/.config.vsh.yaml @@ -238,8 +238,8 @@ build_info: output: "target/executable/bbmap_bbsplit" executable: "target/executable/bbmap_bbsplit/bbmap_bbsplit" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/bbmap_bbsplit/bbmap_bbsplit b/target/executable/bbmap_bbsplit/bbmap_bbsplit index 0965814..b9f9c39 100755 --- a/target/executable/bbmap_bbsplit/bbmap_bbsplit +++ b/target/executable/bbmap_bbsplit/bbmap_bbsplit @@ -506,9 +506,9 @@ tar xzf BBMap_39.01.tar.gz && \ cp -r bbmap/* /usr/local/bin LABEL org.opencontainers.image.description="Companion container for running component bbmap_bbsplit" -LABEL org.opencontainers.image.created="2024-09-24T10:12:43Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df" +LABEL org.opencontainers.image.created="2024-09-30T07:15:18Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/bedtools_genomecov/.config.vsh.yaml b/target/executable/bedtools_genomecov/.config.vsh.yaml index 0e75f20..c6b5f07 100644 --- a/target/executable/bedtools_genomecov/.config.vsh.yaml +++ b/target/executable/bedtools_genomecov/.config.vsh.yaml @@ -178,8 +178,8 @@ build_info: output: "target/executable/bedtools_genomecov" executable: "target/executable/bedtools_genomecov/bedtools_genomecov" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/bedtools_genomecov/bedtools_genomecov b/target/executable/bedtools_genomecov/bedtools_genomecov index 201ffd4..e2e87f6 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="2024-09-24T10:12:44Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df" +LABEL org.opencontainers.image.created="2024-09-30T07:15:18Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/cat_additional_fasta/.config.vsh.yaml b/target/executable/cat_additional_fasta/.config.vsh.yaml index 53bd1b4..295eff3 100644 --- a/target/executable/cat_additional_fasta/.config.vsh.yaml +++ b/target/executable/cat_additional_fasta/.config.vsh.yaml @@ -182,8 +182,8 @@ build_info: output: "target/executable/cat_additional_fasta" executable: "target/executable/cat_additional_fasta/cat_additional_fasta" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/cat_additional_fasta/cat_additional_fasta b/target/executable/cat_additional_fasta/cat_additional_fasta index 28a5eb3..90169b7 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="2024-09-24T10:12:50Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df" +LABEL org.opencontainers.image.created="2024-09-30T07:15:25Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/cat_fastq/.config.vsh.yaml b/target/executable/cat_fastq/.config.vsh.yaml index 807fae2..328f39b 100644 --- a/target/executable/cat_fastq/.config.vsh.yaml +++ b/target/executable/cat_fastq/.config.vsh.yaml @@ -169,8 +169,8 @@ build_info: output: "target/executable/cat_fastq" executable: "target/executable/cat_fastq/cat_fastq" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/cat_fastq/cat_fastq b/target/executable/cat_fastq/cat_fastq index e1192ba..3b14491 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="2024-09-24T10:12:51Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df" +LABEL org.opencontainers.image.created="2024-09-30T07:15:26Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/deseq2_qc/.config.vsh.yaml b/target/executable/deseq2_qc/.config.vsh.yaml index 7d36289..0b1c35a 100644 --- a/target/executable/deseq2_qc/.config.vsh.yaml +++ b/target/executable/deseq2_qc/.config.vsh.yaml @@ -237,8 +237,8 @@ build_info: output: "target/executable/deseq2_qc" executable: "target/executable/deseq2_qc/deseq2_qc" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/deseq2_qc/deseq2_qc b/target/executable/deseq2_qc/deseq2_qc index 4adde1f..de9eb5b 100755 --- a/target/executable/deseq2_qc/deseq2_qc +++ b/target/executable/deseq2_qc/deseq2_qc @@ -502,9 +502,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag Rscript -e 'remotes::install_url(c("https://cran.r-project.org/src/contrib/Archive/matrixStats/matrixStats_1.1.0.tar.gz"), repos = "https://cran.rstudio.com")' LABEL org.opencontainers.image.description="Companion container for running component deseq2_qc" -LABEL org.opencontainers.image.created="2024-09-24T10:13:00Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df" +LABEL org.opencontainers.image.created="2024-09-30T07:15:35Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/dupradar/.config.vsh.yaml b/target/executable/dupradar/.config.vsh.yaml index 68c9cf8..2ff7324 100644 --- a/target/executable/dupradar/.config.vsh.yaml +++ b/target/executable/dupradar/.config.vsh.yaml @@ -266,8 +266,8 @@ build_info: output: "target/executable/dupradar" executable: "target/executable/dupradar/dupradar" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/dupradar/dupradar b/target/executable/dupradar/dupradar index 323cd7c..3b1be76 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="2024-09-24T10:12:52Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df" +LABEL org.opencontainers.image.created="2024-09-30T07:15:27Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/fastqc/.config.vsh.yaml b/target/executable/fastqc/.config.vsh.yaml index 5aaceb5..af17ff0 100644 --- a/target/executable/fastqc/.config.vsh.yaml +++ b/target/executable/fastqc/.config.vsh.yaml @@ -198,8 +198,8 @@ build_info: output: "target/executable/fastqc" executable: "target/executable/fastqc/fastqc" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/fastqc/fastqc b/target/executable/fastqc/fastqc index 4e08100..32410ab 100755 --- a/target/executable/fastqc/fastqc +++ b/target/executable/fastqc/fastqc @@ -490,9 +490,9 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* LABEL org.opencontainers.image.description="Companion container for running component fastqc" -LABEL org.opencontainers.image.created="2024-09-24T10:12:45Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df" +LABEL org.opencontainers.image.created="2024-09-30T07:15:19Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/fq_subsample/.config.vsh.yaml b/target/executable/fq_subsample/.config.vsh.yaml index 24f3888..c34ffc9 100644 --- a/target/executable/fq_subsample/.config.vsh.yaml +++ b/target/executable/fq_subsample/.config.vsh.yaml @@ -177,8 +177,8 @@ build_info: output: "target/executable/fq_subsample" executable: "target/executable/fq_subsample/fq_subsample" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/fq_subsample/fq_subsample b/target/executable/fq_subsample/fq_subsample index f69a298..734a432 100755 --- a/target/executable/fq_subsample/fq_subsample +++ b/target/executable/fq_subsample/fq_subsample @@ -485,9 +485,9 @@ cargo install --locked --path . && \ mv /usr/local/fq/target/release/fq /usr/local/bin/ LABEL org.opencontainers.image.description="Companion container for running component fq_subsample" -LABEL org.opencontainers.image.created="2024-09-24T10:12:44Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df" +LABEL org.opencontainers.image.created="2024-09-30T07:15:19Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/getchromsizes/.config.vsh.yaml b/target/executable/getchromsizes/.config.vsh.yaml index 7b2adc0..99f3aa7 100644 --- a/target/executable/getchromsizes/.config.vsh.yaml +++ b/target/executable/getchromsizes/.config.vsh.yaml @@ -167,8 +167,8 @@ build_info: output: "target/executable/getchromsizes" executable: "target/executable/getchromsizes/getchromsizes" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/getchromsizes/getchromsizes b/target/executable/getchromsizes/getchromsizes index b4deb9a..0ae4e40 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="2024-09-24T10:12:45Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df" +LABEL org.opencontainers.image.created="2024-09-30T07:15:20Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/gtf2bed/.config.vsh.yaml b/target/executable/gtf2bed/.config.vsh.yaml index 9c63bc2..dc4b624 100644 --- a/target/executable/gtf2bed/.config.vsh.yaml +++ b/target/executable/gtf2bed/.config.vsh.yaml @@ -145,8 +145,8 @@ build_info: output: "target/executable/gtf2bed" executable: "target/executable/gtf2bed/gtf2bed" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/gtf2bed/gtf2bed b/target/executable/gtf2bed/gtf2bed index af121e5..f4458fc 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="2024-09-24T10:12:56Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df" +LABEL org.opencontainers.image.created="2024-09-30T07:15:31Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/gtf_filter/.config.vsh.yaml b/target/executable/gtf_filter/.config.vsh.yaml index 26b6161..6dfdc3b 100644 --- a/target/executable/gtf_filter/.config.vsh.yaml +++ b/target/executable/gtf_filter/.config.vsh.yaml @@ -155,8 +155,8 @@ build_info: output: "target/executable/gtf_filter" executable: "target/executable/gtf_filter/gtf_filter" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/gtf_filter/gtf_filter b/target/executable/gtf_filter/gtf_filter index f8021ef..5e9d73f 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="2024-09-24T10:12:59Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df" +LABEL org.opencontainers.image.created="2024-09-30T07:15:34Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/gunzip/.config.vsh.yaml b/target/executable/gunzip/.config.vsh.yaml index 33095bd..7846252 100644 --- a/target/executable/gunzip/.config.vsh.yaml +++ b/target/executable/gunzip/.config.vsh.yaml @@ -144,8 +144,8 @@ build_info: output: "target/executable/gunzip" executable: "target/executable/gunzip/gunzip" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/gunzip/gunzip b/target/executable/gunzip/gunzip index 2bfe369..11210a1 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="2024-09-24T10:12:45Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df" +LABEL org.opencontainers.image.created="2024-09-30T07:15:20Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/kallisto/kallisto_index/.config.vsh.yaml b/target/executable/kallisto/kallisto_index/.config.vsh.yaml index e40bb9f..aca24c2 100644 --- a/target/executable/kallisto/kallisto_index/.config.vsh.yaml +++ b/target/executable/kallisto/kallisto_index/.config.vsh.yaml @@ -155,8 +155,8 @@ build_info: output: "target/executable/kallisto/kallisto_index" executable: "target/executable/kallisto/kallisto_index/kallisto_index" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/kallisto/kallisto_index/kallisto_index b/target/executable/kallisto/kallisto_index/kallisto_index index 42ed391..b370ff0 100755 --- a/target/executable/kallisto/kallisto_index/kallisto_index +++ b/target/executable/kallisto/kallisto_index/kallisto_index @@ -471,9 +471,9 @@ tar -xzf kallisto_linux-v0.50.1.tar.gz && \ mv kallisto/kallisto /usr/local/bin/ LABEL org.opencontainers.image.description="Companion container for running component kallisto kallisto_index" -LABEL org.opencontainers.image.created="2024-09-24T10:12:57Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df" +LABEL org.opencontainers.image.created="2024-09-30T07:15:32Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/kallisto/kallisto_quant/.config.vsh.yaml b/target/executable/kallisto/kallisto_quant/.config.vsh.yaml index 5480d07..792012a 100644 --- a/target/executable/kallisto/kallisto_quant/.config.vsh.yaml +++ b/target/executable/kallisto/kallisto_quant/.config.vsh.yaml @@ -253,8 +253,8 @@ build_info: output: "target/executable/kallisto/kallisto_quant" executable: "target/executable/kallisto/kallisto_quant/kallisto_quant" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/kallisto/kallisto_quant/kallisto_quant b/target/executable/kallisto/kallisto_quant/kallisto_quant index af1a404..3cfff21 100755 --- a/target/executable/kallisto/kallisto_quant/kallisto_quant +++ b/target/executable/kallisto/kallisto_quant/kallisto_quant @@ -515,9 +515,9 @@ tar -xzf kallisto_linux-v0.50.1.tar.gz && \ mv kallisto/kallisto /usr/local/bin/ LABEL org.opencontainers.image.description="Companion container for running component kallisto kallisto_quant" -LABEL org.opencontainers.image.created="2024-09-24T10:12:57Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df" +LABEL org.opencontainers.image.created="2024-09-30T07:15:32Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/multiqc_custom_biotype/.config.vsh.yaml b/target/executable/multiqc_custom_biotype/.config.vsh.yaml index 7502225..caec3cd 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: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/multiqc_custom_biotype/multiqc_custom_biotype b/target/executable/multiqc_custom_biotype/multiqc_custom_biotype index 31e962f..2a9ae0e 100755 --- a/target/executable/multiqc_custom_biotype/multiqc_custom_biotype +++ b/target/executable/multiqc_custom_biotype/multiqc_custom_biotype @@ -481,9 +481,9 @@ RUN apt-get update && \ RUN pip install --upgrade pip LABEL org.opencontainers.image.description="Companion container for running component multiqc_custom_biotype" -LABEL org.opencontainers.image.created="2024-09-24T10:12:52Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df" +LABEL org.opencontainers.image.created="2024-09-30T07:15:27Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/picard_markduplicates/.config.vsh.yaml b/target/executable/picard_markduplicates/.config.vsh.yaml index 57de8b9..44d0d9e 100644 --- a/target/executable/picard_markduplicates/.config.vsh.yaml +++ b/target/executable/picard_markduplicates/.config.vsh.yaml @@ -207,8 +207,8 @@ build_info: output: "target/executable/picard_markduplicates" executable: "target/executable/picard_markduplicates/picard_markduplicates" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/picard_markduplicates/picard_markduplicates b/target/executable/picard_markduplicates/picard_markduplicates index 6d4cb8e..b2c0902 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="2024-09-24T10:12:59Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df" +LABEL org.opencontainers.image.created="2024-09-30T07:15:34Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/prepare_multiqc_input/.config.vsh.yaml b/target/executable/prepare_multiqc_input/.config.vsh.yaml index 1067cb7..3db4d8f 100644 --- a/target/executable/prepare_multiqc_input/.config.vsh.yaml +++ b/target/executable/prepare_multiqc_input/.config.vsh.yaml @@ -409,8 +409,8 @@ build_info: output: "target/executable/prepare_multiqc_input" executable: "target/executable/prepare_multiqc_input/prepare_multiqc_input" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/prepare_multiqc_input/prepare_multiqc_input b/target/executable/prepare_multiqc_input/prepare_multiqc_input index 7f618fc..9496d5a 100755 --- a/target/executable/prepare_multiqc_input/prepare_multiqc_input +++ b/target/executable/prepare_multiqc_input/prepare_multiqc_input @@ -557,9 +557,9 @@ function ViashDockerfile { FROM ubuntu:22.04 ENTRYPOINT [] LABEL org.opencontainers.image.description="Companion container for running component prepare_multiqc_input" -LABEL org.opencontainers.image.created="2024-09-24T10:12:55Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df" +LABEL org.opencontainers.image.created="2024-09-30T07:15:30Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER @@ -2285,8 +2285,9 @@ IFS="," read -ra star_multiqc <<< \$par_star_multiqc && for file in "\${star_mul IFS="," read -ra rsem_multiqc <<< \$par_rsem_multiqc && for file in "\${rsem_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done -# TODO: Fetch Salmon meta info -# IFS="," read -ra salmon_multiqc <<< \$par_salmon_multiqc && for file in "\${salmon_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done +IFS="," read -ra salmon_multiqc <<< \$par_salmon_multiqc && for file in "\${salmon_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done + +IFS="," read -ra pseudo_multiqc <<< \$par_pseudo_multiqc && for file in "\${pseudo_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done IFS="," read -ra samtools_stats <<< \$par_samtools_stats && for file in "\${samtools_stats[@]}"; do [ -e "\$file" ] && cp -r "\$file" \$par_output/; done @@ -2296,9 +2297,6 @@ IFS="," read -ra samtools_idxstats <<< \$par_samtools_idxstats && for file in "\ IFS="," read -ra markduplicates_multiqc <<< \$par_markduplicates_multiqc && for file in "\${markduplicates_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done -IFS="," read -ra pseudo_multiqc <<< \$par_pseudo_multiqc && for file in "\${pseudo_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done - - IFS="," read -ra featurecounts_multiqc <<< \$par_featurecounts_multiqc && for file in "\${featurecounts_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done IFS="," read -ra featurecounts_rrna_multiqc <<< \$par_featurecounts_rrna_multiqc && for file in "\${featurecounts_rrna_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done diff --git a/target/executable/preprocess_transcripts_fasta/.config.vsh.yaml b/target/executable/preprocess_transcripts_fasta/.config.vsh.yaml index 09423de..8a3b76c 100644 --- a/target/executable/preprocess_transcripts_fasta/.config.vsh.yaml +++ b/target/executable/preprocess_transcripts_fasta/.config.vsh.yaml @@ -138,8 +138,8 @@ build_info: output: "target/executable/preprocess_transcripts_fasta" executable: "target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta b/target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta index cac17c8..94346d7 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="2024-09-24T10:12:55Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df" +LABEL org.opencontainers.image.created="2024-09-30T07:15:30Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/preseq_lcextrap/.config.vsh.yaml b/target/executable/preseq_lcextrap/.config.vsh.yaml index bab38e9..bea730e 100644 --- a/target/executable/preseq_lcextrap/.config.vsh.yaml +++ b/target/executable/preseq_lcextrap/.config.vsh.yaml @@ -191,8 +191,8 @@ build_info: output: "target/executable/preseq_lcextrap" executable: "target/executable/preseq_lcextrap/preseq_lcextrap" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/preseq_lcextrap/preseq_lcextrap b/target/executable/preseq_lcextrap/preseq_lcextrap index d0fe596..84c42c1 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="2024-09-24T10:12:46Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df" +LABEL org.opencontainers.image.created="2024-09-30T07:15:20Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/qualimap/.config.vsh.yaml b/target/executable/qualimap/.config.vsh.yaml index c3f1f74..c9168b7 100644 --- a/target/executable/qualimap/.config.vsh.yaml +++ b/target/executable/qualimap/.config.vsh.yaml @@ -271,8 +271,8 @@ build_info: output: "target/executable/qualimap" executable: "target/executable/qualimap/qualimap" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/qualimap/qualimap b/target/executable/qualimap/qualimap index dd23aac..459d05b 100755 --- a/target/executable/qualimap/qualimap +++ b/target/executable/qualimap/qualimap @@ -537,9 +537,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag Rscript -e 'remotes::install_cran(c("optparse"), repos = "https://cran.rstudio.com")' LABEL org.opencontainers.image.description="Companion container for running component qualimap" -LABEL org.opencontainers.image.created="2024-09-24T10:12:44Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df" +LABEL org.opencontainers.image.created="2024-09-30T07:15:19Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml b/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml index 79d281f..b6787a7 100644 --- a/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml +++ b/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml @@ -299,8 +299,8 @@ build_info: output: "target/executable/rsem/rsem_calculate_expression" executable: "target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression b/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression index 2aa6ac3..15551c9 100755 --- a/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression +++ b/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression @@ -542,9 +542,9 @@ echo 'export PATH=$PATH:/usr/local/bin' >> ~/.bashrc && \ /bin/bash -c "source /etc/profile && source ~/.bashrc && echo $PATH && which STAR" LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_calculate_expression" -LABEL org.opencontainers.image.created="2024-09-24T10:12:57Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df" +LABEL org.opencontainers.image.created="2024-09-30T07:15:32Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/rsem/rsem_merge_counts/.config.vsh.yaml b/target/executable/rsem/rsem_merge_counts/.config.vsh.yaml index d0ddc73..e3f2126 100644 --- a/target/executable/rsem/rsem_merge_counts/.config.vsh.yaml +++ b/target/executable/rsem/rsem_merge_counts/.config.vsh.yaml @@ -182,8 +182,8 @@ build_info: output: "target/executable/rsem/rsem_merge_counts" executable: "target/executable/rsem/rsem_merge_counts/rsem_merge_counts" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/rsem/rsem_merge_counts/rsem_merge_counts b/target/executable/rsem/rsem_merge_counts/rsem_merge_counts index 2cc9720..fe7690f 100755 --- a/target/executable/rsem/rsem_merge_counts/rsem_merge_counts +++ b/target/executable/rsem/rsem_merge_counts/rsem_merge_counts @@ -483,9 +483,9 @@ function ViashDockerfile { FROM ubuntu:22.04 ENTRYPOINT [] LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_merge_counts" -LABEL org.opencontainers.image.created="2024-09-24T10:12:56Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df" +LABEL org.opencontainers.image.created="2024-09-30T07:15:31Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml b/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml index 254cf28..b065fdc 100644 --- a/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml @@ -163,8 +163,8 @@ build_info: output: "target/executable/rseqc/rseqc_bamstat" executable: "target/executable/rseqc/rseqc_bamstat/rseqc_bamstat" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat b/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat index cf65807..0bf42ee 100755 --- a/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat +++ b/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat @@ -477,9 +477,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "RSeQC" LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_bamstat" -LABEL org.opencontainers.image.created="2024-09-24T10:12:54Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df" +LABEL org.opencontainers.image.created="2024-09-30T07:15:29Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml b/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml index f68c948..b3d4cb6 100644 --- a/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml @@ -186,8 +186,8 @@ build_info: output: "target/executable/rseqc/rseqc_inferexperiment" executable: "target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment b/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment index f551b09..aea74ad 100755 --- a/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment +++ b/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment @@ -487,9 +487,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "RSeQC" LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_inferexperiment" -LABEL org.opencontainers.image.created="2024-09-24T10:12:52Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df" +LABEL org.opencontainers.image.created="2024-09-30T07:15:27Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml b/target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml index 6585195..a981793 100644 --- a/target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml @@ -272,8 +272,8 @@ build_info: output: "target/executable/rseqc/rseqc_innerdistance" executable: "target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance b/target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance index 6642bb0..f09313f 100755 --- a/target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance +++ b/target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance @@ -529,9 +529,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "RSeQC" LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_innerdistance" -LABEL org.opencontainers.image.created="2024-09-24T10:12:54Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df" +LABEL org.opencontainers.image.created="2024-09-30T07:15:29Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml b/target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml index 86ce891..0c389c9 100644 --- a/target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml @@ -260,8 +260,8 @@ build_info: output: "target/executable/rseqc/rseqc_junctionannotation" executable: "target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation b/target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation index d0ebb83..78ca45c 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="2024-09-24T10:12:53Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df" +LABEL org.opencontainers.image.created="2024-09-30T07:15:29Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_junctionsaturation/.config.vsh.yaml b/target/executable/rseqc/rseqc_junctionsaturation/.config.vsh.yaml index 81962a8..49b8c6c 100644 --- a/target/executable/rseqc/rseqc_junctionsaturation/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_junctionsaturation/.config.vsh.yaml @@ -249,8 +249,8 @@ build_info: output: "target/executable/rseqc/rseqc_junctionsaturation" executable: "target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation b/target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation index bcb40bd..069d0fa 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="2024-09-24T10:12:53Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df" +LABEL org.opencontainers.image.created="2024-09-30T07:15:28Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_readdistribution/.config.vsh.yaml b/target/executable/rseqc/rseqc_readdistribution/.config.vsh.yaml index b6a15cb..d3b73ba 100644 --- a/target/executable/rseqc/rseqc_readdistribution/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_readdistribution/.config.vsh.yaml @@ -162,8 +162,8 @@ build_info: output: "target/executable/rseqc/rseqc_readdistribution" executable: "target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution b/target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution index 9285ab0..a412b48 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="2024-09-24T10:12:54Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df" +LABEL org.opencontainers.image.created="2024-09-30T07:15:30Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_readduplication/.config.vsh.yaml b/target/executable/rseqc/rseqc_readduplication/.config.vsh.yaml index e0f7439..cc534cd 100644 --- a/target/executable/rseqc/rseqc_readduplication/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_readduplication/.config.vsh.yaml @@ -211,8 +211,8 @@ build_info: output: "target/executable/rseqc/rseqc_readduplication" executable: "target/executable/rseqc/rseqc_readduplication/rseqc_readduplication" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/rseqc/rseqc_readduplication/rseqc_readduplication b/target/executable/rseqc/rseqc_readduplication/rseqc_readduplication index 4454469..c0c67d6 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="2024-09-24T10:12:52Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df" +LABEL org.opencontainers.image.created="2024-09-30T07:15:28Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_tin/.config.vsh.yaml b/target/executable/rseqc/rseqc_tin/.config.vsh.yaml index b7f5aa1..f23874e 100644 --- a/target/executable/rseqc/rseqc_tin/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_tin/.config.vsh.yaml @@ -214,8 +214,8 @@ build_info: output: "target/executable/rseqc/rseqc_tin" executable: "target/executable/rseqc/rseqc_tin/rseqc_tin" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/rseqc/rseqc_tin/rseqc_tin b/target/executable/rseqc/rseqc_tin/rseqc_tin index 2b82598..88d51d1 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="2024-09-24T10:12:53Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df" +LABEL org.opencontainers.image.created="2024-09-30T07:15:28Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/sortmerna/.config.vsh.yaml b/target/executable/sortmerna/.config.vsh.yaml index 1c96f6e..d2c3d15 100644 --- a/target/executable/sortmerna/.config.vsh.yaml +++ b/target/executable/sortmerna/.config.vsh.yaml @@ -198,8 +198,8 @@ build_info: output: "target/executable/sortmerna" executable: "target/executable/sortmerna/sortmerna" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/sortmerna/sortmerna b/target/executable/sortmerna/sortmerna index bcd3f2c..1f23aa9 100755 --- a/target/executable/sortmerna/sortmerna +++ b/target/executable/sortmerna/sortmerna @@ -492,9 +492,9 @@ wget --no-check-certificate https://github.com/sortmerna/sortmerna/releases/down bash sortmerna-4.3.6-Linux.sh --skip-license LABEL org.opencontainers.image.description="Companion container for running component sortmerna" -LABEL org.opencontainers.image.created="2024-09-24T10:12:59Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df" +LABEL org.opencontainers.image.created="2024-09-30T07:15:34Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/stringtie/.config.vsh.yaml b/target/executable/stringtie/.config.vsh.yaml index 54e6c2e..60ae24b 100644 --- a/target/executable/stringtie/.config.vsh.yaml +++ b/target/executable/stringtie/.config.vsh.yaml @@ -216,8 +216,8 @@ build_info: output: "target/executable/stringtie" executable: "target/executable/stringtie/stringtie" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/stringtie/stringtie b/target/executable/stringtie/stringtie index 27a5459..6b33336 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="2024-09-24T10:12:56Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df" +LABEL org.opencontainers.image.created="2024-09-30T07:15:31Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/summarizedexperiment/.config.vsh.yaml b/target/executable/summarizedexperiment/.config.vsh.yaml index fef6d95..bd9b788 100644 --- a/target/executable/summarizedexperiment/.config.vsh.yaml +++ b/target/executable/summarizedexperiment/.config.vsh.yaml @@ -199,8 +199,8 @@ build_info: output: "target/executable/summarizedexperiment" executable: "target/executable/summarizedexperiment/summarizedexperiment" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/summarizedexperiment/summarizedexperiment b/target/executable/summarizedexperiment/summarizedexperiment index 275fda0..907ce28 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="2024-09-24T10:13:00Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df" +LABEL org.opencontainers.image.created="2024-09-30T07:15:35Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/trimgalore/.config.vsh.yaml b/target/executable/trimgalore/.config.vsh.yaml index 01db2e5..898d214 100644 --- a/target/executable/trimgalore/.config.vsh.yaml +++ b/target/executable/trimgalore/.config.vsh.yaml @@ -788,8 +788,8 @@ build_info: output: "target/executable/trimgalore" executable: "target/executable/trimgalore/trimgalore" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/trimgalore/trimgalore b/target/executable/trimgalore/trimgalore index 13d445b..2e8a60b 100755 --- a/target/executable/trimgalore/trimgalore +++ b/target/executable/trimgalore/trimgalore @@ -858,9 +858,9 @@ ENTRYPOINT [] RUN echo "TrimGalore: `trim_galore --version | sed -n 's/.*version\s\+\([0-9]\+\.[0-9]\+\.[0-9]\+\).*/\1/p'`" > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component trimgalore" -LABEL org.opencontainers.image.created="2024-09-24T10:12:58Z" +LABEL org.opencontainers.image.created="2024-09-30T07:15:33Z" LABEL org.opencontainers.image.source="https://github.com/FelixKrueger/TrimGalore" -LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df" +LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/tx2gene/.config.vsh.yaml b/target/executable/tx2gene/.config.vsh.yaml index bff44b4..c25ed48 100644 --- a/target/executable/tx2gene/.config.vsh.yaml +++ b/target/executable/tx2gene/.config.vsh.yaml @@ -192,8 +192,8 @@ build_info: output: "target/executable/tx2gene" executable: "target/executable/tx2gene/tx2gene" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/tx2gene/tx2gene b/target/executable/tx2gene/tx2gene index 28ce13d..dd1b6d7 100755 --- a/target/executable/tx2gene/tx2gene +++ b/target/executable/tx2gene/tx2gene @@ -487,9 +487,9 @@ RUN apt-get update && \ RUN pip install --upgrade pip LABEL org.opencontainers.image.description="Companion container for running component tx2gene" -LABEL org.opencontainers.image.created="2024-09-24T10:12:55Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df" +LABEL org.opencontainers.image.created="2024-09-30T07:15:31Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/tximport/.config.vsh.yaml b/target/executable/tximport/.config.vsh.yaml index 6934f09..07598cc 100644 --- a/target/executable/tximport/.config.vsh.yaml +++ b/target/executable/tximport/.config.vsh.yaml @@ -247,8 +247,8 @@ build_info: output: "target/executable/tximport" executable: "target/executable/tximport/tximport" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/tximport/tximport b/target/executable/tximport/tximport index 6304815..5879b58 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="2024-09-24T10:12:50Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df" +LABEL org.opencontainers.image.created="2024-09-30T07:15:25Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/ucsc/bedclip/.config.vsh.yaml b/target/executable/ucsc/bedclip/.config.vsh.yaml index 5ac1aec..ab06846 100644 --- a/target/executable/ucsc/bedclip/.config.vsh.yaml +++ b/target/executable/ucsc/bedclip/.config.vsh.yaml @@ -164,8 +164,8 @@ build_info: output: "target/executable/ucsc/bedclip" executable: "target/executable/ucsc/bedclip/bedclip" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/ucsc/bedclip/bedclip b/target/executable/ucsc/bedclip/bedclip index 7822e23..2dbdd1b 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="2024-09-24T10:12:51Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df" +LABEL org.opencontainers.image.created="2024-09-30T07:15:26Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/ucsc/bedgraphtobigwig/.config.vsh.yaml b/target/executable/ucsc/bedgraphtobigwig/.config.vsh.yaml index 278e3ba..39a7bf5 100644 --- a/target/executable/ucsc/bedgraphtobigwig/.config.vsh.yaml +++ b/target/executable/ucsc/bedgraphtobigwig/.config.vsh.yaml @@ -164,8 +164,8 @@ build_info: output: "target/executable/ucsc/bedgraphtobigwig" executable: "target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig b/target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig index 92c98fc..c6e03a9 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="2024-09-24T10:12:51Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df" +LABEL org.opencontainers.image.created="2024-09-30T07:15:26Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/umitools/umitools_dedup/.config.vsh.yaml b/target/executable/umitools/umitools_dedup/.config.vsh.yaml index 3bcefc3..ad64664 100644 --- a/target/executable/umitools/umitools_dedup/.config.vsh.yaml +++ b/target/executable/umitools/umitools_dedup/.config.vsh.yaml @@ -195,8 +195,8 @@ build_info: output: "target/executable/umitools/umitools_dedup" executable: "target/executable/umitools/umitools_dedup/umitools_dedup" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/umitools/umitools_dedup/umitools_dedup b/target/executable/umitools/umitools_dedup/umitools_dedup index a7f87ac..a227866 100755 --- a/target/executable/umitools/umitools_dedup/umitools_dedup +++ b/target/executable/umitools/umitools_dedup/umitools_dedup @@ -489,9 +489,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "umi_tools" LABEL org.opencontainers.image.description="Companion container for running component umitools umitools_dedup" -LABEL org.opencontainers.image.created="2024-09-24T10:12:58Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df" +LABEL org.opencontainers.image.created="2024-09-30T07:15:33Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/umitools/umitools_extract/.config.vsh.yaml b/target/executable/umitools/umitools_extract/.config.vsh.yaml index ff6f057..690c1e0 100644 --- a/target/executable/umitools/umitools_extract/.config.vsh.yaml +++ b/target/executable/umitools/umitools_extract/.config.vsh.yaml @@ -253,8 +253,8 @@ build_info: output: "target/executable/umitools/umitools_extract" executable: "target/executable/umitools/umitools_extract/umitools_extract" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/umitools/umitools_extract/umitools_extract b/target/executable/umitools/umitools_extract/umitools_extract index a30a893..7f68e3e 100755 --- a/target/executable/umitools/umitools_extract/umitools_extract +++ b/target/executable/umitools/umitools_extract/umitools_extract @@ -521,9 +521,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "umi_tools" LABEL org.opencontainers.image.description="Companion container for running component umitools umitools_extract" -LABEL org.opencontainers.image.created="2024-09-24T10:12:58Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df" +LABEL org.opencontainers.image.created="2024-09-30T07:15:33Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/umitools_prepareforquant/.config.vsh.yaml b/target/executable/umitools_prepareforquant/.config.vsh.yaml index e84775c..cdc52d7 100644 --- a/target/executable/umitools_prepareforquant/.config.vsh.yaml +++ b/target/executable/umitools_prepareforquant/.config.vsh.yaml @@ -156,8 +156,8 @@ build_info: output: "target/executable/umitools_prepareforquant" executable: "target/executable/umitools_prepareforquant/umitools_prepareforquant" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/umitools_prepareforquant/umitools_prepareforquant b/target/executable/umitools_prepareforquant/umitools_prepareforquant index e8edfa6..de782d4 100755 --- a/target/executable/umitools_prepareforquant/umitools_prepareforquant +++ b/target/executable/umitools_prepareforquant/umitools_prepareforquant @@ -473,9 +473,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "umi_tools" "pysam" LABEL org.opencontainers.image.description="Companion container for running component umitools_prepareforquant" -LABEL org.opencontainers.image.created="2024-09-24T10:13:00Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df" +LABEL org.opencontainers.image.created="2024-09-30T07:15:35Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" LABEL org.opencontainers.image.version="multiple_fixes" 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 77b672d..90674b9 100644 --- a/target/executable/workflows/genome_alignment_and_quant/.config.vsh.yaml +++ b/target/executable/workflows/genome_alignment_and_quant/.config.vsh.yaml @@ -381,6 +381,15 @@ argument_groups: direction: "output" multiple: false multiple_sep: ";" + - type: "file" + name: "--salmon_multiqc" + info: null + must_exist: true + create_parent: true + required: false + direction: "output" + multiple: false + multiple_sep: ";" - type: "file" name: "--rsem_counts_gene" description: "Expression counts on gene level" @@ -594,8 +603,8 @@ build_info: output: "target/executable/workflows/genome_alignment_and_quant" executable: "target/executable/workflows/genome_alignment_and_quant/genome_alignment_and_quant" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" dependencies: - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_align_reads" - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort" diff --git a/target/executable/workflows/genome_alignment_and_quant/genome_alignment_and_quant b/target/executable/workflows/genome_alignment_and_quant/genome_alignment_and_quant index 87a84a5..b522878 100755 --- a/target/executable/workflows/genome_alignment_and_quant/genome_alignment_and_quant +++ b/target/executable/workflows/genome_alignment_and_quant/genome_alignment_and_quant @@ -341,6 +341,9 @@ function ViashHelp { echo " type: file, output, file must exist" echo " default: \$id.quant.sf" echo "" + echo " --salmon_multiqc" + echo " type: file, output, file must exist" + echo "" echo " --rsem_counts_gene" echo " type: file, output, file must exist" echo " default: \$id.genes.results" @@ -792,6 +795,17 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_QUANT_RESULTS_FILE=$(ViashRemoveFlags "$1") shift 1 ;; + --salmon_multiqc) + [ -n "$VIASH_PAR_SALMON_MULTIQC" ] && ViashError Bad arguments for option \'--salmon_multiqc\': \'$VIASH_PAR_SALMON_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_SALMON_MULTIQC="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --salmon_multiqc. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --salmon_multiqc=*) + [ -n "$VIASH_PAR_SALMON_MULTIQC" ] && ViashError Bad arguments for option \'--salmon_multiqc=*\': \'$VIASH_PAR_SALMON_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_SALMON_MULTIQC=$(ViashRemoveFlags "$1") + shift 1 + ;; --rsem_counts_gene) [ -n "$VIASH_PAR_RSEM_COUNTS_GENE" ] && ViashError Bad arguments for option \'--rsem_counts_gene\': \'$VIASH_PAR_RSEM_COUNTS_GENE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 VIASH_PAR_RSEM_COUNTS_GENE="$2" @@ -1273,6 +1287,9 @@ fi if [ ! -z "$VIASH_PAR_QUANT_RESULTS_FILE" ] && [ ! -d "$(dirname "$VIASH_PAR_QUANT_RESULTS_FILE")" ]; then mkdir -p "$(dirname "$VIASH_PAR_QUANT_RESULTS_FILE")" fi +if [ ! -z "$VIASH_PAR_SALMON_MULTIQC" ] && [ ! -d "$(dirname "$VIASH_PAR_SALMON_MULTIQC")" ]; then + mkdir -p "$(dirname "$VIASH_PAR_SALMON_MULTIQC")" +fi if [ ! -z "$VIASH_PAR_RSEM_COUNTS_GENE" ] && [ ! -d "$(dirname "$VIASH_PAR_RSEM_COUNTS_GENE")" ]; then mkdir -p "$(dirname "$VIASH_PAR_RSEM_COUNTS_GENE")" fi @@ -1614,6 +1631,11 @@ workflow run_wf { ] ) + | map { id, state -> + def mod_state = (state.aligner == 'star_salmon') ? state + [salmon_multiqc: state.quant_out_dir] : state + [ id, mod_state ] + } + | niceView() | rsem_calculate_expression.run ( runIf: { id, state -> state.aligner == 'star_rsem' }, fromState: [ @@ -1691,6 +1713,7 @@ workflow run_wf { [ "star_alignment": "star_alignment", "star_multiqc": "star_multiqc", "rsem_multiqc": "rsem_multiqc", + "salmon_multiqc": "salmon_multiqc", "genome_bam_sorted": "genome_bam_sorted", "genome_bam_index": "genome_bam_index", "genome_bam_stats": "genome_bam_stats", @@ -1772,6 +1795,10 @@ if [ ! -z "$VIASH_PAR_QUANT_RESULTS_FILE" ] && [ ! -e "$VIASH_PAR_QUANT_RESULTS_ ViashError "Output file '$VIASH_PAR_QUANT_RESULTS_FILE' does not exist." exit 1 fi +if [ ! -z "$VIASH_PAR_SALMON_MULTIQC" ] && [ ! -e "$VIASH_PAR_SALMON_MULTIQC" ]; then + ViashError "Output file '$VIASH_PAR_SALMON_MULTIQC' does not exist." + exit 1 +fi if [ ! -z "$VIASH_PAR_RSEM_COUNTS_GENE" ] && [ ! -e "$VIASH_PAR_RSEM_COUNTS_GENE" ]; then ViashError "Output file '$VIASH_PAR_RSEM_COUNTS_GENE' does not exist." exit 1 diff --git a/target/executable/workflows/merge_quant_results/.config.vsh.yaml b/target/executable/workflows/merge_quant_results/.config.vsh.yaml index fcc338a..0da79e4 100644 --- a/target/executable/workflows/merge_quant_results/.config.vsh.yaml +++ b/target/executable/workflows/merge_quant_results/.config.vsh.yaml @@ -278,8 +278,8 @@ build_info: output: "target/executable/workflows/merge_quant_results" executable: "target/executable/workflows/merge_quant_results/merge_quant_results" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/tx2gene" - "target/nextflow/tximport" diff --git a/target/executable/workflows/post_processing/.config.vsh.yaml b/target/executable/workflows/post_processing/.config.vsh.yaml index b8c2bb3..f0f92d7 100644 --- a/target/executable/workflows/post_processing/.config.vsh.yaml +++ b/target/executable/workflows/post_processing/.config.vsh.yaml @@ -199,7 +199,7 @@ argument_groups: name: "--processed_genome_bam" info: null default: - - "$id.markdup.sorted.bam" + - "$id..genome.bam" must_exist: true create_parent: true required: false @@ -210,7 +210,7 @@ argument_groups: name: "--genome_bam_index" info: null default: - - "$id.markdup.sorted.bam" + - "$id.genome.bam.bai" must_exist: true create_parent: true required: false @@ -221,7 +221,7 @@ argument_groups: name: "--genome_bam_stats" info: null default: - - "$id.markdup.sorted.bam.stats" + - "$id.genome.stats" must_exist: true create_parent: true required: false @@ -232,7 +232,7 @@ argument_groups: name: "--genome_bam_flagstat" info: null default: - - "$id.markdup.sorted.bam.flagstat" + - "$id.genome.flagstat" must_exist: true create_parent: true required: false @@ -243,7 +243,7 @@ argument_groups: name: "--genome_bam_idxstats" info: null default: - - "$id.markdup.sorted.bam.idxstats" + - "$id.genome.idxstats" must_exist: true create_parent: true required: false @@ -254,7 +254,7 @@ argument_groups: name: "--markduplicates_metrics" info: null default: - - "$id.markdup.sorted.MarkDuplicates.metrics.txt" + - "$id.MarkDuplicates.metrics.txt" must_exist: true create_parent: true required: false @@ -486,8 +486,8 @@ build_info: output: "target/executable/workflows/post_processing" executable: "target/executable/workflows/post_processing/post_processing" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/picard_markduplicates" - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort" diff --git a/target/executable/workflows/post_processing/post_processing b/target/executable/workflows/post_processing/post_processing index 983b007..ad15b5c 100755 --- a/target/executable/workflows/post_processing/post_processing +++ b/target/executable/workflows/post_processing/post_processing @@ -269,27 +269,27 @@ function ViashHelp { echo "Output:" echo " --processed_genome_bam" echo " type: file, output, file must exist" - echo " default: \$id.markdup.sorted.bam" + echo " default: \$id..genome.bam" echo "" echo " --genome_bam_index" echo " type: file, output, file must exist" - echo " default: \$id.markdup.sorted.bam" + echo " default: \$id.genome.bam.bai" echo "" echo " --genome_bam_stats" echo " type: file, output, file must exist" - echo " default: \$id.markdup.sorted.bam.stats" + echo " default: \$id.genome.stats" echo "" echo " --genome_bam_flagstat" echo " type: file, output, file must exist" - echo " default: \$id.markdup.sorted.bam.flagstat" + echo " default: \$id.genome.flagstat" echo "" echo " --genome_bam_idxstats" echo " type: file, output, file must exist" - echo " default: \$id.markdup.sorted.bam.idxstats" + echo " default: \$id.genome.idxstats" echo "" echo " --markduplicates_metrics" echo " type: file, output, file must exist" - echo " default: \$id.markdup.sorted.MarkDuplicates.metrics.txt" + echo " default: \$id.MarkDuplicates.metrics.txt" echo "" echo " --stringtie_transcript_gtf" echo " type: file, output, file must exist" @@ -887,22 +887,22 @@ if [ -z ${VIASH_PAR_WITH_UMI+x} ]; then VIASH_PAR_WITH_UMI="false" fi if [ -z ${VIASH_PAR_PROCESSED_GENOME_BAM+x} ]; then - VIASH_PAR_PROCESSED_GENOME_BAM="\$id.markdup.sorted.bam" + VIASH_PAR_PROCESSED_GENOME_BAM="\$id..genome.bam" fi if [ -z ${VIASH_PAR_GENOME_BAM_INDEX+x} ]; then - VIASH_PAR_GENOME_BAM_INDEX="\$id.markdup.sorted.bam" + VIASH_PAR_GENOME_BAM_INDEX="\$id.genome.bam.bai" fi if [ -z ${VIASH_PAR_GENOME_BAM_STATS+x} ]; then - VIASH_PAR_GENOME_BAM_STATS="\$id.markdup.sorted.bam.stats" + VIASH_PAR_GENOME_BAM_STATS="\$id.genome.stats" fi if [ -z ${VIASH_PAR_GENOME_BAM_FLAGSTAT+x} ]; then - VIASH_PAR_GENOME_BAM_FLAGSTAT="\$id.markdup.sorted.bam.flagstat" + VIASH_PAR_GENOME_BAM_FLAGSTAT="\$id.genome.flagstat" fi if [ -z ${VIASH_PAR_GENOME_BAM_IDXSTATS+x} ]; then - VIASH_PAR_GENOME_BAM_IDXSTATS="\$id.markdup.sorted.bam.idxstats" + VIASH_PAR_GENOME_BAM_IDXSTATS="\$id.genome.idxstats" fi if [ -z ${VIASH_PAR_MARKDUPLICATES_METRICS+x} ]; then - VIASH_PAR_MARKDUPLICATES_METRICS="\$id.markdup.sorted.MarkDuplicates.metrics.txt" + VIASH_PAR_MARKDUPLICATES_METRICS="\$id.MarkDuplicates.metrics.txt" fi if [ -z ${VIASH_PAR_STRINGTIE_TRANSCRIPT_GTF+x} ]; then VIASH_PAR_STRINGTIE_TRANSCRIPT_GTF="\$id.stringtie.transcripts.gtf" diff --git a/target/executable/workflows/pre_processing/.config.vsh.yaml b/target/executable/workflows/pre_processing/.config.vsh.yaml index 491ed9c..d8c8d3a 100644 --- a/target/executable/workflows/pre_processing/.config.vsh.yaml +++ b/target/executable/workflows/pre_processing/.config.vsh.yaml @@ -353,7 +353,7 @@ argument_groups: description: "Path to output directory" info: null default: - - "$id.$key.read_1.fastq" + - "$id.read_1.fastq" must_exist: false create_parent: true required: false @@ -365,7 +365,7 @@ argument_groups: description: "Path to output directory" info: null default: - - "$id.$key.read_2.fastq" + - "$id.read_2.fastq" must_exist: false create_parent: true required: false @@ -673,8 +673,8 @@ build_info: output: "target/executable/workflows/pre_processing" executable: "target/executable/workflows/pre_processing/pre_processing" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/fastqc" - "target/nextflow/umitools/umitools_extract" diff --git a/target/executable/workflows/pre_processing/pre_processing b/target/executable/workflows/pre_processing/pre_processing index d89842b..32b38c3 100755 --- a/target/executable/workflows/pre_processing/pre_processing +++ b/target/executable/workflows/pre_processing/pre_processing @@ -350,12 +350,12 @@ function ViashHelp { echo "Output:" echo " --qc_output1" echo " type: file, output" - echo " default: \$id.\$key.read_1.fastq" + echo " default: \$id.read_1.fastq" echo " Path to output directory" echo "" echo " --qc_output2" echo " type: file, output" - echo " default: \$id.\$key.read_2.fastq" + echo " default: \$id.read_2.fastq" echo " Path to output directory" echo "" echo " --fastqc_html_1" @@ -1167,10 +1167,10 @@ if [ -z ${VIASH_PAR_EXTRA_FQ_SUBSAMPLE_ARGS+x} ]; then VIASH_PAR_EXTRA_FQ_SUBSAMPLE_ARGS="--record-count 1000000 --seed 1" fi if [ -z ${VIASH_PAR_QC_OUTPUT1+x} ]; then - VIASH_PAR_QC_OUTPUT1="\$id.\$key.read_1.fastq" + VIASH_PAR_QC_OUTPUT1="\$id.read_1.fastq" fi if [ -z ${VIASH_PAR_QC_OUTPUT2+x} ]; then - VIASH_PAR_QC_OUTPUT2="\$id.\$key.read_2.fastq" + VIASH_PAR_QC_OUTPUT2="\$id.read_2.fastq" fi if [ -z ${VIASH_PAR_FASTQC_HTML_1+x} ]; then VIASH_PAR_FASTQC_HTML_1="\$id.read_1.fastqc.html" @@ -1609,7 +1609,7 @@ workflow run_wf { "trim_html_1": "trimmed_fastqc_html_1", "trim_html_2": "trimmed_fastqc_html_2" ], - args: [gzip: true] + args: [gzip: true, fastqc: true] ) // Trim reads using fastp diff --git a/target/executable/workflows/prepare_genome/.config.vsh.yaml b/target/executable/workflows/prepare_genome/.config.vsh.yaml index 60b87fa..a69e47e 100644 --- a/target/executable/workflows/prepare_genome/.config.vsh.yaml +++ b/target/executable/workflows/prepare_genome/.config.vsh.yaml @@ -496,8 +496,8 @@ build_info: output: "target/executable/workflows/prepare_genome" executable: "target/executable/workflows/prepare_genome/prepare_genome" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/gunzip" - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/gffread" diff --git a/target/executable/workflows/pseudo_alignment_and_quant/.config.vsh.yaml b/target/executable/workflows/pseudo_alignment_and_quant/.config.vsh.yaml index 4ef2cc5..1a41217 100644 --- a/target/executable/workflows/pseudo_alignment_and_quant/.config.vsh.yaml +++ b/target/executable/workflows/pseudo_alignment_and_quant/.config.vsh.yaml @@ -139,8 +139,6 @@ argument_groups: - type: "file" name: "--pseudo_multiqc" info: null - default: - - "$id.quant.log" must_exist: true create_parent: true required: false @@ -285,8 +283,8 @@ build_info: output: "target/executable/workflows/pseudo_alignment_and_quant" executable: "target/executable/workflows/pseudo_alignment_and_quant/pseudo_alignment_and_quant" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" dependencies: - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant" - "target/nextflow/kallisto/kallisto_quant" diff --git a/target/executable/workflows/pseudo_alignment_and_quant/pseudo_alignment_and_quant b/target/executable/workflows/pseudo_alignment_and_quant/pseudo_alignment_and_quant index 085e2d6..39b4fdf 100755 --- a/target/executable/workflows/pseudo_alignment_and_quant/pseudo_alignment_and_quant +++ b/target/executable/workflows/pseudo_alignment_and_quant/pseudo_alignment_and_quant @@ -239,7 +239,6 @@ function ViashHelp { echo "Output:" echo " --pseudo_multiqc" echo " type: file, output, file must exist" - echo " default: \$id.quant.log" echo "" echo " --quant_out_dir" echo " type: file, output, file must exist" @@ -608,9 +607,6 @@ fi if [ -z ${VIASH_PAR_LIB_TYPE+x} ]; then VIASH_PAR_LIB_TYPE="" fi -if [ -z ${VIASH_PAR_PSEUDO_MULTIQC+x} ]; then - VIASH_PAR_PSEUDO_MULTIQC="\$id.quant.log" -fi if [ -z ${VIASH_PAR_QUANT_OUT_DIR+x} ]; then VIASH_PAR_QUANT_OUT_DIR="\$id.quant" fi @@ -852,11 +848,16 @@ workflow run_wf { lib_type: state.lib_type ] }, toState: [ - "quant_outs_dir": "output", + "quant_out_dir": "output", "salmon_quant_results_file": "quant_results" ] ) + | map { id, state -> + def mod_state = (state.pseudo_aligner == 'salmon') ? state + [pseudo_multiqc: state.quant_out_dir] : state + [ id, mod_state ] + } + | kallisto_quant.run ( runIf: { id, state -> state.pseudo_aligner == 'kallisto'}, fromState: [ diff --git a/target/executable/workflows/quality_control/.config.vsh.yaml b/target/executable/workflows/quality_control/.config.vsh.yaml index fa2aa6c..ad74eb3 100644 --- a/target/executable/workflows/quality_control/.config.vsh.yaml +++ b/target/executable/workflows/quality_control/.config.vsh.yaml @@ -632,25 +632,6 @@ argument_groups: direction: "input" multiple: false multiple_sep: ";" - - type: "file" - name: "--mqc_yml" - description: "Software versions" - info: null - must_exist: true - create_parent: true - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--workflow_summary" - info: null - must_exist: true - create_parent: true - required: false - direction: "input" - multiple: false - multiple_sep: ";" - type: "boolean" name: "--passed_trimmed_reads" info: null @@ -751,6 +732,15 @@ argument_groups: direction: "input" multiple: false multiple_sep: ";" + - type: "file" + name: "--rsem_multiqc" + info: null + must_exist: true + create_parent: true + required: false + direction: "input" + multiple: false + multiple_sep: ";" - type: "file" name: "--genome_bam_stats" info: null @@ -1253,15 +1243,6 @@ argument_groups: direction: "output" multiple: false multiple_sep: ";" - - type: "file" - name: "--multiqc_versions" - info: null - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - type: "file" name: "--featurecounts" info: null @@ -1615,8 +1596,8 @@ build_info: output: "target/executable/workflows/quality_control" executable: "target/executable/workflows/quality_control/quality_control" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/rseqc/rseqc_bamstat" - "target/nextflow/rseqc/rseqc_inferexperiment" diff --git a/target/executable/workflows/quality_control/quality_control b/target/executable/workflows/quality_control/quality_control index 5bd09a5..d699ac5 100755 --- a/target/executable/workflows/quality_control/quality_control +++ b/target/executable/workflows/quality_control/quality_control @@ -491,13 +491,6 @@ function ViashHelp { echo " --multiqc_methods_description" echo " type: file, file must exist" echo "" - echo " --mqc_yml" - echo " type: file, file must exist" - echo " Software versions" - echo "" - echo " --workflow_summary" - echo " type: file, file must exist" - echo "" echo " --passed_trimmed_reads" echo " type: boolean" echo "" @@ -534,6 +527,9 @@ function ViashHelp { echo " --star_multiqc" echo " type: file" echo "" + echo " --rsem_multiqc" + echo " type: file, file must exist" + echo "" echo " --genome_bam_stats" echo " type: file" echo "" @@ -739,9 +735,6 @@ function ViashHelp { echo " type: file, output, file must exist" echo " default: multiqc_plots" echo "" - echo " --multiqc_versions" - echo " type: file, output, file must exist" - echo "" echo " --featurecounts" echo " type: file, output" echo " default: \$id.featureCounts.txt" @@ -1509,28 +1502,6 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_MULTIQC_METHODS_DESCRIPTION=$(ViashRemoveFlags "$1") shift 1 ;; - --mqc_yml) - [ -n "$VIASH_PAR_MQC_YML" ] && ViashError Bad arguments for option \'--mqc_yml\': \'$VIASH_PAR_MQC_YML\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_MQC_YML="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --mqc_yml. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --mqc_yml=*) - [ -n "$VIASH_PAR_MQC_YML" ] && ViashError Bad arguments for option \'--mqc_yml=*\': \'$VIASH_PAR_MQC_YML\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_MQC_YML=$(ViashRemoveFlags "$1") - shift 1 - ;; - --workflow_summary) - [ -n "$VIASH_PAR_WORKFLOW_SUMMARY" ] && ViashError Bad arguments for option \'--workflow_summary\': \'$VIASH_PAR_WORKFLOW_SUMMARY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_WORKFLOW_SUMMARY="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --workflow_summary. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --workflow_summary=*) - [ -n "$VIASH_PAR_WORKFLOW_SUMMARY" ] && ViashError Bad arguments for option \'--workflow_summary=*\': \'$VIASH_PAR_WORKFLOW_SUMMARY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_WORKFLOW_SUMMARY=$(ViashRemoveFlags "$1") - shift 1 - ;; --passed_trimmed_reads) [ -n "$VIASH_PAR_PASSED_TRIMMED_READS" ] && ViashError Bad arguments for option \'--passed_trimmed_reads\': \'$VIASH_PAR_PASSED_TRIMMED_READS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 VIASH_PAR_PASSED_TRIMMED_READS="$2" @@ -1663,6 +1634,17 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_STAR_MULTIQC=$(ViashRemoveFlags "$1") shift 1 ;; + --rsem_multiqc) + [ -n "$VIASH_PAR_RSEM_MULTIQC" ] && ViashError Bad arguments for option \'--rsem_multiqc\': \'$VIASH_PAR_RSEM_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_RSEM_MULTIQC="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --rsem_multiqc. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --rsem_multiqc=*) + [ -n "$VIASH_PAR_RSEM_MULTIQC" ] && ViashError Bad arguments for option \'--rsem_multiqc=*\': \'$VIASH_PAR_RSEM_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_RSEM_MULTIQC=$(ViashRemoveFlags "$1") + shift 1 + ;; --genome_bam_stats) [ -n "$VIASH_PAR_GENOME_BAM_STATS" ] && ViashError Bad arguments for option \'--genome_bam_stats\': \'$VIASH_PAR_GENOME_BAM_STATS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 VIASH_PAR_GENOME_BAM_STATS="$2" @@ -2136,17 +2118,6 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_MULTIQC_PLOTS=$(ViashRemoveFlags "$1") shift 1 ;; - --multiqc_versions) - [ -n "$VIASH_PAR_MULTIQC_VERSIONS" ] && ViashError Bad arguments for option \'--multiqc_versions\': \'$VIASH_PAR_MULTIQC_VERSIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_MULTIQC_VERSIONS="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --multiqc_versions. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --multiqc_versions=*) - [ -n "$VIASH_PAR_MULTIQC_VERSIONS" ] && ViashError Bad arguments for option \'--multiqc_versions=*\': \'$VIASH_PAR_MULTIQC_VERSIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_MULTIQC_VERSIONS=$(ViashRemoveFlags "$1") - shift 1 - ;; --featurecounts) [ -n "$VIASH_PAR_FEATURECOUNTS" ] && ViashError Bad arguments for option \'--featurecounts\': \'$VIASH_PAR_FEATURECOUNTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 VIASH_PAR_FEATURECOUNTS="$2" @@ -2820,12 +2791,8 @@ if [ ! -z "$VIASH_PAR_MULTIQC_METHODS_DESCRIPTION" ] && [ ! -e "$VIASH_PAR_MULTI ViashError "Input file '$VIASH_PAR_MULTIQC_METHODS_DESCRIPTION' does not exist." exit 1 fi -if [ ! -z "$VIASH_PAR_MQC_YML" ] && [ ! -e "$VIASH_PAR_MQC_YML" ]; then - ViashError "Input file '$VIASH_PAR_MQC_YML' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_WORKFLOW_SUMMARY" ] && [ ! -e "$VIASH_PAR_WORKFLOW_SUMMARY" ]; then - ViashError "Input file '$VIASH_PAR_WORKFLOW_SUMMARY' does not exist." +if [ ! -z "$VIASH_PAR_RSEM_MULTIQC" ] && [ ! -e "$VIASH_PAR_RSEM_MULTIQC" ]; then + ViashError "Input file '$VIASH_PAR_RSEM_MULTIQC' does not exist." exit 1 fi @@ -3297,9 +3264,6 @@ fi if [ ! -z "$VIASH_PAR_MULTIQC_PLOTS" ] && [ ! -d "$(dirname "$VIASH_PAR_MULTIQC_PLOTS")" ]; then mkdir -p "$(dirname "$VIASH_PAR_MULTIQC_PLOTS")" fi -if [ ! -z "$VIASH_PAR_MULTIQC_VERSIONS" ] && [ ! -d "$(dirname "$VIASH_PAR_MULTIQC_VERSIONS")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_MULTIQC_VERSIONS")" -fi if [ ! -z "$VIASH_PAR_FEATURECOUNTS" ] && [ ! -d "$(dirname "$VIASH_PAR_FEATURECOUNTS")" ]; then mkdir -p "$(dirname "$VIASH_PAR_FEATURECOUNTS")" fi @@ -3460,7 +3424,7 @@ workflow run_wf { "input": "genome_bam", "extra_preseq_args": "extra_preseq_args" ], - toState: [ "preseq_output": "output" ], + toState: [ "preseq_output": "output" ] ) | rseqc_bamstat.run ( @@ -3619,11 +3583,49 @@ workflow run_wf { merged_ch = qc_ch | toSortedList - - // TODO: Get Salmon meta info | map { list -> def ids = list.collect { id, state -> state.id } def strandedness = list.collect { id, state -> state.strandedness } + def num_trimmed_reads = list.collect { id, state -> state.num_trimmed_reads } + def passed_trimmed_reads = list.collect { id, state -> state.passed_trimmed_reads } + def passed_mapping = list.collect { id, state -> state.passed_mapping } + def percent_mapped = list.collect { id, state -> state.percent_mapped } + def inferred_strand = list.collect { id, state -> state.inferred_strand } + def passed_strand_check = list.collect { id, state -> state.passed_strand_check } + def gtf = list.collect { id, state -> state.gtf }.unique()[0] + def gtf_extra_attributes = list.collect { id, state -> state.gtf_extra_attributes }.unique()[0] + def gtf_group_features = list.collect { id, state -> state.gtf_group_features }.unique()[0] + def pca_header_multiqc = list.collect { id, state -> state.pca_header_multiqc }.unique()[0] + def clustering_header_multiqc = list.collect { id, state -> state.clustering_header_multiqc }.unique()[0] + def aligner = list.collect { id, state -> state.aligner }.unique()[0] + def pseudo_aligner = list.collect { id, state -> state.pseudo_aligner }.unique()[0] + def deseq2_vst = list.collect { id, state -> state.deseq2_vst }.unique()[0] + def extra_deseq2_args = list.collect { id, state -> state.extra_deseq2_args }.unique()[0] + def extra_deseq2_args2 = list.collect { id, state -> state.extra_deseq2_args2 }.unique()[0] + def skip_deseq2_qc = list.collect { id, state -> state.skip_deseq2_qc }.unique()[0] + def skip_qc = list.collect { id, state -> state.skip_qc }.unique()[0] + def skip_align = list.collect { id, state -> state.skip_align }.unique()[0] + def skip_pseudo_align = list.collect { id, state -> state.skip_pseudo_align }.unique()[0] + def quant_results = list.collect { id, state -> + (state.quant_results_file instanceof java.nio.file.Path && state.quant_results_file.exists()) ? + state.quant_results_file : + null } + def rsem_counts_gene = list.collect { id, state -> + (state.rsem_counts_gene instanceof java.nio.file.Path && state.rsem_counts_gene.exists()) ? + state.rsem_counts_gene : + null } + def rsem_counts_transcripts = list.collect { id, state -> + (state.rsem_counts_transcripts instanceof java.nio.file.Path && state.rsem_counts_transcripts.exists()) ? + state.rsem_counts_transcripts : + null } + def pseudo_salmon_quant_results = list.collect { id, state -> + (state.pseudo_salmon_quant_results_file instanceof java.nio.file.Path && state.pseudo_salmon_quant_results_file.exists()) ? + state.pseudo_salmon_quant_results_file : + null } + def pseudo_kallisto_quant_results = list.collect { id, state -> + (state.pseudo_kallisto_quant_results_file instanceof java.nio.file.Path && state.pseudo_kallisto_quant_results_file.exists()) ? + state.pseudo_kallisto_quant_results_file : + null } def fastqc_zip_1 = list.collect { id, state -> (state.fastqc_zip_1 instanceof java.nio.file.Path && state.fastqc_zip_1.exists()) ? state.fastqc_zip_1 : @@ -3648,34 +3650,14 @@ workflow run_wf { (state.trim_log_2 instanceof java.nio.file.Path && state.trim_log_2.exists()) ? state.trim_log_2 : null } - def sortmerna_log = list.collect { id, state -> - (state.sortmerna_log instanceof java.nio.file.Path && state.sortmerna_log.exists()) ? - state.sortmerna_log : + def sortmerna_multiqc = list.collect { id, state -> + (state.sortmerna_multiqc instanceof java.nio.file.Path && state.sortmerna_multiqc.exists()) ? + state.sortmerna_multiqc : null } def star_multiqc = list.collect { id, state -> (state.star_multiqc instanceof java.nio.file.Path && state.star_multiqc.exists()) ? state.star_multiqc : null } - def quant_results = list.collect { id, state -> - (state.quant_results_file instanceof java.nio.file.Path && state.quant_results_file.exists()) ? - state.quant_results_file : - null } - def rsem_counts_gene = list.collect { id, state -> - (state.rsem_counts_gene instanceof java.nio.file.Path && state.rsem_counts_gene.exists()) ? - state.rsem_counts_gene : - null } - def rsem_counts_transcripts = list.collect { id, state -> - (state.rsem_counts_transcripts instanceof java.nio.file.Path && state.rsem_counts_transcripts.exists()) ? - state.rsem_counts_transcripts : - null } - def pseudo_salmon_quant_results = list.collect { id, state -> - (state.pseudo_salmon_quant_results_file instanceof java.nio.file.Path && state.pseudo_salmon_quant_results_file.exists()) ? - state.pseudo_salmon_quant_results_file : - null } - def pseudo_kallisto_quant_results = list.collect { id, state -> - (state.pseudo_kallisto_quant_results_file instanceof java.nio.file.Path && state.pseudo_kallisto_quant_results_file.exists()) ? - state.pseudo_kallisto_quant_results_file : - null } def genome_bam_stats = list.collect { id, state -> (state.genome_bam_stats instanceof java.nio.file.Path && state.genome_bam_stats.exists()) ? state.genome_bam_stats : @@ -3692,6 +3674,14 @@ workflow run_wf { (state.markduplicates_multiqc instanceof java.nio.file.Path && state.markduplicates_multiqc.exists()) ? state.markduplicates_multiqc : null } + def salmon_multiqc = list.collect { id, state -> + (state.salmon_multiqc instanceof java.nio.file.Path && state.salmon_multiqc.exists()) ? + state.salmon_multiqc : + null } + def rsem_multiqc = list.collect { id, state -> + (state.rsem_multiqc instanceof java.nio.file.Path && state.rsem_multiqc.exists()) ? + state.rsem_multiqc : + null } def pseudo_multiqc = list.collect { id, state -> (state.pseudo_multiqc instanceof java.nio.file.Path && state.pseudo_multiqc.exists()) ? state.pseudo_multiqc : @@ -3752,55 +3742,18 @@ workflow run_wf { (state.tin_output_summary instanceof java.nio.file.Path && state.tin_output_summary.exists()) ? state.tin_output_summary : null } - def num_trimmed_reads = list.collect { id, state -> state.num_trimmed_reads } - def passed_trimmed_reads = list.collect { id, state -> state.passed_trimmed_reads } - def passed_mapping = list.collect { id, state -> state.passed_mapping } - def percent_mapped = list.collect { id, state -> state.percent_mapped } - def inferred_strand = list.collect { id, state -> state.inferred_strand } - def passed_strand_check = list.collect { id, state -> state.passed_strand_check } - def gtf = list.collect { id, state -> state.gtf }.unique()[0] - def gtf_extra_attributes = list.collect { id, state -> state.gtf_extra_attributes }.unique()[0] - def gtf_group_features = list.collect { id, state -> state.gtf_group_features }.unique()[0] - def pca_header_multiqc = list.collect { id, state -> state.pca_header_multiqc }.unique()[0] - def clustering_header_multiqc = list.collect { id, state -> state.clustering_header_multiqc }.unique()[0] - def aligner = list.collect { id, state -> state.aligner }.unique()[0] - def pseudo_aligner = list.collect { id, state -> state.pseudo_aligner }.unique()[0] - def deseq2_vst = list.collect { id, state -> state.deseq2_vst }.unique()[0] - def extra_deseq2_args = list.collect { id, state -> state.extra_deseq2_args }.unique()[0] - def extra_deseq2_args2 = list.collect { id, state -> state.extra_deseq2_args2 }.unique()[0] - def skip_deseq2_qc = list.collect { id, state -> state.skip_deseq2_qc }.unique()[0] def multiqc_custom_config = list.collect { id, state -> state.multiqc_custom_config }.unique()[0] - def skip_qc = list.collect { id, state -> state.skip_qc }.unique()[0] - def skip_align = list.collect { id, state -> state.skip_align }.unique()[0] - def skip_pseudo_align = list.collect { id, state -> state.skip_pseudo_align }.unique()[0] ["merged", [ ids: ids, strandedness: strandedness, - fastqc_zip: fastqc_zip_1 + fastqc_zip_2, - trim_zip: trim_zip_1 + trim_zip_2, - trim_log: trim_log_1 + trim_log_2, - sortmerna_log: sortmerna_log, - star_multiqc: star_multiqc, - salmon_multiqc: quant_results, - genome_bam_stats: genome_bam_stats, - genome_bam_flagstat: genome_bam_flagstat, - genome_bam_idxstats: genome_bam_idxstats, - markduplicates_multiqc: markduplicates_multiqc, - pseudo_multiqc: pseudo_multiqc, - featurecounts_multiqc: featurecounts_multiqc, - featurecounts_rrna_multiqc: featurecounts_rrna_multiqc, - preseq_output: preseq_output, - qualimap_output_dir: qualimap_output_dir, - dupradar_output_dup_intercept_mqc: dupradar_output_dup_intercept_mqc, - dupradar_output_duprate_exp_denscurve_mqc: dupradar_output_duprate_exp_denscurve_mqc, - bamstat_output: bamstat_output, - inner_dist_output_freq: inner_dist_output_freq, - inferexperiment_multiqc: inferexperiment_multiqc, - junction_annotation_output_log: junction_annotation_output_log, - junction_saturation_output_plot_r: junction_saturation_output_plot_r, - read_distribution_output: read_distribution_output, - read_duplication_output_duplication_rate_mapping: read_duplication_output_duplication_rate_mapping, - tin_output_summary: tin_output_summary, + num_trimmed_reads: num_trimmed_reads, + passed_trimmed_reads: passed_trimmed_reads, + passed_mapping: passed_mapping, + percent_mapped: percent_mapped, + inferred_strand: inferred_strand, + passed_strand_check: passed_strand_check, + skip_align: skip_align, + skip_pseudo_align: skip_pseudo_align, quant_results: quant_results, rsem_counts_gene: rsem_counts_gene, rsem_counts_transcripts: rsem_counts_transcripts, @@ -3817,21 +3770,143 @@ workflow run_wf { extra_deseq2_args: extra_deseq2_args, extra_deseq2_args2: extra_deseq2_args2, skip_deseq2_qc: skip_deseq2_qc, - num_trimmed_reads: num_trimmed_reads, - passed_trimmed_reads: passed_trimmed_reads, - passed_mapping: passed_mapping, - percent_mapped: percent_mapped, - inferred_strand: inferred_strand, - passed_strand_check: passed_strand_check, - multiqc_custom_config: multiqc_custom_config, - skip_align: skip_align, - skip_pseudo_align: skip_pseudo_align + fastqc_zip: fastqc_zip_1 + fastqc_zip_2, + trim_zip: trim_zip_1 + trim_zip_2, + trim_log: trim_log_1 + trim_log_2, + sortmerna_multiqc: sortmerna_multiqc, + star_multiqc: star_multiqc, + genome_bam_stats: genome_bam_stats, + genome_bam_flagstat: genome_bam_flagstat, + genome_bam_idxstats: genome_bam_idxstats, + markduplicates_multiqc: markduplicates_multiqc, + salmon_multiqc: salmon_multiqc, + rsem_multiqc: rsem_multiqc, + pseudo_multiqc: pseudo_multiqc, + featurecounts_multiqc: featurecounts_multiqc, + featurecounts_rrna_multiqc: featurecounts_rrna_multiqc, + preseq_output: preseq_output, + qualimap_output_dir: qualimap_output_dir, + dupradar_output_dup_intercept_mqc: dupradar_output_dup_intercept_mqc, + dupradar_output_duprate_exp_denscurve_mqc: dupradar_output_duprate_exp_denscurve_mqc, + bamstat_output: bamstat_output, + inner_dist_output_freq: inner_dist_output_freq, + inferexperiment_multiqc: inferexperiment_multiqc, + junction_annotation_output_log: junction_annotation_output_log, + junction_saturation_output_plot_r: junction_saturation_output_plot_r, + read_distribution_output: read_distribution_output, + read_duplication_output_duplication_rate_mapping: read_duplication_output_duplication_rate_mapping, + tin_output_summary: tin_output_summary, + multiqc_custom_config: multiqc_custom_config ] ] } - + + // | map { list -> + // def ids = list.collect { id, state -> state.id } + // def strandedness = list.collect { id, state -> state.strandedness } + // def num_trimmed_reads = list.collect { id, state -> state.num_trimmed_reads } + // def passed_trimmed_reads = list.collect { id, state -> state.passed_trimmed_reads } + // def passed_mapping = list.collect { id, state -> state.passed_mapping } + // def percent_mapped = list.collect { id, state -> state.percent_mapped } + // def inferred_strand = list.collect { id, state -> state.inferred_strand } + // def passed_strand_check = list.collect { id, state -> state.passed_strand_check } + // def gtf = list.collect { id, state -> state.gtf }.unique()[0] + // def gtf_extra_attributes = list.collect { id, state -> state.gtf_extra_attributes }.unique()[0] + // def gtf_group_features = list.collect { id, state -> state.gtf_group_features }.unique()[0] + // def pca_header_multiqc = list.collect { id, state -> state.pca_header_multiqc }.unique()[0] + // def clustering_header_multiqc = list.collect { id, state -> state.clustering_header_multiqc }.unique()[0] + // def aligner = list.collect { id, state -> state.aligner }.unique()[0] + // def pseudo_aligner = list.collect { id, state -> state.pseudo_aligner }.unique()[0] + // def deseq2_vst = list.collect { id, state -> state.deseq2_vst }.unique()[0] + // def extra_deseq2_args = list.collect { id, state -> state.extra_deseq2_args }.unique()[0] + // def extra_deseq2_args2 = list.collect { id, state -> state.extra_deseq2_args2 }.unique()[0] + // def skip_deseq2_qc = list.collect { id, state -> state.skip_deseq2_qc }.unique()[0] + // def skip_qc = list.collect { id, state -> state.skip_qc }.unique()[0] + // def skip_align = list.collect { id, state -> state.skip_align }.unique()[0] + // def skip_pseudo_align = list.collect { id, state -> state.skip_pseudo_align }.unique()[0] + // def quant_results = list.collect { id, state -> + // (state.quant_results_file instanceof java.nio.file.Path && state.quant_results_file.exists()) ? + // state.quant_results_file : + // null } + // def rsem_counts_gene = list.collect { id, state -> + // (state.rsem_counts_gene instanceof java.nio.file.Path && state.rsem_counts_gene.exists()) ? + // state.rsem_counts_gene : + // null } + // def rsem_counts_transcripts = list.collect { id, state -> + // (state.rsem_counts_transcripts instanceof java.nio.file.Path && state.rsem_counts_transcripts.exists()) ? + // state.rsem_counts_transcripts : + // null } + // def pseudo_salmon_quant_results = list.collect { id, state -> + // (state.pseudo_salmon_quant_results_file instanceof java.nio.file.Path && state.pseudo_salmon_quant_results_file.exists()) ? + // state.pseudo_salmon_quant_results_file : + // null } + // def pseudo_kallisto_quant_results = list.collect { id, state -> + // (state.pseudo_kallisto_quant_results_file instanceof java.nio.file.Path && state.pseudo_kallisto_quant_results_file.exists()) ? + // state.pseudo_kallisto_quant_results_file : + // null } + // def fastqc_zip_1_dirs = list.collect{it[1].fastqc_zip_1.getParent()} + // def fastqc_zip_2_dirs = list.collect{it[1].fastqc_zip_2.getParent()} + // def trim_zip_1_dirs = list.collect{it[1].trim_zip_1.getParent()} + // def trim_zip_2_dirs = list.collect{it[1].trim_zip_2.getParent()} + // def trim_log_1_dirs = list.collect{it[1].trim_log_1.getParent()} + // def trim_log_2_dirs = list.collect{it[1].trim_log_2.getParent()} + // def sortmerna_multiqc_dirs = list.collect{it[1].sortmerna_multiqc.getParent()} + // def star_multiqc_dirs = list.collect{it[1].star_multiqc.getParent()} + // def genome_bam_stats_dirs = list.collect{it[1].genome_bam_stats.getParent()} + // def genome_bam_flagstat_dirs = list.collect{it[1].genome_bam_flagstat.getParent()} + // def genome_bam_idxstats_dirs = list.collect{it[1].genome_bam_idxstats} + // def markduplicates_multiqc_dirs = list.collect{it[1].markduplicates_multiqc.getParent()} + // def salmon_multiqc_dirs = list.collect{it[1].salmon_multiqc} + // def rsem_multiqc_dirs = list.collect{it[1].rsem_multiqc.getParent()} + // def pseudo_multiqc_dirs = list.collect{it[1].pseudo_multiqc.getParent()} + // def featurecounts_multiqc_dirs = list.collect{it[1].featurecounts_multiqc.getParent()} + // def featurecounts_rrna_multiqc_dirs = list.collect{it[1].featurecounts_rrna_multiqc.getParent()} + // def preseq_output_dirs = list.collect{it[1].preseq_output.getParent()} + // def qualimap_output_dirs = list.collect{it[1].qualimap_output_dir} + // def dupradar_output_dup_intercept_mqc_dirs = list.collect{it[1].dupradar_output_dup_intercept_mqc.getParent()} + // def dupradar_output_duprate_exp_denscurve_mqc_dirs = list.collect{it[1].dupradar_output_duprate_exp_denscurve_mqc.getParent()} + // def bamstat_output_dirs = list.collect{it[1].bamstat_output.getParent()} + // def strandedness_output_dirs = list.collect{it[1].strandedness_output.getParent()} + // def inner_dist_output_freq_dirs = list.collect{it[1].inner_dist_output_freq.getParent()} + // def junction_annotation_output_log_dirs = list.collect{it[1].junction_annotation_output_log.getParent()} + // def junction_saturation_output_plot_r_dirs = list.collect{it[1].junction_saturation_output_plot_r.getParent()} + // def read_distribution_output_dirs = list.collect{it[1].read_distribution_output.getParent()} + // def read_duplication_output_duplication_rate_mapping_dirs = list.collect{it[1].read_duplication_output_duplication_rate_mapping.getParent()} + // def tin_output_summary_dirs = list.collect{it[1].tin_output_summary.getParent()} + // def multiqc_custom_config_dirs = list.collect{it[1].multiqc_custom_config.getParent()} + // ["merged", [ + // ids: ids, + // strandedness: strandedness, + // num_trimmed_reads: num_trimmed_reads, + // passed_trimmed_reads: passed_trimmed_reads, + // passed_mapping: passed_mapping, + // percent_mapped: percent_mapped, + // inferred_strand: inferred_strand, + // passed_strand_check: passed_strand_check, + // skip_align: skip_align, + // skip_pseudo_align: skip_pseudo_align, + // quant_results: quant_results, + // rsem_counts_gene: rsem_counts_gene, + // rsem_counts_transcripts: rsem_counts_transcripts, + // pseudo_salmon_quant_results: pseudo_salmon_quant_results, + // pseudo_kallisto_quant_results: pseudo_kallisto_quant_results, + // gtf: gtf, + // gtf_extra_attributes: gtf_extra_attributes, + // gtf_group_features: gtf_group_features, + // pca_header_multiqc: pca_header_multiqc, + // clustering_header_multiqc: clustering_header_multiqc, + // aligner: aligner, + // pseudo_aligner: pseudo_aligner, + // deseq2_vst: deseq2_vst, + // extra_deseq2_args: extra_deseq2_args, + // extra_deseq2_args2: extra_deseq2_args2, + // skip_deseq2_qc: skip_deseq2_qc, + // multiqc_input: fastqc_zip_1_dirs + fastqc_zip_2_dirs + trim_zip_1_dirs + trim_zip_2_dirs + trim_log_1_dirs + trim_log_2_dirs + sortmerna_multiqc_dirs + star_multiqc_dirs + genome_bam_stats_dirs + genome_bam_flagstat_dirs + genome_bam_idxstats_dirs + markduplicates_multiqc_dirs + salmon_multiqc_dirs + rsem_multiqc_dirs + pseudo_multiqc_dirs + featurecounts_multiqc_dirs + featurecounts_rrna_multiqc_dirs + preseq_output_dirs + qualimap_output_dirs + dupradar_output_dup_intercept_mqc_dirs + dupradar_output_duprate_exp_denscurve_mqc_dirs + bamstat_output_dirs + strandedness_output_dirs + inner_dist_output_freq_dirs + junction_annotation_output_log_dirs + junction_saturation_output_plot_r_dirs + read_distribution_output_dirs + read_duplication_output_duplication_rate_mapping_dirs + tin_output_summary_dirs + multiqc_custom_config_dirs + // ] ] + // } + // Merge quantification results of alignment | merge_quant_results.run ( - runIf: { id, state -> (!state.skip_align && state.aligner == 'star_salmon') || !skip_pseudo_align }, + runIf: { id, state -> !state.skip_align && state.aligner == 'star_salmon' }, fromState: [ "salmon_quant_results": "quant_results", "gtf": "gtf", @@ -3850,7 +3925,7 @@ workflow run_wf { "lengths_transcript": "lengths_transcript", "quant_merged_summarizedexperiment": "quant_merged_summarizedexperiment" ], - key: "merge_qunat_results" + key: "merge_quant_results" ) | rsem_merge_counts.run ( @@ -3980,14 +4055,15 @@ workflow run_wf { "fastqc_raw_multiqc": "fastqc_zip", "fastqc_trim_multiqc": "trim_zip", "trim_log_multiqc": "trim_log", - "sortmerna_multiqc": "sortmerna_log", + "sortmerna_multiqc": "sortmerna_multiqc", "star_multiqc": "star_multiqc", "salmon_multiqc": "salmon_multiqc", + "rsem_multiqc": "rsem_multiqc", + "pseudo_multiqc": "pseudo_multiqc", "samtools_stats": "genome_bam_stats", "samtools_flagstat": "genome_bam_flagstat", "samtools_idxstats": "genome_bam_idxstats", - "markduplicates_multiqc": "markduplicates_multiqc", - "pseudo_multiqc": "pseudo_multiqc", + "markduplicates_multiqc": "markduplicates_multiqc", "featurecounts_multiqc": "featurecounts_multiqc", "featurecounts_rrna_multiqc": "featurecounts_rrna_multiqc", "aligner_pca_multiqc": "deseq2_pca_multiqc", @@ -4019,7 +4095,7 @@ workflow run_wf { toState: [ "multiqc_report": "output_report", "multiqc_data": "output_data", - "multiqc_plots": "output_plots", + "multiqc_plots": "output_plots" ] ) @@ -4121,8 +4197,7 @@ workflow run_wf { "deseq2_output_pseudo": "deseq2_output_pseudo", "multiqc_report": "multiqc_report", "multiqc_data": "multiqc_data", - "multiqc_plots": "multiqc_plots", - "multiqc_versions": "multiqc_versions" + "multiqc_plots": "multiqc_plots" ] ) @@ -4317,10 +4392,6 @@ if [ ! -z "$VIASH_PAR_MULTIQC_PLOTS" ] && [ ! -e "$VIASH_PAR_MULTIQC_PLOTS" ]; t ViashError "Output file '$VIASH_PAR_MULTIQC_PLOTS' does not exist." exit 1 fi -if [ ! -z "$VIASH_PAR_MULTIQC_VERSIONS" ] && [ ! -e "$VIASH_PAR_MULTIQC_VERSIONS" ]; then - ViashError "Output file '$VIASH_PAR_MULTIQC_VERSIONS' does not exist." - exit 1 -fi if [ ! -z "$VIASH_PAR_TPM_GENE" ] && [ ! -e "$VIASH_PAR_TPM_GENE" ]; then ViashError "Output file '$VIASH_PAR_TPM_GENE' does not exist." exit 1 diff --git a/target/executable/workflows/rnaseq/.config.vsh.yaml b/target/executable/workflows/rnaseq/.config.vsh.yaml index f49eb48..7335a78 100644 --- a/target/executable/workflows/rnaseq/.config.vsh.yaml +++ b/target/executable/workflows/rnaseq/.config.vsh.yaml @@ -1172,7 +1172,18 @@ argument_groups: name: "--salmon_quant_results" info: null default: - - "Salmon/$id" + - "STAR_Salmon/$id" + must_exist: true + create_parent: true + required: false + direction: "output" + multiple: false + multiple_sep: ";" + - type: "file" + name: "--pseudo_quant_results" + info: null + default: + - "Pseudo_align_quant/$id" must_exist: true create_parent: true required: false @@ -2095,8 +2106,8 @@ build_info: output: "target/executable/workflows/rnaseq" executable: "target/executable/workflows/rnaseq/rnaseq" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@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 aad28fd..f0eb778 100755 --- a/target/executable/workflows/rnaseq/rnaseq +++ b/target/executable/workflows/rnaseq/rnaseq @@ -738,7 +738,11 @@ function ViashHelp { echo "" echo " --salmon_quant_results" echo " type: file, output, file must exist" - echo " default: Salmon/\$id" + echo " default: STAR_Salmon/\$id" + echo "" + echo " --pseudo_quant_results" + echo " type: file, output, file must exist" + echo " default: Pseudo_align_quant/\$id" echo "" echo " --rsem_counts_gene" echo " type: file, output, file must exist" @@ -2231,6 +2235,17 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_SALMON_QUANT_RESULTS=$(ViashRemoveFlags "$1") shift 1 ;; + --pseudo_quant_results) + [ -n "$VIASH_PAR_PSEUDO_QUANT_RESULTS" ] && ViashError Bad arguments for option \'--pseudo_quant_results\': \'$VIASH_PAR_PSEUDO_QUANT_RESULTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_PSEUDO_QUANT_RESULTS="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --pseudo_quant_results. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --pseudo_quant_results=*) + [ -n "$VIASH_PAR_PSEUDO_QUANT_RESULTS" ] && ViashError Bad arguments for option \'--pseudo_quant_results=*\': \'$VIASH_PAR_PSEUDO_QUANT_RESULTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_PSEUDO_QUANT_RESULTS=$(ViashRemoveFlags "$1") + shift 1 + ;; --rsem_counts_gene) [ -n "$VIASH_PAR_RSEM_COUNTS_GENE" ] && ViashError Bad arguments for option \'--rsem_counts_gene\': \'$VIASH_PAR_RSEM_COUNTS_GENE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 VIASH_PAR_RSEM_COUNTS_GENE="$2" @@ -3416,7 +3431,10 @@ if [ -z ${VIASH_PAR_TRANSCRIPTOME_BAM_IDXSTATS+x} ]; then VIASH_PAR_TRANSCRIPTOME_BAM_IDXSTATS="samtools_stats/\$id.transcriptome.idxstats" fi if [ -z ${VIASH_PAR_SALMON_QUANT_RESULTS+x} ]; then - VIASH_PAR_SALMON_QUANT_RESULTS="Salmon/\$id" + VIASH_PAR_SALMON_QUANT_RESULTS="STAR_Salmon/\$id" +fi +if [ -z ${VIASH_PAR_PSEUDO_QUANT_RESULTS+x} ]; then + VIASH_PAR_PSEUDO_QUANT_RESULTS="Pseudo_align_quant/\$id" fi if [ -z ${VIASH_PAR_RSEM_COUNTS_GENE+x} ]; then VIASH_PAR_RSEM_COUNTS_GENE="RSEM/\$id.genes.results" @@ -4174,6 +4192,9 @@ fi if [ ! -z "$VIASH_PAR_SALMON_QUANT_RESULTS" ] && [ ! -d "$(dirname "$VIASH_PAR_SALMON_QUANT_RESULTS")" ]; then mkdir -p "$(dirname "$VIASH_PAR_SALMON_QUANT_RESULTS")" fi +if [ ! -z "$VIASH_PAR_PSEUDO_QUANT_RESULTS" ] && [ ! -d "$(dirname "$VIASH_PAR_PSEUDO_QUANT_RESULTS")" ]; then + mkdir -p "$(dirname "$VIASH_PAR_PSEUDO_QUANT_RESULTS")" +fi if [ ! -z "$VIASH_PAR_RSEM_COUNTS_GENE" ] && [ ! -d "$(dirname "$VIASH_PAR_RSEM_COUNTS_GENE")" ]; then mkdir -p "$(dirname "$VIASH_PAR_RSEM_COUNTS_GENE")" fi @@ -4640,6 +4661,8 @@ workflow run_wf { toState: [ "star_alignment": "star_alignment", "star_multiqc": "star_multiqc", + "rsem_multiqc": "rsem_multiqc", + "salmon_multiqc": "salmon_multiqc", "genome_bam_sorted": "genome_bam_sorted", "genome_bam_index": "genome_bam_index", "genome_bam_stats": "genome_bam_stats", @@ -4665,7 +4688,7 @@ workflow run_wf { def passed_mapping = (percent_mapped >= state.min_mapped_reads) ? true : false [ id, state + [percent_mapped: percent_mapped, passed_mapping: passed_mapping] ] } - + // Pseudo-alignment and quantification | pseudo_alignment_and_quant.run ( runIf: { id, state -> !state.skip_pseudo_alignment && state.passed_trimmed_reads }, @@ -4757,18 +4780,23 @@ workflow run_wf { "skip_align": "skip_alignment", "skip_pseudo_align": "skip_pseudo_alignment", "gtf": "gtf", + "num_trimmed_reads": "num_trimmed_reads", + "passed_trimmed_reads": "passed_trimmed_reads", + "passed_mapping": "passed_mapping", + "percent_mapped": "percent_mapped", "genome_bam": "genome_bam_sorted", "genome_bam_index": "genome_bam_index", - "quant_out_dir": "quant_out_dir", + "salmon_multiqc": "salmon_multiqc", "quant_results_file": "quant_results_file", + "rsem_multiqc": "rsem_multiqc", "rsem_counts_gene": "rsem_counts_gene", "rsem_counts_transcripts": "rsem_counts_transcripts", + "pseudo_multiqc": "pseudo_multiqc", "pseudo_quant_out_dir": "pseudo_quant_out_dir", "pseudo_salmon_quant_results_file": "pseudo_salmon_quant_results_file", "pseudo_kallisto_quant_results_file": "pseudo_kallisto_quant_results_file", "aligner": "aligner", "pseudo_aligner": "pseudo_aligner", - "pseudo_multiqc": "pseudo_multiqc", "gene_bed": "gene_bed", "extra_preseq_args": "extra_preseq_args", "extra_featurecounts_args": "extra_featurecounts_args", @@ -4796,11 +4824,7 @@ workflow run_wf { "genome_bam_flagstat": "genome_bam_flagstat", "genome_bam_idxstats": "genome_bam_idxstats", "markduplicates_multiqc": "markduplicates_metrics", - "rseqc_modules": "rseqc_modules", - "num_trimmed_reads": "num_trimmed_reads", - "passed_trimmed_reads": "passed_trimmed_reads", - "passed_mapping": "passed_mapping", - "percent_mapped": "percent_mapped" + "rseqc_modules": "rseqc_modules" ], toState: [ "preseq_output": "preseq_output", @@ -4846,7 +4870,7 @@ workflow run_wf { "counts_gene_scaled": "counts_gene_scaled", "tpm_transcript": "tpm_transcript", "counts_transcript": "counts_transcript", - "salmon_merged_summarizedexperiment": "salmon_merged_summarizedexperiment", + "qunat_merged_summarizedexperiment": "quant_merged_summarizedexperiment", "deseq2_output": "deseq2_output", "multiqc_report": "multiqc_report", "multiqc_data": "multiqc_data", @@ -4893,7 +4917,8 @@ workflow run_wf { "transcriptome_bam_stats": "transcriptome_bam_stats", "transcriptome_bam_flagstat": "transcriptome_bam_flagstat", "transcriptome_bam_idxstats": "transcriptome_bam_idxstats", - "salmon_quant_results": "salmon_quant_results", + "salmon_quant_results": "quant_out_dir", + "pseudo_quant_results": "pseudo_quant_out_dir", "stringtie_transcript_gtf": "stringtie_transcript_gtf", "stringtie_coverage_gtf": "stringtie_coverage_gtf", "stringtie_abundance": "stringtie_abundance", @@ -4959,8 +4984,7 @@ workflow run_wf { "deseq2_output_pseudo": "deseq2_output_pseudo", "multiqc_report": "multiqc_report", "multiqc_data": "multiqc_data", - "multiqc_plots": "multiqc_plots", - "multiqc_versions": "multiqc_versions" + "multiqc_plots": "multiqc_plots" ] ) @@ -5039,7 +5063,7 @@ def getFastpReadsAfterFiltering(json_file) { } // -// Function that parses and returns the alignment rate from the STAR log output +// Function that parses and returns the alignment rate from the STAR log outputs // def getStarPercentMapped(align_log) { def percent_aligned = 0 @@ -5148,6 +5172,10 @@ if [ ! -z "$VIASH_PAR_SALMON_QUANT_RESULTS" ] && [ ! -e "$VIASH_PAR_SALMON_QUANT ViashError "Output file '$VIASH_PAR_SALMON_QUANT_RESULTS' does not exist." exit 1 fi +if [ ! -z "$VIASH_PAR_PSEUDO_QUANT_RESULTS" ] && [ ! -e "$VIASH_PAR_PSEUDO_QUANT_RESULTS" ]; then + ViashError "Output file '$VIASH_PAR_PSEUDO_QUANT_RESULTS' does not exist." + exit 1 +fi if [ ! -z "$VIASH_PAR_RSEM_COUNTS_GENE" ] && [ ! -e "$VIASH_PAR_RSEM_COUNTS_GENE" ]; then ViashError "Output file '$VIASH_PAR_RSEM_COUNTS_GENE' does not exist." exit 1 diff --git a/target/nextflow/bbmap_bbsplit/.config.vsh.yaml b/target/nextflow/bbmap_bbsplit/.config.vsh.yaml index 64e6336..7dc77d4 100644 --- a/target/nextflow/bbmap_bbsplit/.config.vsh.yaml +++ b/target/nextflow/bbmap_bbsplit/.config.vsh.yaml @@ -238,8 +238,8 @@ build_info: output: "target/nextflow/bbmap_bbsplit" executable: "target/nextflow/bbmap_bbsplit/main.nf" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/bbmap_bbsplit/main.nf b/target/nextflow/bbmap_bbsplit/main.nf index 1a75a6e..720900a 100644 --- a/target/nextflow/bbmap_bbsplit/main.nf +++ b/target/nextflow/bbmap_bbsplit/main.nf @@ -3104,8 +3104,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/bbmap_bbsplit", "viash_version" : "0.9.0", - "git_commit" : "b291665ddc01d0f8072d9d3d7b4aa9932afb84df", - "git_remote" : "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", + "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/bedtools_genomecov/.config.vsh.yaml b/target/nextflow/bedtools_genomecov/.config.vsh.yaml index 07124fa..c032ec3 100644 --- a/target/nextflow/bedtools_genomecov/.config.vsh.yaml +++ b/target/nextflow/bedtools_genomecov/.config.vsh.yaml @@ -178,8 +178,8 @@ build_info: output: "target/nextflow/bedtools_genomecov" executable: "target/nextflow/bedtools_genomecov/main.nf" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/bedtools_genomecov/main.nf b/target/nextflow/bedtools_genomecov/main.nf index d277231..b3e55bf 100644 --- a/target/nextflow/bedtools_genomecov/main.nf +++ b/target/nextflow/bedtools_genomecov/main.nf @@ -3031,8 +3031,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/bedtools_genomecov", "viash_version" : "0.9.0", - "git_commit" : "b291665ddc01d0f8072d9d3d7b4aa9932afb84df", - "git_remote" : "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", + "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/cat_additional_fasta/.config.vsh.yaml b/target/nextflow/cat_additional_fasta/.config.vsh.yaml index a35c0f0..a362039 100644 --- a/target/nextflow/cat_additional_fasta/.config.vsh.yaml +++ b/target/nextflow/cat_additional_fasta/.config.vsh.yaml @@ -182,8 +182,8 @@ build_info: output: "target/nextflow/cat_additional_fasta" executable: "target/nextflow/cat_additional_fasta/main.nf" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/cat_additional_fasta/main.nf b/target/nextflow/cat_additional_fasta/main.nf index 9532f38..cf67de5 100644 --- a/target/nextflow/cat_additional_fasta/main.nf +++ b/target/nextflow/cat_additional_fasta/main.nf @@ -3032,8 +3032,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/cat_additional_fasta", "viash_version" : "0.9.0", - "git_commit" : "b291665ddc01d0f8072d9d3d7b4aa9932afb84df", - "git_remote" : "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", + "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/cat_fastq/.config.vsh.yaml b/target/nextflow/cat_fastq/.config.vsh.yaml index 86477ea..ac4e3cf 100644 --- a/target/nextflow/cat_fastq/.config.vsh.yaml +++ b/target/nextflow/cat_fastq/.config.vsh.yaml @@ -169,8 +169,8 @@ build_info: output: "target/nextflow/cat_fastq" executable: "target/nextflow/cat_fastq/main.nf" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/cat_fastq/main.nf b/target/nextflow/cat_fastq/main.nf index c580310..7ea24f2 100644 --- a/target/nextflow/cat_fastq/main.nf +++ b/target/nextflow/cat_fastq/main.nf @@ -3023,8 +3023,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/cat_fastq", "viash_version" : "0.9.0", - "git_commit" : "b291665ddc01d0f8072d9d3d7b4aa9932afb84df", - "git_remote" : "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", + "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/deseq2_qc/.config.vsh.yaml b/target/nextflow/deseq2_qc/.config.vsh.yaml index 6db5730..e4bdbda 100644 --- a/target/nextflow/deseq2_qc/.config.vsh.yaml +++ b/target/nextflow/deseq2_qc/.config.vsh.yaml @@ -237,8 +237,8 @@ build_info: output: "target/nextflow/deseq2_qc" executable: "target/nextflow/deseq2_qc/main.nf" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/deseq2_qc/main.nf b/target/nextflow/deseq2_qc/main.nf index 4246a2c..455d9bc 100644 --- a/target/nextflow/deseq2_qc/main.nf +++ b/target/nextflow/deseq2_qc/main.nf @@ -3110,8 +3110,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/deseq2_qc", "viash_version" : "0.9.0", - "git_commit" : "b291665ddc01d0f8072d9d3d7b4aa9932afb84df", - "git_remote" : "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", + "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/dupradar/.config.vsh.yaml b/target/nextflow/dupradar/.config.vsh.yaml index ddce089..04ef101 100644 --- a/target/nextflow/dupradar/.config.vsh.yaml +++ b/target/nextflow/dupradar/.config.vsh.yaml @@ -266,8 +266,8 @@ build_info: output: "target/nextflow/dupradar" executable: "target/nextflow/dupradar/main.nf" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/dupradar/main.nf b/target/nextflow/dupradar/main.nf index 0f6e557..d1328b3 100644 --- a/target/nextflow/dupradar/main.nf +++ b/target/nextflow/dupradar/main.nf @@ -3136,8 +3136,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/dupradar", "viash_version" : "0.9.0", - "git_commit" : "b291665ddc01d0f8072d9d3d7b4aa9932afb84df", - "git_remote" : "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", + "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/fastqc/.config.vsh.yaml b/target/nextflow/fastqc/.config.vsh.yaml index 07b83ce..34ca15b 100644 --- a/target/nextflow/fastqc/.config.vsh.yaml +++ b/target/nextflow/fastqc/.config.vsh.yaml @@ -198,8 +198,8 @@ build_info: output: "target/nextflow/fastqc" executable: "target/nextflow/fastqc/main.nf" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/fastqc/main.nf b/target/nextflow/fastqc/main.nf index 25eff25..a103813 100644 --- a/target/nextflow/fastqc/main.nf +++ b/target/nextflow/fastqc/main.nf @@ -3056,8 +3056,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/fastqc", "viash_version" : "0.9.0", - "git_commit" : "b291665ddc01d0f8072d9d3d7b4aa9932afb84df", - "git_remote" : "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", + "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/fq_subsample/.config.vsh.yaml b/target/nextflow/fq_subsample/.config.vsh.yaml index d9b081a..9fad7a1 100644 --- a/target/nextflow/fq_subsample/.config.vsh.yaml +++ b/target/nextflow/fq_subsample/.config.vsh.yaml @@ -177,8 +177,8 @@ build_info: output: "target/nextflow/fq_subsample" executable: "target/nextflow/fq_subsample/main.nf" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/fq_subsample/main.nf b/target/nextflow/fq_subsample/main.nf index 01234a1..5c3736d 100644 --- a/target/nextflow/fq_subsample/main.nf +++ b/target/nextflow/fq_subsample/main.nf @@ -3027,8 +3027,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/fq_subsample", "viash_version" : "0.9.0", - "git_commit" : "b291665ddc01d0f8072d9d3d7b4aa9932afb84df", - "git_remote" : "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", + "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/getchromsizes/.config.vsh.yaml b/target/nextflow/getchromsizes/.config.vsh.yaml index 1c73533..b6d5135 100644 --- a/target/nextflow/getchromsizes/.config.vsh.yaml +++ b/target/nextflow/getchromsizes/.config.vsh.yaml @@ -167,8 +167,8 @@ build_info: output: "target/nextflow/getchromsizes" executable: "target/nextflow/getchromsizes/main.nf" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/getchromsizes/main.nf b/target/nextflow/getchromsizes/main.nf index 1ba2c7c..896b467 100644 --- a/target/nextflow/getchromsizes/main.nf +++ b/target/nextflow/getchromsizes/main.nf @@ -3013,8 +3013,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/getchromsizes", "viash_version" : "0.9.0", - "git_commit" : "b291665ddc01d0f8072d9d3d7b4aa9932afb84df", - "git_remote" : "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", + "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/gtf2bed/.config.vsh.yaml b/target/nextflow/gtf2bed/.config.vsh.yaml index 40e1e39..662f239 100644 --- a/target/nextflow/gtf2bed/.config.vsh.yaml +++ b/target/nextflow/gtf2bed/.config.vsh.yaml @@ -145,8 +145,8 @@ build_info: output: "target/nextflow/gtf2bed" executable: "target/nextflow/gtf2bed/main.nf" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/gtf2bed/main.nf b/target/nextflow/gtf2bed/main.nf index 2b46fbb..9cb1653 100644 --- a/target/nextflow/gtf2bed/main.nf +++ b/target/nextflow/gtf2bed/main.nf @@ -2995,8 +2995,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/gtf2bed", "viash_version" : "0.9.0", - "git_commit" : "b291665ddc01d0f8072d9d3d7b4aa9932afb84df", - "git_remote" : "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", + "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/gtf_filter/.config.vsh.yaml b/target/nextflow/gtf_filter/.config.vsh.yaml index 96888a6..9e17a10 100644 --- a/target/nextflow/gtf_filter/.config.vsh.yaml +++ b/target/nextflow/gtf_filter/.config.vsh.yaml @@ -155,8 +155,8 @@ build_info: output: "target/nextflow/gtf_filter" executable: "target/nextflow/gtf_filter/main.nf" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/gtf_filter/main.nf b/target/nextflow/gtf_filter/main.nf index 50995cc..591b219 100644 --- a/target/nextflow/gtf_filter/main.nf +++ b/target/nextflow/gtf_filter/main.nf @@ -3003,8 +3003,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/gtf_filter", "viash_version" : "0.9.0", - "git_commit" : "b291665ddc01d0f8072d9d3d7b4aa9932afb84df", - "git_remote" : "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", + "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/gunzip/.config.vsh.yaml b/target/nextflow/gunzip/.config.vsh.yaml index 0c94c20..5fec39c 100644 --- a/target/nextflow/gunzip/.config.vsh.yaml +++ b/target/nextflow/gunzip/.config.vsh.yaml @@ -144,8 +144,8 @@ build_info: output: "target/nextflow/gunzip" executable: "target/nextflow/gunzip/main.nf" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/gunzip/main.nf b/target/nextflow/gunzip/main.nf index 7a797c1..e18e223 100644 --- a/target/nextflow/gunzip/main.nf +++ b/target/nextflow/gunzip/main.nf @@ -2992,8 +2992,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/gunzip", "viash_version" : "0.9.0", - "git_commit" : "b291665ddc01d0f8072d9d3d7b4aa9932afb84df", - "git_remote" : "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", + "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml b/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml index ddccae7..9426f89 100644 --- a/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml +++ b/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml @@ -155,8 +155,8 @@ build_info: output: "target/nextflow/kallisto/kallisto_index" executable: "target/nextflow/kallisto/kallisto_index/main.nf" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/kallisto/kallisto_index/main.nf b/target/nextflow/kallisto/kallisto_index/main.nf index 20d37b3..26766c3 100644 --- a/target/nextflow/kallisto/kallisto_index/main.nf +++ b/target/nextflow/kallisto/kallisto_index/main.nf @@ -3002,8 +3002,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/kallisto/kallisto_index", "viash_version" : "0.9.0", - "git_commit" : "b291665ddc01d0f8072d9d3d7b4aa9932afb84df", - "git_remote" : "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", + "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml b/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml index 0dcc719..b18063c 100644 --- a/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml +++ b/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml @@ -253,8 +253,8 @@ build_info: output: "target/nextflow/kallisto/kallisto_quant" executable: "target/nextflow/kallisto/kallisto_quant/main.nf" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/kallisto/kallisto_quant/main.nf b/target/nextflow/kallisto/kallisto_quant/main.nf index b6c3b85..96fb786 100644 --- a/target/nextflow/kallisto/kallisto_quant/main.nf +++ b/target/nextflow/kallisto/kallisto_quant/main.nf @@ -3114,8 +3114,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/kallisto/kallisto_quant", "viash_version" : "0.9.0", - "git_commit" : "b291665ddc01d0f8072d9d3d7b4aa9932afb84df", - "git_remote" : "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", + "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/multiqc_custom_biotype/.config.vsh.yaml b/target/nextflow/multiqc_custom_biotype/.config.vsh.yaml index 8310944..6db45e5 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: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/multiqc_custom_biotype/main.nf b/target/nextflow/multiqc_custom_biotype/main.nf index 85c9cdd..ecd67e3 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" : "b291665ddc01d0f8072d9d3d7b4aa9932afb84df", - "git_remote" : "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", + "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/picard_markduplicates/.config.vsh.yaml b/target/nextflow/picard_markduplicates/.config.vsh.yaml index d98e5dd..a4cb0e7 100644 --- a/target/nextflow/picard_markduplicates/.config.vsh.yaml +++ b/target/nextflow/picard_markduplicates/.config.vsh.yaml @@ -207,8 +207,8 @@ build_info: output: "target/nextflow/picard_markduplicates" executable: "target/nextflow/picard_markduplicates/main.nf" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/picard_markduplicates/main.nf b/target/nextflow/picard_markduplicates/main.nf index 460e4f4..c5a3ddc 100644 --- a/target/nextflow/picard_markduplicates/main.nf +++ b/target/nextflow/picard_markduplicates/main.nf @@ -3063,8 +3063,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/picard_markduplicates", "viash_version" : "0.9.0", - "git_commit" : "b291665ddc01d0f8072d9d3d7b4aa9932afb84df", - "git_remote" : "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", + "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/prepare_multiqc_input/.config.vsh.yaml b/target/nextflow/prepare_multiqc_input/.config.vsh.yaml index 7ea83e7..fad4c69 100644 --- a/target/nextflow/prepare_multiqc_input/.config.vsh.yaml +++ b/target/nextflow/prepare_multiqc_input/.config.vsh.yaml @@ -409,8 +409,8 @@ build_info: output: "target/nextflow/prepare_multiqc_input" executable: "target/nextflow/prepare_multiqc_input/main.nf" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/prepare_multiqc_input/main.nf b/target/nextflow/prepare_multiqc_input/main.nf index be6aa88..da34f40 100644 --- a/target/nextflow/prepare_multiqc_input/main.nf +++ b/target/nextflow/prepare_multiqc_input/main.nf @@ -3277,8 +3277,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/prepare_multiqc_input", "viash_version" : "0.9.0", - "git_commit" : "b291665ddc01d0f8072d9d3d7b4aa9932afb84df", - "git_remote" : "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", + "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", @@ -3407,8 +3407,9 @@ IFS="," read -ra star_multiqc <<< \\$par_star_multiqc && for file in "\\${star_m IFS="," read -ra rsem_multiqc <<< \\$par_rsem_multiqc && for file in "\\${rsem_multiqc[@]}"; do [ -e "\\$file" ] && cp -r "\\$file" "\\$par_output/"; done -# TODO: Fetch Salmon meta info -# IFS="," read -ra salmon_multiqc <<< \\$par_salmon_multiqc && for file in "\\${salmon_multiqc[@]}"; do [ -e "\\$file" ] && cp -r "\\$file" "\\$par_output/"; done +IFS="," read -ra salmon_multiqc <<< \\$par_salmon_multiqc && for file in "\\${salmon_multiqc[@]}"; do [ -e "\\$file" ] && cp -r "\\$file" "\\$par_output/"; done + +IFS="," read -ra pseudo_multiqc <<< \\$par_pseudo_multiqc && for file in "\\${pseudo_multiqc[@]}"; do [ -e "\\$file" ] && cp -r "\\$file" "\\$par_output/"; done IFS="," read -ra samtools_stats <<< \\$par_samtools_stats && for file in "\\${samtools_stats[@]}"; do [ -e "\\$file" ] && cp -r "\\$file" \\$par_output/; done @@ -3418,9 +3419,6 @@ IFS="," read -ra samtools_idxstats <<< \\$par_samtools_idxstats && for file in " IFS="," read -ra markduplicates_multiqc <<< \\$par_markduplicates_multiqc && for file in "\\${markduplicates_multiqc[@]}"; do [ -e "\\$file" ] && cp -r "\\$file" "\\$par_output/"; done -IFS="," read -ra pseudo_multiqc <<< \\$par_pseudo_multiqc && for file in "\\${pseudo_multiqc[@]}"; do [ -e "\\$file" ] && cp -r "\\$file" "\\$par_output/"; done - - IFS="," read -ra featurecounts_multiqc <<< \\$par_featurecounts_multiqc && for file in "\\${featurecounts_multiqc[@]}"; do [ -e "\\$file" ] && cp -r "\\$file" "\\$par_output/"; done IFS="," read -ra featurecounts_rrna_multiqc <<< \\$par_featurecounts_rrna_multiqc && for file in "\\${featurecounts_rrna_multiqc[@]}"; do [ -e "\\$file" ] && cp -r "\\$file" "\\$par_output/"; done diff --git a/target/nextflow/preprocess_transcripts_fasta/.config.vsh.yaml b/target/nextflow/preprocess_transcripts_fasta/.config.vsh.yaml index cf87a43..63df6ed 100644 --- a/target/nextflow/preprocess_transcripts_fasta/.config.vsh.yaml +++ b/target/nextflow/preprocess_transcripts_fasta/.config.vsh.yaml @@ -138,8 +138,8 @@ build_info: output: "target/nextflow/preprocess_transcripts_fasta" executable: "target/nextflow/preprocess_transcripts_fasta/main.nf" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/preprocess_transcripts_fasta/main.nf b/target/nextflow/preprocess_transcripts_fasta/main.nf index 5578069..d6d1c9f 100644 --- a/target/nextflow/preprocess_transcripts_fasta/main.nf +++ b/target/nextflow/preprocess_transcripts_fasta/main.nf @@ -2982,8 +2982,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/preprocess_transcripts_fasta", "viash_version" : "0.9.0", - "git_commit" : "b291665ddc01d0f8072d9d3d7b4aa9932afb84df", - "git_remote" : "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", + "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/preseq_lcextrap/.config.vsh.yaml b/target/nextflow/preseq_lcextrap/.config.vsh.yaml index a04529b..bb3cf56 100644 --- a/target/nextflow/preseq_lcextrap/.config.vsh.yaml +++ b/target/nextflow/preseq_lcextrap/.config.vsh.yaml @@ -191,8 +191,8 @@ build_info: output: "target/nextflow/preseq_lcextrap" executable: "target/nextflow/preseq_lcextrap/main.nf" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/preseq_lcextrap/main.nf b/target/nextflow/preseq_lcextrap/main.nf index e8e6405..a81907c 100644 --- a/target/nextflow/preseq_lcextrap/main.nf +++ b/target/nextflow/preseq_lcextrap/main.nf @@ -3035,8 +3035,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/preseq_lcextrap", "viash_version" : "0.9.0", - "git_commit" : "b291665ddc01d0f8072d9d3d7b4aa9932afb84df", - "git_remote" : "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", + "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/qualimap/.config.vsh.yaml b/target/nextflow/qualimap/.config.vsh.yaml index 75ab775..75719f2 100644 --- a/target/nextflow/qualimap/.config.vsh.yaml +++ b/target/nextflow/qualimap/.config.vsh.yaml @@ -271,8 +271,8 @@ build_info: output: "target/nextflow/qualimap" executable: "target/nextflow/qualimap/main.nf" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/qualimap/main.nf b/target/nextflow/qualimap/main.nf index e51c09d..454943d 100644 --- a/target/nextflow/qualimap/main.nf +++ b/target/nextflow/qualimap/main.nf @@ -3144,8 +3144,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/qualimap", "viash_version" : "0.9.0", - "git_commit" : "b291665ddc01d0f8072d9d3d7b4aa9932afb84df", - "git_remote" : "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", + "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml b/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml index bc6df1e..742c544 100644 --- a/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml +++ b/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml @@ -299,8 +299,8 @@ build_info: output: "target/nextflow/rsem/rsem_calculate_expression" executable: "target/nextflow/rsem/rsem_calculate_expression/main.nf" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/rsem/rsem_calculate_expression/main.nf b/target/nextflow/rsem/rsem_calculate_expression/main.nf index 9acc5f9..c591cec 100644 --- a/target/nextflow/rsem/rsem_calculate_expression/main.nf +++ b/target/nextflow/rsem/rsem_calculate_expression/main.nf @@ -3163,8 +3163,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rsem/rsem_calculate_expression", "viash_version" : "0.9.0", - "git_commit" : "b291665ddc01d0f8072d9d3d7b4aa9932afb84df", - "git_remote" : "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", + "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/rsem/rsem_merge_counts/.config.vsh.yaml b/target/nextflow/rsem/rsem_merge_counts/.config.vsh.yaml index b449647..62ad579 100644 --- a/target/nextflow/rsem/rsem_merge_counts/.config.vsh.yaml +++ b/target/nextflow/rsem/rsem_merge_counts/.config.vsh.yaml @@ -182,8 +182,8 @@ build_info: output: "target/nextflow/rsem/rsem_merge_counts" executable: "target/nextflow/rsem/rsem_merge_counts/main.nf" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/rsem/rsem_merge_counts/main.nf b/target/nextflow/rsem/rsem_merge_counts/main.nf index 468920d..60ba527 100644 --- a/target/nextflow/rsem/rsem_merge_counts/main.nf +++ b/target/nextflow/rsem/rsem_merge_counts/main.nf @@ -3028,8 +3028,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rsem/rsem_merge_counts", "viash_version" : "0.9.0", - "git_commit" : "b291665ddc01d0f8072d9d3d7b4aa9932afb84df", - "git_remote" : "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", + "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml index 26952a9..cad890e 100644 --- a/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml @@ -163,8 +163,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_bamstat" executable: "target/nextflow/rseqc/rseqc_bamstat/main.nf" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/rseqc/rseqc_bamstat/main.nf b/target/nextflow/rseqc/rseqc_bamstat/main.nf index 1786cba..078b1cf 100644 --- a/target/nextflow/rseqc/rseqc_bamstat/main.nf +++ b/target/nextflow/rseqc/rseqc_bamstat/main.nf @@ -3016,8 +3016,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_bamstat", "viash_version" : "0.9.0", - "git_commit" : "b291665ddc01d0f8072d9d3d7b4aa9932afb84df", - "git_remote" : "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", + "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml index 27f66f2..91deacd 100644 --- a/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml @@ -186,8 +186,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_inferexperiment" executable: "target/nextflow/rseqc/rseqc_inferexperiment/main.nf" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/rseqc/rseqc_inferexperiment/main.nf b/target/nextflow/rseqc/rseqc_inferexperiment/main.nf index 066e16a..cee1b2f 100644 --- a/target/nextflow/rseqc/rseqc_inferexperiment/main.nf +++ b/target/nextflow/rseqc/rseqc_inferexperiment/main.nf @@ -3044,8 +3044,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_inferexperiment", "viash_version" : "0.9.0", - "git_commit" : "b291665ddc01d0f8072d9d3d7b4aa9932afb84df", - "git_remote" : "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", + "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/rseqc/rseqc_innerdistance/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_innerdistance/.config.vsh.yaml index 6814e7a..58644ec 100644 --- a/target/nextflow/rseqc/rseqc_innerdistance/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_innerdistance/.config.vsh.yaml @@ -272,8 +272,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_innerdistance" executable: "target/nextflow/rseqc/rseqc_innerdistance/main.nf" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/rseqc/rseqc_innerdistance/main.nf b/target/nextflow/rseqc/rseqc_innerdistance/main.nf index 786e3b0..77e7f64 100644 --- a/target/nextflow/rseqc/rseqc_innerdistance/main.nf +++ b/target/nextflow/rseqc/rseqc_innerdistance/main.nf @@ -3137,8 +3137,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_innerdistance", "viash_version" : "0.9.0", - "git_commit" : "b291665ddc01d0f8072d9d3d7b4aa9932afb84df", - "git_remote" : "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", + "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/rseqc/rseqc_junctionannotation/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_junctionannotation/.config.vsh.yaml index f89355a..fb160cd 100644 --- a/target/nextflow/rseqc/rseqc_junctionannotation/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_junctionannotation/.config.vsh.yaml @@ -260,8 +260,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_junctionannotation" executable: "target/nextflow/rseqc/rseqc_junctionannotation/main.nf" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/rseqc/rseqc_junctionannotation/main.nf b/target/nextflow/rseqc/rseqc_junctionannotation/main.nf index f078f23..523a3f8 100644 --- a/target/nextflow/rseqc/rseqc_junctionannotation/main.nf +++ b/target/nextflow/rseqc/rseqc_junctionannotation/main.nf @@ -3128,8 +3128,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_junctionannotation", "viash_version" : "0.9.0", - "git_commit" : "b291665ddc01d0f8072d9d3d7b4aa9932afb84df", - "git_remote" : "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", + "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/rseqc/rseqc_junctionsaturation/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_junctionsaturation/.config.vsh.yaml index b452e16..f3d2a45 100644 --- a/target/nextflow/rseqc/rseqc_junctionsaturation/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_junctionsaturation/.config.vsh.yaml @@ -249,8 +249,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_junctionsaturation" executable: "target/nextflow/rseqc/rseqc_junctionsaturation/main.nf" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/rseqc/rseqc_junctionsaturation/main.nf b/target/nextflow/rseqc/rseqc_junctionsaturation/main.nf index adb8c3c..3ed2a7d 100644 --- a/target/nextflow/rseqc/rseqc_junctionsaturation/main.nf +++ b/target/nextflow/rseqc/rseqc_junctionsaturation/main.nf @@ -3113,8 +3113,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_junctionsaturation", "viash_version" : "0.9.0", - "git_commit" : "b291665ddc01d0f8072d9d3d7b4aa9932afb84df", - "git_remote" : "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", + "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/rseqc/rseqc_readdistribution/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_readdistribution/.config.vsh.yaml index 3904d47..35dee3e 100644 --- a/target/nextflow/rseqc/rseqc_readdistribution/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_readdistribution/.config.vsh.yaml @@ -162,8 +162,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_readdistribution" executable: "target/nextflow/rseqc/rseqc_readdistribution/main.nf" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/rseqc/rseqc_readdistribution/main.nf b/target/nextflow/rseqc/rseqc_readdistribution/main.nf index 3676803..374001e 100644 --- a/target/nextflow/rseqc/rseqc_readdistribution/main.nf +++ b/target/nextflow/rseqc/rseqc_readdistribution/main.nf @@ -3017,8 +3017,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_readdistribution", "viash_version" : "0.9.0", - "git_commit" : "b291665ddc01d0f8072d9d3d7b4aa9932afb84df", - "git_remote" : "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", + "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/rseqc/rseqc_readduplication/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_readduplication/.config.vsh.yaml index 1a21d43..183b2b3 100644 --- a/target/nextflow/rseqc/rseqc_readduplication/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_readduplication/.config.vsh.yaml @@ -211,8 +211,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_readduplication" executable: "target/nextflow/rseqc/rseqc_readduplication/main.nf" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/rseqc/rseqc_readduplication/main.nf b/target/nextflow/rseqc/rseqc_readduplication/main.nf index e40c4d3..4bbe152 100644 --- a/target/nextflow/rseqc/rseqc_readduplication/main.nf +++ b/target/nextflow/rseqc/rseqc_readduplication/main.nf @@ -3071,8 +3071,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_readduplication", "viash_version" : "0.9.0", - "git_commit" : "b291665ddc01d0f8072d9d3d7b4aa9932afb84df", - "git_remote" : "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", + "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/rseqc/rseqc_tin/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_tin/.config.vsh.yaml index 9246438..f10b6ae 100644 --- a/target/nextflow/rseqc/rseqc_tin/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_tin/.config.vsh.yaml @@ -214,8 +214,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_tin" executable: "target/nextflow/rseqc/rseqc_tin/main.nf" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/rseqc/rseqc_tin/main.nf b/target/nextflow/rseqc/rseqc_tin/main.nf index 4b732ee..d0963e5 100644 --- a/target/nextflow/rseqc/rseqc_tin/main.nf +++ b/target/nextflow/rseqc/rseqc_tin/main.nf @@ -3076,8 +3076,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_tin", "viash_version" : "0.9.0", - "git_commit" : "b291665ddc01d0f8072d9d3d7b4aa9932afb84df", - "git_remote" : "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", + "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/sortmerna/.config.vsh.yaml b/target/nextflow/sortmerna/.config.vsh.yaml index 05ae3a4..dabbcd1 100644 --- a/target/nextflow/sortmerna/.config.vsh.yaml +++ b/target/nextflow/sortmerna/.config.vsh.yaml @@ -198,8 +198,8 @@ build_info: output: "target/nextflow/sortmerna" executable: "target/nextflow/sortmerna/main.nf" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/sortmerna/main.nf b/target/nextflow/sortmerna/main.nf index f8097d5..87840ff 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" : "b291665ddc01d0f8072d9d3d7b4aa9932afb84df", - "git_remote" : "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", + "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/stringtie/.config.vsh.yaml b/target/nextflow/stringtie/.config.vsh.yaml index cf5deb8..43545b3 100644 --- a/target/nextflow/stringtie/.config.vsh.yaml +++ b/target/nextflow/stringtie/.config.vsh.yaml @@ -216,8 +216,8 @@ build_info: output: "target/nextflow/stringtie" executable: "target/nextflow/stringtie/main.nf" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/stringtie/main.nf b/target/nextflow/stringtie/main.nf index 3c9ddb8..100bd0d 100644 --- a/target/nextflow/stringtie/main.nf +++ b/target/nextflow/stringtie/main.nf @@ -3073,8 +3073,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/stringtie", "viash_version" : "0.9.0", - "git_commit" : "b291665ddc01d0f8072d9d3d7b4aa9932afb84df", - "git_remote" : "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", + "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/summarizedexperiment/.config.vsh.yaml b/target/nextflow/summarizedexperiment/.config.vsh.yaml index 5a7481f..5556760 100644 --- a/target/nextflow/summarizedexperiment/.config.vsh.yaml +++ b/target/nextflow/summarizedexperiment/.config.vsh.yaml @@ -199,8 +199,8 @@ build_info: output: "target/nextflow/summarizedexperiment" executable: "target/nextflow/summarizedexperiment/main.nf" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/summarizedexperiment/main.nf b/target/nextflow/summarizedexperiment/main.nf index 3bf1104..d5bd2e2 100644 --- a/target/nextflow/summarizedexperiment/main.nf +++ b/target/nextflow/summarizedexperiment/main.nf @@ -3054,8 +3054,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/summarizedexperiment", "viash_version" : "0.9.0", - "git_commit" : "b291665ddc01d0f8072d9d3d7b4aa9932afb84df", - "git_remote" : "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", + "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/trimgalore/.config.vsh.yaml b/target/nextflow/trimgalore/.config.vsh.yaml index abb7acb..1f9a8d3 100644 --- a/target/nextflow/trimgalore/.config.vsh.yaml +++ b/target/nextflow/trimgalore/.config.vsh.yaml @@ -788,8 +788,8 @@ build_info: output: "target/nextflow/trimgalore" executable: "target/nextflow/trimgalore/main.nf" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/trimgalore/main.nf b/target/nextflow/trimgalore/main.nf index 2079209..f8a631f 100644 --- a/target/nextflow/trimgalore/main.nf +++ b/target/nextflow/trimgalore/main.nf @@ -3576,8 +3576,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/trimgalore", "viash_version" : "0.9.0", - "git_commit" : "b291665ddc01d0f8072d9d3d7b4aa9932afb84df", - "git_remote" : "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", + "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/tx2gene/.config.vsh.yaml b/target/nextflow/tx2gene/.config.vsh.yaml index 124bffa..733b1a6 100644 --- a/target/nextflow/tx2gene/.config.vsh.yaml +++ b/target/nextflow/tx2gene/.config.vsh.yaml @@ -192,8 +192,8 @@ build_info: output: "target/nextflow/tx2gene" executable: "target/nextflow/tx2gene/main.nf" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/tx2gene/main.nf b/target/nextflow/tx2gene/main.nf index 3a64b44..d5a9570 100644 --- a/target/nextflow/tx2gene/main.nf +++ b/target/nextflow/tx2gene/main.nf @@ -3049,8 +3049,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/tx2gene", "viash_version" : "0.9.0", - "git_commit" : "b291665ddc01d0f8072d9d3d7b4aa9932afb84df", - "git_remote" : "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", + "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/tximport/.config.vsh.yaml b/target/nextflow/tximport/.config.vsh.yaml index d5f697a..7244d11 100644 --- a/target/nextflow/tximport/.config.vsh.yaml +++ b/target/nextflow/tximport/.config.vsh.yaml @@ -247,8 +247,8 @@ build_info: output: "target/nextflow/tximport" executable: "target/nextflow/tximport/main.nf" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/tximport/main.nf b/target/nextflow/tximport/main.nf index 7755b4d..29e9d8c 100644 --- a/target/nextflow/tximport/main.nf +++ b/target/nextflow/tximport/main.nf @@ -3114,8 +3114,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/tximport", "viash_version" : "0.9.0", - "git_commit" : "b291665ddc01d0f8072d9d3d7b4aa9932afb84df", - "git_remote" : "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", + "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/ucsc/bedclip/.config.vsh.yaml b/target/nextflow/ucsc/bedclip/.config.vsh.yaml index 7ed0942..2d4ac7f 100644 --- a/target/nextflow/ucsc/bedclip/.config.vsh.yaml +++ b/target/nextflow/ucsc/bedclip/.config.vsh.yaml @@ -164,8 +164,8 @@ build_info: output: "target/nextflow/ucsc/bedclip" executable: "target/nextflow/ucsc/bedclip/main.nf" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/ucsc/bedclip/main.nf b/target/nextflow/ucsc/bedclip/main.nf index 1202ac3..ab23566 100644 --- a/target/nextflow/ucsc/bedclip/main.nf +++ b/target/nextflow/ucsc/bedclip/main.nf @@ -3018,8 +3018,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/ucsc/bedclip", "viash_version" : "0.9.0", - "git_commit" : "b291665ddc01d0f8072d9d3d7b4aa9932afb84df", - "git_remote" : "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", + "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/ucsc/bedgraphtobigwig/.config.vsh.yaml b/target/nextflow/ucsc/bedgraphtobigwig/.config.vsh.yaml index 945b0ff..0c64dce 100644 --- a/target/nextflow/ucsc/bedgraphtobigwig/.config.vsh.yaml +++ b/target/nextflow/ucsc/bedgraphtobigwig/.config.vsh.yaml @@ -164,8 +164,8 @@ build_info: output: "target/nextflow/ucsc/bedgraphtobigwig" executable: "target/nextflow/ucsc/bedgraphtobigwig/main.nf" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/ucsc/bedgraphtobigwig/main.nf b/target/nextflow/ucsc/bedgraphtobigwig/main.nf index ff6bf05..83d042f 100644 --- a/target/nextflow/ucsc/bedgraphtobigwig/main.nf +++ b/target/nextflow/ucsc/bedgraphtobigwig/main.nf @@ -3018,8 +3018,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/ucsc/bedgraphtobigwig", "viash_version" : "0.9.0", - "git_commit" : "b291665ddc01d0f8072d9d3d7b4aa9932afb84df", - "git_remote" : "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", + "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/umitools/umitools_dedup/.config.vsh.yaml b/target/nextflow/umitools/umitools_dedup/.config.vsh.yaml index a4a6574..c307ef0 100644 --- a/target/nextflow/umitools/umitools_dedup/.config.vsh.yaml +++ b/target/nextflow/umitools/umitools_dedup/.config.vsh.yaml @@ -195,8 +195,8 @@ build_info: output: "target/nextflow/umitools/umitools_dedup" executable: "target/nextflow/umitools/umitools_dedup/main.nf" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/umitools/umitools_dedup/main.nf b/target/nextflow/umitools/umitools_dedup/main.nf index 3017e55..ce33562 100644 --- a/target/nextflow/umitools/umitools_dedup/main.nf +++ b/target/nextflow/umitools/umitools_dedup/main.nf @@ -3054,8 +3054,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/umitools/umitools_dedup", "viash_version" : "0.9.0", - "git_commit" : "b291665ddc01d0f8072d9d3d7b4aa9932afb84df", - "git_remote" : "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", + "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/umitools/umitools_extract/.config.vsh.yaml b/target/nextflow/umitools/umitools_extract/.config.vsh.yaml index 718aa2e..70af5a7 100644 --- a/target/nextflow/umitools/umitools_extract/.config.vsh.yaml +++ b/target/nextflow/umitools/umitools_extract/.config.vsh.yaml @@ -253,8 +253,8 @@ build_info: output: "target/nextflow/umitools/umitools_extract" executable: "target/nextflow/umitools/umitools_extract/main.nf" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/umitools/umitools_extract/main.nf b/target/nextflow/umitools/umitools_extract/main.nf index b77ffb0..6d18628 100644 --- a/target/nextflow/umitools/umitools_extract/main.nf +++ b/target/nextflow/umitools/umitools_extract/main.nf @@ -3119,8 +3119,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/umitools/umitools_extract", "viash_version" : "0.9.0", - "git_commit" : "b291665ddc01d0f8072d9d3d7b4aa9932afb84df", - "git_remote" : "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", + "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/umitools_prepareforquant/.config.vsh.yaml b/target/nextflow/umitools_prepareforquant/.config.vsh.yaml index d9d664c..5928840 100644 --- a/target/nextflow/umitools_prepareforquant/.config.vsh.yaml +++ b/target/nextflow/umitools_prepareforquant/.config.vsh.yaml @@ -156,8 +156,8 @@ build_info: output: "target/nextflow/umitools_prepareforquant" executable: "target/nextflow/umitools_prepareforquant/main.nf" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/umitools_prepareforquant/main.nf b/target/nextflow/umitools_prepareforquant/main.nf index 0e1f82a..b53a124 100644 --- a/target/nextflow/umitools_prepareforquant/main.nf +++ b/target/nextflow/umitools_prepareforquant/main.nf @@ -3007,8 +3007,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/umitools_prepareforquant", "viash_version" : "0.9.0", - "git_commit" : "b291665ddc01d0f8072d9d3d7b4aa9932afb84df", - "git_remote" : "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", + "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", 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 62be1dc..d3b76a9 100644 --- a/target/nextflow/workflows/genome_alignment_and_quant/.config.vsh.yaml +++ b/target/nextflow/workflows/genome_alignment_and_quant/.config.vsh.yaml @@ -381,6 +381,15 @@ argument_groups: direction: "output" multiple: false multiple_sep: ";" + - type: "file" + name: "--salmon_multiqc" + info: null + must_exist: true + create_parent: true + required: false + direction: "output" + multiple: false + multiple_sep: ";" - type: "file" name: "--rsem_counts_gene" description: "Expression counts on gene level" @@ -594,8 +603,8 @@ build_info: output: "target/nextflow/workflows/genome_alignment_and_quant" executable: "target/nextflow/workflows/genome_alignment_and_quant/main.nf" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" dependencies: - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_align_reads" - "target/dependencies/vsh/vsh/biobox/v0.2.0/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 58b366b..ccad37d 100644 --- a/target/nextflow/workflows/genome_alignment_and_quant/main.nf +++ b/target/nextflow/workflows/genome_alignment_and_quant/main.nf @@ -3243,6 +3243,16 @@ meta = [ "multiple" : false, "multiple_sep" : ";" }, + { + "type" : "file", + "name" : "--salmon_multiqc", + "must_exist" : true, + "create_parent" : true, + "required" : false, + "direction" : "output", + "multiple" : false, + "multiple_sep" : ";" + }, { "type" : "file", "name" : "--rsem_counts_gene", @@ -3521,8 +3531,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/genome_alignment_and_quant", "viash_version" : "0.9.0", - "git_commit" : "b291665ddc01d0f8072d9d3d7b4aa9932afb84df", - "git_remote" : "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", + "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", @@ -3859,6 +3869,11 @@ workflow run_wf { ] ) + | map { id, state -> + def mod_state = (state.aligner == 'star_salmon') ? state + [salmon_multiqc: state.quant_out_dir] : state + [ id, mod_state ] + } + | niceView() | rsem_calculate_expression.run ( runIf: { id, state -> state.aligner == 'star_rsem' }, fromState: [ @@ -3936,6 +3951,7 @@ workflow run_wf { [ "star_alignment": "star_alignment", "star_multiqc": "star_multiqc", "rsem_multiqc": "rsem_multiqc", + "salmon_multiqc": "salmon_multiqc", "genome_bam_sorted": "genome_bam_sorted", "genome_bam_index": "genome_bam_index", "genome_bam_stats": "genome_bam_stats", diff --git a/target/nextflow/workflows/genome_alignment_and_quant/nextflow_schema.json b/target/nextflow/workflows/genome_alignment_and_quant/nextflow_schema.json index 6bc17f4..dfe1afe 100644 --- a/target/nextflow/workflows/genome_alignment_and_quant/nextflow_schema.json +++ b/target/nextflow/workflows/genome_alignment_and_quant/nextflow_schema.json @@ -399,6 +399,17 @@ } + , + "salmon_multiqc": { + "type": + "string", + "description": "Type: `file`, default: `$id.$key.salmon_multiqc.salmon_multiqc`. ", + "help_text": "Type: `file`, default: `$id.$key.salmon_multiqc.salmon_multiqc`. " + , + "default": "$id.$key.salmon_multiqc.salmon_multiqc" + } + + , "rsem_counts_gene": { "type": diff --git a/target/nextflow/workflows/merge_quant_results/.config.vsh.yaml b/target/nextflow/workflows/merge_quant_results/.config.vsh.yaml index 9b6dde8..bc44897 100644 --- a/target/nextflow/workflows/merge_quant_results/.config.vsh.yaml +++ b/target/nextflow/workflows/merge_quant_results/.config.vsh.yaml @@ -278,8 +278,8 @@ build_info: output: "target/nextflow/workflows/merge_quant_results" executable: "target/nextflow/workflows/merge_quant_results/main.nf" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@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 3de319b..864b7fd 100644 --- a/target/nextflow/workflows/merge_quant_results/main.nf +++ b/target/nextflow/workflows/merge_quant_results/main.nf @@ -3149,8 +3149,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/merge_quant_results", "viash_version" : "0.9.0", - "git_commit" : "b291665ddc01d0f8072d9d3d7b4aa9932afb84df", - "git_remote" : "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", + "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/workflows/post_processing/.config.vsh.yaml b/target/nextflow/workflows/post_processing/.config.vsh.yaml index f56c28f..ca96f59 100644 --- a/target/nextflow/workflows/post_processing/.config.vsh.yaml +++ b/target/nextflow/workflows/post_processing/.config.vsh.yaml @@ -199,7 +199,7 @@ argument_groups: name: "--processed_genome_bam" info: null default: - - "$id.markdup.sorted.bam" + - "$id..genome.bam" must_exist: true create_parent: true required: false @@ -210,7 +210,7 @@ argument_groups: name: "--genome_bam_index" info: null default: - - "$id.markdup.sorted.bam" + - "$id.genome.bam.bai" must_exist: true create_parent: true required: false @@ -221,7 +221,7 @@ argument_groups: name: "--genome_bam_stats" info: null default: - - "$id.markdup.sorted.bam.stats" + - "$id.genome.stats" must_exist: true create_parent: true required: false @@ -232,7 +232,7 @@ argument_groups: name: "--genome_bam_flagstat" info: null default: - - "$id.markdup.sorted.bam.flagstat" + - "$id.genome.flagstat" must_exist: true create_parent: true required: false @@ -243,7 +243,7 @@ argument_groups: name: "--genome_bam_idxstats" info: null default: - - "$id.markdup.sorted.bam.idxstats" + - "$id.genome.idxstats" must_exist: true create_parent: true required: false @@ -254,7 +254,7 @@ argument_groups: name: "--markduplicates_metrics" info: null default: - - "$id.markdup.sorted.MarkDuplicates.metrics.txt" + - "$id.MarkDuplicates.metrics.txt" must_exist: true create_parent: true required: false @@ -486,8 +486,8 @@ build_info: output: "target/nextflow/workflows/post_processing" executable: "target/nextflow/workflows/post_processing/main.nf" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/picard_markduplicates" - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort" diff --git a/target/nextflow/workflows/post_processing/main.nf b/target/nextflow/workflows/post_processing/main.nf index 656a45a..10a6131 100644 --- a/target/nextflow/workflows/post_processing/main.nf +++ b/target/nextflow/workflows/post_processing/main.nf @@ -3029,7 +3029,7 @@ meta = [ "type" : "file", "name" : "--processed_genome_bam", "default" : [ - "$id.markdup.sorted.bam" + "$id..genome.bam" ], "must_exist" : true, "create_parent" : true, @@ -3042,7 +3042,7 @@ meta = [ "type" : "file", "name" : "--genome_bam_index", "default" : [ - "$id.markdup.sorted.bam" + "$id.genome.bam.bai" ], "must_exist" : true, "create_parent" : true, @@ -3055,7 +3055,7 @@ meta = [ "type" : "file", "name" : "--genome_bam_stats", "default" : [ - "$id.markdup.sorted.bam.stats" + "$id.genome.stats" ], "must_exist" : true, "create_parent" : true, @@ -3068,7 +3068,7 @@ meta = [ "type" : "file", "name" : "--genome_bam_flagstat", "default" : [ - "$id.markdup.sorted.bam.flagstat" + "$id.genome.flagstat" ], "must_exist" : true, "create_parent" : true, @@ -3081,7 +3081,7 @@ meta = [ "type" : "file", "name" : "--genome_bam_idxstats", "default" : [ - "$id.markdup.sorted.bam.idxstats" + "$id.genome.idxstats" ], "must_exist" : true, "create_parent" : true, @@ -3094,7 +3094,7 @@ meta = [ "type" : "file", "name" : "--markduplicates_metrics", "default" : [ - "$id.markdup.sorted.MarkDuplicates.metrics.txt" + "$id.MarkDuplicates.metrics.txt" ], "must_exist" : true, "create_parent" : true, @@ -3397,8 +3397,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/post_processing", "viash_version" : "0.9.0", - "git_commit" : "b291665ddc01d0f8072d9d3d7b4aa9932afb84df", - "git_remote" : "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", + "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/workflows/post_processing/nextflow_schema.json b/target/nextflow/workflows/post_processing/nextflow_schema.json index 26bdcd3..ca7d7bf 100644 --- a/target/nextflow/workflows/post_processing/nextflow_schema.json +++ b/target/nextflow/workflows/post_processing/nextflow_schema.json @@ -244,10 +244,10 @@ "genome_bam_index": { "type": "string", - "description": "Type: `file`, default: `$id.$key.genome_bam_index.bam`. ", - "help_text": "Type: `file`, default: `$id.$key.genome_bam_index.bam`. " + "description": "Type: `file`, default: `$id.$key.genome_bam_index.bai`. ", + "help_text": "Type: `file`, default: `$id.$key.genome_bam_index.bai`. " , - "default": "$id.$key.genome_bam_index.bam" + "default": "$id.$key.genome_bam_index.bai" } diff --git a/target/nextflow/workflows/pre_processing/.config.vsh.yaml b/target/nextflow/workflows/pre_processing/.config.vsh.yaml index 806201a..5d219f2 100644 --- a/target/nextflow/workflows/pre_processing/.config.vsh.yaml +++ b/target/nextflow/workflows/pre_processing/.config.vsh.yaml @@ -353,7 +353,7 @@ argument_groups: description: "Path to output directory" info: null default: - - "$id.$key.read_1.fastq" + - "$id.read_1.fastq" must_exist: false create_parent: true required: false @@ -365,7 +365,7 @@ argument_groups: description: "Path to output directory" info: null default: - - "$id.$key.read_2.fastq" + - "$id.read_2.fastq" must_exist: false create_parent: true required: false @@ -673,8 +673,8 @@ build_info: output: "target/nextflow/workflows/pre_processing" executable: "target/nextflow/workflows/pre_processing/main.nf" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/fastqc" - "target/nextflow/umitools/umitools_extract" diff --git a/target/nextflow/workflows/pre_processing/main.nf b/target/nextflow/workflows/pre_processing/main.nf index 616ec40..1a5ddb8 100644 --- a/target/nextflow/workflows/pre_processing/main.nf +++ b/target/nextflow/workflows/pre_processing/main.nf @@ -3222,7 +3222,7 @@ meta = [ "name" : "--qc_output1", "description" : "Path to output directory", "default" : [ - "$id.$key.read_1.fastq" + "$id.read_1.fastq" ], "must_exist" : false, "create_parent" : true, @@ -3236,7 +3236,7 @@ meta = [ "name" : "--qc_output2", "description" : "Path to output directory", "default" : [ - "$id.$key.read_2.fastq" + "$id.read_2.fastq" ], "must_exist" : false, "create_parent" : true, @@ -3626,8 +3626,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/pre_processing", "viash_version" : "0.9.0", - "git_commit" : "b291665ddc01d0f8072d9d3d7b4aa9932afb84df", - "git_remote" : "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", + "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", @@ -3758,7 +3758,7 @@ workflow run_wf { "trim_html_1": "trimmed_fastqc_html_1", "trim_html_2": "trimmed_fastqc_html_2" ], - args: [gzip: true] + args: [gzip: true, fastqc: true] ) // Trim reads using fastp diff --git a/target/nextflow/workflows/prepare_genome/.config.vsh.yaml b/target/nextflow/workflows/prepare_genome/.config.vsh.yaml index 623b325..b9fd063 100644 --- a/target/nextflow/workflows/prepare_genome/.config.vsh.yaml +++ b/target/nextflow/workflows/prepare_genome/.config.vsh.yaml @@ -496,8 +496,8 @@ build_info: output: "target/nextflow/workflows/prepare_genome" executable: "target/nextflow/workflows/prepare_genome/main.nf" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/gunzip" - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/gffread" diff --git a/target/nextflow/workflows/prepare_genome/main.nf b/target/nextflow/workflows/prepare_genome/main.nf index 98b6ca1..cfcc084 100644 --- a/target/nextflow/workflows/prepare_genome/main.nf +++ b/target/nextflow/workflows/prepare_genome/main.nf @@ -3407,8 +3407,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/prepare_genome", "viash_version" : "0.9.0", - "git_commit" : "b291665ddc01d0f8072d9d3d7b4aa9932afb84df", - "git_remote" : "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", + "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", 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 a1ca5b6..899e630 100644 --- a/target/nextflow/workflows/pseudo_alignment_and_quant/.config.vsh.yaml +++ b/target/nextflow/workflows/pseudo_alignment_and_quant/.config.vsh.yaml @@ -139,8 +139,6 @@ argument_groups: - type: "file" name: "--pseudo_multiqc" info: null - default: - - "$id.quant.log" must_exist: true create_parent: true required: false @@ -285,8 +283,8 @@ build_info: output: "target/nextflow/workflows/pseudo_alignment_and_quant" executable: "target/nextflow/workflows/pseudo_alignment_and_quant/main.nf" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" dependencies: - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant" - "target/nextflow/kallisto/kallisto_quant" diff --git a/target/nextflow/workflows/pseudo_alignment_and_quant/main.nf b/target/nextflow/workflows/pseudo_alignment_and_quant/main.nf index 0c64db6..6c7ad31 100644 --- a/target/nextflow/workflows/pseudo_alignment_and_quant/main.nf +++ b/target/nextflow/workflows/pseudo_alignment_and_quant/main.nf @@ -2963,9 +2963,6 @@ meta = [ { "type" : "file", "name" : "--pseudo_multiqc", - "default" : [ - "$id.quant.log" - ], "must_exist" : true, "create_parent" : true, "required" : false, @@ -3146,8 +3143,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/pseudo_alignment_and_quant", "viash_version" : "0.9.0", - "git_commit" : "b291665ddc01d0f8072d9d3d7b4aa9932afb84df", - "git_remote" : "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", + "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", @@ -3242,11 +3239,16 @@ workflow run_wf { lib_type: state.lib_type ] }, toState: [ - "quant_outs_dir": "output", + "quant_out_dir": "output", "salmon_quant_results_file": "quant_results" ] ) + | map { id, state -> + def mod_state = (state.pseudo_aligner == 'salmon') ? state + [pseudo_multiqc: state.quant_out_dir] : state + [ id, mod_state ] + } + | kallisto_quant.run ( runIf: { id, state -> state.pseudo_aligner == 'kallisto'}, fromState: [ diff --git a/target/nextflow/workflows/pseudo_alignment_and_quant/nextflow_schema.json b/target/nextflow/workflows/pseudo_alignment_and_quant/nextflow_schema.json index 3ecd375..bbfd08f 100644 --- a/target/nextflow/workflows/pseudo_alignment_and_quant/nextflow_schema.json +++ b/target/nextflow/workflows/pseudo_alignment_and_quant/nextflow_schema.json @@ -153,10 +153,10 @@ "pseudo_multiqc": { "type": "string", - "description": "Type: `file`, default: `$id.$key.pseudo_multiqc.log`. ", - "help_text": "Type: `file`, default: `$id.$key.pseudo_multiqc.log`. " + "description": "Type: `file`, default: `$id.$key.pseudo_multiqc.pseudo_multiqc`. ", + "help_text": "Type: `file`, default: `$id.$key.pseudo_multiqc.pseudo_multiqc`. " , - "default": "$id.$key.pseudo_multiqc.log" + "default": "$id.$key.pseudo_multiqc.pseudo_multiqc" } diff --git a/target/nextflow/workflows/quality_control/.config.vsh.yaml b/target/nextflow/workflows/quality_control/.config.vsh.yaml index 3a6825d..15eb460 100644 --- a/target/nextflow/workflows/quality_control/.config.vsh.yaml +++ b/target/nextflow/workflows/quality_control/.config.vsh.yaml @@ -632,25 +632,6 @@ argument_groups: direction: "input" multiple: false multiple_sep: ";" - - type: "file" - name: "--mqc_yml" - description: "Software versions" - info: null - must_exist: true - create_parent: true - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--workflow_summary" - info: null - must_exist: true - create_parent: true - required: false - direction: "input" - multiple: false - multiple_sep: ";" - type: "boolean" name: "--passed_trimmed_reads" info: null @@ -751,6 +732,15 @@ argument_groups: direction: "input" multiple: false multiple_sep: ";" + - type: "file" + name: "--rsem_multiqc" + info: null + must_exist: true + create_parent: true + required: false + direction: "input" + multiple: false + multiple_sep: ";" - type: "file" name: "--genome_bam_stats" info: null @@ -1253,15 +1243,6 @@ argument_groups: direction: "output" multiple: false multiple_sep: ";" - - type: "file" - name: "--multiqc_versions" - info: null - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - type: "file" name: "--featurecounts" info: null @@ -1615,8 +1596,8 @@ build_info: output: "target/nextflow/workflows/quality_control" executable: "target/nextflow/workflows/quality_control/main.nf" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/rseqc/rseqc_bamstat" - "target/nextflow/rseqc/rseqc_inferexperiment" diff --git a/target/nextflow/workflows/quality_control/main.nf b/target/nextflow/workflows/quality_control/main.nf index 47c7568..ec54d2c 100644 --- a/target/nextflow/workflows/quality_control/main.nf +++ b/target/nextflow/workflows/quality_control/main.nf @@ -3510,27 +3510,6 @@ meta = [ "multiple" : false, "multiple_sep" : ";" }, - { - "type" : "file", - "name" : "--mqc_yml", - "description" : "Software versions", - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--workflow_summary", - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - }, { "type" : "boolean", "name" : "--passed_trimmed_reads", @@ -3643,6 +3622,16 @@ meta = [ "multiple" : false, "multiple_sep" : ";" }, + { + "type" : "file", + "name" : "--rsem_multiqc", + "must_exist" : true, + "create_parent" : true, + "required" : false, + "direction" : "input", + "multiple" : false, + "multiple_sep" : ";" + }, { "type" : "file", "name" : "--genome_bam_stats", @@ -4221,16 +4210,6 @@ meta = [ "multiple" : false, "multiple_sep" : ";" }, - { - "type" : "file", - "name" : "--multiqc_versions", - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, { "type" : "file", "name" : "--featurecounts", @@ -4697,8 +4676,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/quality_control", "viash_version" : "0.9.0", - "git_commit" : "b291665ddc01d0f8072d9d3d7b4aa9932afb84df", - "git_remote" : "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", + "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", @@ -4818,7 +4797,7 @@ workflow run_wf { "input": "genome_bam", "extra_preseq_args": "extra_preseq_args" ], - toState: [ "preseq_output": "output" ], + toState: [ "preseq_output": "output" ] ) | rseqc_bamstat.run ( @@ -4977,11 +4956,49 @@ workflow run_wf { merged_ch = qc_ch | toSortedList - - // TODO: Get Salmon meta info | map { list -> def ids = list.collect { id, state -> state.id } def strandedness = list.collect { id, state -> state.strandedness } + def num_trimmed_reads = list.collect { id, state -> state.num_trimmed_reads } + def passed_trimmed_reads = list.collect { id, state -> state.passed_trimmed_reads } + def passed_mapping = list.collect { id, state -> state.passed_mapping } + def percent_mapped = list.collect { id, state -> state.percent_mapped } + def inferred_strand = list.collect { id, state -> state.inferred_strand } + def passed_strand_check = list.collect { id, state -> state.passed_strand_check } + def gtf = list.collect { id, state -> state.gtf }.unique()[0] + def gtf_extra_attributes = list.collect { id, state -> state.gtf_extra_attributes }.unique()[0] + def gtf_group_features = list.collect { id, state -> state.gtf_group_features }.unique()[0] + def pca_header_multiqc = list.collect { id, state -> state.pca_header_multiqc }.unique()[0] + def clustering_header_multiqc = list.collect { id, state -> state.clustering_header_multiqc }.unique()[0] + def aligner = list.collect { id, state -> state.aligner }.unique()[0] + def pseudo_aligner = list.collect { id, state -> state.pseudo_aligner }.unique()[0] + def deseq2_vst = list.collect { id, state -> state.deseq2_vst }.unique()[0] + def extra_deseq2_args = list.collect { id, state -> state.extra_deseq2_args }.unique()[0] + def extra_deseq2_args2 = list.collect { id, state -> state.extra_deseq2_args2 }.unique()[0] + def skip_deseq2_qc = list.collect { id, state -> state.skip_deseq2_qc }.unique()[0] + def skip_qc = list.collect { id, state -> state.skip_qc }.unique()[0] + def skip_align = list.collect { id, state -> state.skip_align }.unique()[0] + def skip_pseudo_align = list.collect { id, state -> state.skip_pseudo_align }.unique()[0] + def quant_results = list.collect { id, state -> + (state.quant_results_file instanceof java.nio.file.Path && state.quant_results_file.exists()) ? + state.quant_results_file : + null } + def rsem_counts_gene = list.collect { id, state -> + (state.rsem_counts_gene instanceof java.nio.file.Path && state.rsem_counts_gene.exists()) ? + state.rsem_counts_gene : + null } + def rsem_counts_transcripts = list.collect { id, state -> + (state.rsem_counts_transcripts instanceof java.nio.file.Path && state.rsem_counts_transcripts.exists()) ? + state.rsem_counts_transcripts : + null } + def pseudo_salmon_quant_results = list.collect { id, state -> + (state.pseudo_salmon_quant_results_file instanceof java.nio.file.Path && state.pseudo_salmon_quant_results_file.exists()) ? + state.pseudo_salmon_quant_results_file : + null } + def pseudo_kallisto_quant_results = list.collect { id, state -> + (state.pseudo_kallisto_quant_results_file instanceof java.nio.file.Path && state.pseudo_kallisto_quant_results_file.exists()) ? + state.pseudo_kallisto_quant_results_file : + null } def fastqc_zip_1 = list.collect { id, state -> (state.fastqc_zip_1 instanceof java.nio.file.Path && state.fastqc_zip_1.exists()) ? state.fastqc_zip_1 : @@ -5006,34 +5023,14 @@ workflow run_wf { (state.trim_log_2 instanceof java.nio.file.Path && state.trim_log_2.exists()) ? state.trim_log_2 : null } - def sortmerna_log = list.collect { id, state -> - (state.sortmerna_log instanceof java.nio.file.Path && state.sortmerna_log.exists()) ? - state.sortmerna_log : + def sortmerna_multiqc = list.collect { id, state -> + (state.sortmerna_multiqc instanceof java.nio.file.Path && state.sortmerna_multiqc.exists()) ? + state.sortmerna_multiqc : null } def star_multiqc = list.collect { id, state -> (state.star_multiqc instanceof java.nio.file.Path && state.star_multiqc.exists()) ? state.star_multiqc : null } - def quant_results = list.collect { id, state -> - (state.quant_results_file instanceof java.nio.file.Path && state.quant_results_file.exists()) ? - state.quant_results_file : - null } - def rsem_counts_gene = list.collect { id, state -> - (state.rsem_counts_gene instanceof java.nio.file.Path && state.rsem_counts_gene.exists()) ? - state.rsem_counts_gene : - null } - def rsem_counts_transcripts = list.collect { id, state -> - (state.rsem_counts_transcripts instanceof java.nio.file.Path && state.rsem_counts_transcripts.exists()) ? - state.rsem_counts_transcripts : - null } - def pseudo_salmon_quant_results = list.collect { id, state -> - (state.pseudo_salmon_quant_results_file instanceof java.nio.file.Path && state.pseudo_salmon_quant_results_file.exists()) ? - state.pseudo_salmon_quant_results_file : - null } - def pseudo_kallisto_quant_results = list.collect { id, state -> - (state.pseudo_kallisto_quant_results_file instanceof java.nio.file.Path && state.pseudo_kallisto_quant_results_file.exists()) ? - state.pseudo_kallisto_quant_results_file : - null } def genome_bam_stats = list.collect { id, state -> (state.genome_bam_stats instanceof java.nio.file.Path && state.genome_bam_stats.exists()) ? state.genome_bam_stats : @@ -5050,6 +5047,14 @@ workflow run_wf { (state.markduplicates_multiqc instanceof java.nio.file.Path && state.markduplicates_multiqc.exists()) ? state.markduplicates_multiqc : null } + def salmon_multiqc = list.collect { id, state -> + (state.salmon_multiqc instanceof java.nio.file.Path && state.salmon_multiqc.exists()) ? + state.salmon_multiqc : + null } + def rsem_multiqc = list.collect { id, state -> + (state.rsem_multiqc instanceof java.nio.file.Path && state.rsem_multiqc.exists()) ? + state.rsem_multiqc : + null } def pseudo_multiqc = list.collect { id, state -> (state.pseudo_multiqc instanceof java.nio.file.Path && state.pseudo_multiqc.exists()) ? state.pseudo_multiqc : @@ -5110,55 +5115,18 @@ workflow run_wf { (state.tin_output_summary instanceof java.nio.file.Path && state.tin_output_summary.exists()) ? state.tin_output_summary : null } - def num_trimmed_reads = list.collect { id, state -> state.num_trimmed_reads } - def passed_trimmed_reads = list.collect { id, state -> state.passed_trimmed_reads } - def passed_mapping = list.collect { id, state -> state.passed_mapping } - def percent_mapped = list.collect { id, state -> state.percent_mapped } - def inferred_strand = list.collect { id, state -> state.inferred_strand } - def passed_strand_check = list.collect { id, state -> state.passed_strand_check } - def gtf = list.collect { id, state -> state.gtf }.unique()[0] - def gtf_extra_attributes = list.collect { id, state -> state.gtf_extra_attributes }.unique()[0] - def gtf_group_features = list.collect { id, state -> state.gtf_group_features }.unique()[0] - def pca_header_multiqc = list.collect { id, state -> state.pca_header_multiqc }.unique()[0] - def clustering_header_multiqc = list.collect { id, state -> state.clustering_header_multiqc }.unique()[0] - def aligner = list.collect { id, state -> state.aligner }.unique()[0] - def pseudo_aligner = list.collect { id, state -> state.pseudo_aligner }.unique()[0] - def deseq2_vst = list.collect { id, state -> state.deseq2_vst }.unique()[0] - def extra_deseq2_args = list.collect { id, state -> state.extra_deseq2_args }.unique()[0] - def extra_deseq2_args2 = list.collect { id, state -> state.extra_deseq2_args2 }.unique()[0] - def skip_deseq2_qc = list.collect { id, state -> state.skip_deseq2_qc }.unique()[0] def multiqc_custom_config = list.collect { id, state -> state.multiqc_custom_config }.unique()[0] - def skip_qc = list.collect { id, state -> state.skip_qc }.unique()[0] - def skip_align = list.collect { id, state -> state.skip_align }.unique()[0] - def skip_pseudo_align = list.collect { id, state -> state.skip_pseudo_align }.unique()[0] ["merged", [ ids: ids, strandedness: strandedness, - fastqc_zip: fastqc_zip_1 + fastqc_zip_2, - trim_zip: trim_zip_1 + trim_zip_2, - trim_log: trim_log_1 + trim_log_2, - sortmerna_log: sortmerna_log, - star_multiqc: star_multiqc, - salmon_multiqc: quant_results, - genome_bam_stats: genome_bam_stats, - genome_bam_flagstat: genome_bam_flagstat, - genome_bam_idxstats: genome_bam_idxstats, - markduplicates_multiqc: markduplicates_multiqc, - pseudo_multiqc: pseudo_multiqc, - featurecounts_multiqc: featurecounts_multiqc, - featurecounts_rrna_multiqc: featurecounts_rrna_multiqc, - preseq_output: preseq_output, - qualimap_output_dir: qualimap_output_dir, - dupradar_output_dup_intercept_mqc: dupradar_output_dup_intercept_mqc, - dupradar_output_duprate_exp_denscurve_mqc: dupradar_output_duprate_exp_denscurve_mqc, - bamstat_output: bamstat_output, - inner_dist_output_freq: inner_dist_output_freq, - inferexperiment_multiqc: inferexperiment_multiqc, - junction_annotation_output_log: junction_annotation_output_log, - junction_saturation_output_plot_r: junction_saturation_output_plot_r, - read_distribution_output: read_distribution_output, - read_duplication_output_duplication_rate_mapping: read_duplication_output_duplication_rate_mapping, - tin_output_summary: tin_output_summary, + num_trimmed_reads: num_trimmed_reads, + passed_trimmed_reads: passed_trimmed_reads, + passed_mapping: passed_mapping, + percent_mapped: percent_mapped, + inferred_strand: inferred_strand, + passed_strand_check: passed_strand_check, + skip_align: skip_align, + skip_pseudo_align: skip_pseudo_align, quant_results: quant_results, rsem_counts_gene: rsem_counts_gene, rsem_counts_transcripts: rsem_counts_transcripts, @@ -5175,21 +5143,143 @@ workflow run_wf { extra_deseq2_args: extra_deseq2_args, extra_deseq2_args2: extra_deseq2_args2, skip_deseq2_qc: skip_deseq2_qc, - num_trimmed_reads: num_trimmed_reads, - passed_trimmed_reads: passed_trimmed_reads, - passed_mapping: passed_mapping, - percent_mapped: percent_mapped, - inferred_strand: inferred_strand, - passed_strand_check: passed_strand_check, - multiqc_custom_config: multiqc_custom_config, - skip_align: skip_align, - skip_pseudo_align: skip_pseudo_align + fastqc_zip: fastqc_zip_1 + fastqc_zip_2, + trim_zip: trim_zip_1 + trim_zip_2, + trim_log: trim_log_1 + trim_log_2, + sortmerna_multiqc: sortmerna_multiqc, + star_multiqc: star_multiqc, + genome_bam_stats: genome_bam_stats, + genome_bam_flagstat: genome_bam_flagstat, + genome_bam_idxstats: genome_bam_idxstats, + markduplicates_multiqc: markduplicates_multiqc, + salmon_multiqc: salmon_multiqc, + rsem_multiqc: rsem_multiqc, + pseudo_multiqc: pseudo_multiqc, + featurecounts_multiqc: featurecounts_multiqc, + featurecounts_rrna_multiqc: featurecounts_rrna_multiqc, + preseq_output: preseq_output, + qualimap_output_dir: qualimap_output_dir, + dupradar_output_dup_intercept_mqc: dupradar_output_dup_intercept_mqc, + dupradar_output_duprate_exp_denscurve_mqc: dupradar_output_duprate_exp_denscurve_mqc, + bamstat_output: bamstat_output, + inner_dist_output_freq: inner_dist_output_freq, + inferexperiment_multiqc: inferexperiment_multiqc, + junction_annotation_output_log: junction_annotation_output_log, + junction_saturation_output_plot_r: junction_saturation_output_plot_r, + read_distribution_output: read_distribution_output, + read_duplication_output_duplication_rate_mapping: read_duplication_output_duplication_rate_mapping, + tin_output_summary: tin_output_summary, + multiqc_custom_config: multiqc_custom_config ] ] } - + + // | map { list -> + // def ids = list.collect { id, state -> state.id } + // def strandedness = list.collect { id, state -> state.strandedness } + // def num_trimmed_reads = list.collect { id, state -> state.num_trimmed_reads } + // def passed_trimmed_reads = list.collect { id, state -> state.passed_trimmed_reads } + // def passed_mapping = list.collect { id, state -> state.passed_mapping } + // def percent_mapped = list.collect { id, state -> state.percent_mapped } + // def inferred_strand = list.collect { id, state -> state.inferred_strand } + // def passed_strand_check = list.collect { id, state -> state.passed_strand_check } + // def gtf = list.collect { id, state -> state.gtf }.unique()[0] + // def gtf_extra_attributes = list.collect { id, state -> state.gtf_extra_attributes }.unique()[0] + // def gtf_group_features = list.collect { id, state -> state.gtf_group_features }.unique()[0] + // def pca_header_multiqc = list.collect { id, state -> state.pca_header_multiqc }.unique()[0] + // def clustering_header_multiqc = list.collect { id, state -> state.clustering_header_multiqc }.unique()[0] + // def aligner = list.collect { id, state -> state.aligner }.unique()[0] + // def pseudo_aligner = list.collect { id, state -> state.pseudo_aligner }.unique()[0] + // def deseq2_vst = list.collect { id, state -> state.deseq2_vst }.unique()[0] + // def extra_deseq2_args = list.collect { id, state -> state.extra_deseq2_args }.unique()[0] + // def extra_deseq2_args2 = list.collect { id, state -> state.extra_deseq2_args2 }.unique()[0] + // def skip_deseq2_qc = list.collect { id, state -> state.skip_deseq2_qc }.unique()[0] + // def skip_qc = list.collect { id, state -> state.skip_qc }.unique()[0] + // def skip_align = list.collect { id, state -> state.skip_align }.unique()[0] + // def skip_pseudo_align = list.collect { id, state -> state.skip_pseudo_align }.unique()[0] + // def quant_results = list.collect { id, state -> + // (state.quant_results_file instanceof java.nio.file.Path && state.quant_results_file.exists()) ? + // state.quant_results_file : + // null } + // def rsem_counts_gene = list.collect { id, state -> + // (state.rsem_counts_gene instanceof java.nio.file.Path && state.rsem_counts_gene.exists()) ? + // state.rsem_counts_gene : + // null } + // def rsem_counts_transcripts = list.collect { id, state -> + // (state.rsem_counts_transcripts instanceof java.nio.file.Path && state.rsem_counts_transcripts.exists()) ? + // state.rsem_counts_transcripts : + // null } + // def pseudo_salmon_quant_results = list.collect { id, state -> + // (state.pseudo_salmon_quant_results_file instanceof java.nio.file.Path && state.pseudo_salmon_quant_results_file.exists()) ? + // state.pseudo_salmon_quant_results_file : + // null } + // def pseudo_kallisto_quant_results = list.collect { id, state -> + // (state.pseudo_kallisto_quant_results_file instanceof java.nio.file.Path && state.pseudo_kallisto_quant_results_file.exists()) ? + // state.pseudo_kallisto_quant_results_file : + // null } + // def fastqc_zip_1_dirs = list.collect{it[1].fastqc_zip_1.getParent()} + // def fastqc_zip_2_dirs = list.collect{it[1].fastqc_zip_2.getParent()} + // def trim_zip_1_dirs = list.collect{it[1].trim_zip_1.getParent()} + // def trim_zip_2_dirs = list.collect{it[1].trim_zip_2.getParent()} + // def trim_log_1_dirs = list.collect{it[1].trim_log_1.getParent()} + // def trim_log_2_dirs = list.collect{it[1].trim_log_2.getParent()} + // def sortmerna_multiqc_dirs = list.collect{it[1].sortmerna_multiqc.getParent()} + // def star_multiqc_dirs = list.collect{it[1].star_multiqc.getParent()} + // def genome_bam_stats_dirs = list.collect{it[1].genome_bam_stats.getParent()} + // def genome_bam_flagstat_dirs = list.collect{it[1].genome_bam_flagstat.getParent()} + // def genome_bam_idxstats_dirs = list.collect{it[1].genome_bam_idxstats} + // def markduplicates_multiqc_dirs = list.collect{it[1].markduplicates_multiqc.getParent()} + // def salmon_multiqc_dirs = list.collect{it[1].salmon_multiqc} + // def rsem_multiqc_dirs = list.collect{it[1].rsem_multiqc.getParent()} + // def pseudo_multiqc_dirs = list.collect{it[1].pseudo_multiqc.getParent()} + // def featurecounts_multiqc_dirs = list.collect{it[1].featurecounts_multiqc.getParent()} + // def featurecounts_rrna_multiqc_dirs = list.collect{it[1].featurecounts_rrna_multiqc.getParent()} + // def preseq_output_dirs = list.collect{it[1].preseq_output.getParent()} + // def qualimap_output_dirs = list.collect{it[1].qualimap_output_dir} + // def dupradar_output_dup_intercept_mqc_dirs = list.collect{it[1].dupradar_output_dup_intercept_mqc.getParent()} + // def dupradar_output_duprate_exp_denscurve_mqc_dirs = list.collect{it[1].dupradar_output_duprate_exp_denscurve_mqc.getParent()} + // def bamstat_output_dirs = list.collect{it[1].bamstat_output.getParent()} + // def strandedness_output_dirs = list.collect{it[1].strandedness_output.getParent()} + // def inner_dist_output_freq_dirs = list.collect{it[1].inner_dist_output_freq.getParent()} + // def junction_annotation_output_log_dirs = list.collect{it[1].junction_annotation_output_log.getParent()} + // def junction_saturation_output_plot_r_dirs = list.collect{it[1].junction_saturation_output_plot_r.getParent()} + // def read_distribution_output_dirs = list.collect{it[1].read_distribution_output.getParent()} + // def read_duplication_output_duplication_rate_mapping_dirs = list.collect{it[1].read_duplication_output_duplication_rate_mapping.getParent()} + // def tin_output_summary_dirs = list.collect{it[1].tin_output_summary.getParent()} + // def multiqc_custom_config_dirs = list.collect{it[1].multiqc_custom_config.getParent()} + // ["merged", [ + // ids: ids, + // strandedness: strandedness, + // num_trimmed_reads: num_trimmed_reads, + // passed_trimmed_reads: passed_trimmed_reads, + // passed_mapping: passed_mapping, + // percent_mapped: percent_mapped, + // inferred_strand: inferred_strand, + // passed_strand_check: passed_strand_check, + // skip_align: skip_align, + // skip_pseudo_align: skip_pseudo_align, + // quant_results: quant_results, + // rsem_counts_gene: rsem_counts_gene, + // rsem_counts_transcripts: rsem_counts_transcripts, + // pseudo_salmon_quant_results: pseudo_salmon_quant_results, + // pseudo_kallisto_quant_results: pseudo_kallisto_quant_results, + // gtf: gtf, + // gtf_extra_attributes: gtf_extra_attributes, + // gtf_group_features: gtf_group_features, + // pca_header_multiqc: pca_header_multiqc, + // clustering_header_multiqc: clustering_header_multiqc, + // aligner: aligner, + // pseudo_aligner: pseudo_aligner, + // deseq2_vst: deseq2_vst, + // extra_deseq2_args: extra_deseq2_args, + // extra_deseq2_args2: extra_deseq2_args2, + // skip_deseq2_qc: skip_deseq2_qc, + // multiqc_input: fastqc_zip_1_dirs + fastqc_zip_2_dirs + trim_zip_1_dirs + trim_zip_2_dirs + trim_log_1_dirs + trim_log_2_dirs + sortmerna_multiqc_dirs + star_multiqc_dirs + genome_bam_stats_dirs + genome_bam_flagstat_dirs + genome_bam_idxstats_dirs + markduplicates_multiqc_dirs + salmon_multiqc_dirs + rsem_multiqc_dirs + pseudo_multiqc_dirs + featurecounts_multiqc_dirs + featurecounts_rrna_multiqc_dirs + preseq_output_dirs + qualimap_output_dirs + dupradar_output_dup_intercept_mqc_dirs + dupradar_output_duprate_exp_denscurve_mqc_dirs + bamstat_output_dirs + strandedness_output_dirs + inner_dist_output_freq_dirs + junction_annotation_output_log_dirs + junction_saturation_output_plot_r_dirs + read_distribution_output_dirs + read_duplication_output_duplication_rate_mapping_dirs + tin_output_summary_dirs + multiqc_custom_config_dirs + // ] ] + // } + // Merge quantification results of alignment | merge_quant_results.run ( - runIf: { id, state -> (!state.skip_align && state.aligner == 'star_salmon') || !skip_pseudo_align }, + runIf: { id, state -> !state.skip_align && state.aligner == 'star_salmon' }, fromState: [ "salmon_quant_results": "quant_results", "gtf": "gtf", @@ -5208,7 +5298,7 @@ workflow run_wf { "lengths_transcript": "lengths_transcript", "quant_merged_summarizedexperiment": "quant_merged_summarizedexperiment" ], - key: "merge_qunat_results" + key: "merge_quant_results" ) | rsem_merge_counts.run ( @@ -5338,14 +5428,15 @@ workflow run_wf { "fastqc_raw_multiqc": "fastqc_zip", "fastqc_trim_multiqc": "trim_zip", "trim_log_multiqc": "trim_log", - "sortmerna_multiqc": "sortmerna_log", + "sortmerna_multiqc": "sortmerna_multiqc", "star_multiqc": "star_multiqc", "salmon_multiqc": "salmon_multiqc", + "rsem_multiqc": "rsem_multiqc", + "pseudo_multiqc": "pseudo_multiqc", "samtools_stats": "genome_bam_stats", "samtools_flagstat": "genome_bam_flagstat", "samtools_idxstats": "genome_bam_idxstats", - "markduplicates_multiqc": "markduplicates_multiqc", - "pseudo_multiqc": "pseudo_multiqc", + "markduplicates_multiqc": "markduplicates_multiqc", "featurecounts_multiqc": "featurecounts_multiqc", "featurecounts_rrna_multiqc": "featurecounts_rrna_multiqc", "aligner_pca_multiqc": "deseq2_pca_multiqc", @@ -5377,7 +5468,7 @@ workflow run_wf { toState: [ "multiqc_report": "output_report", "multiqc_data": "output_data", - "multiqc_plots": "output_plots", + "multiqc_plots": "output_plots" ] ) @@ -5479,8 +5570,7 @@ workflow run_wf { "deseq2_output_pseudo": "deseq2_output_pseudo", "multiqc_report": "multiqc_report", "multiqc_data": "multiqc_data", - "multiqc_plots": "multiqc_plots", - "multiqc_versions": "multiqc_versions" + "multiqc_plots": "multiqc_plots" ] ) diff --git a/target/nextflow/workflows/quality_control/nextflow_schema.json b/target/nextflow/workflows/quality_control/nextflow_schema.json index 2366cf6..41438af 100644 --- a/target/nextflow/workflows/quality_control/nextflow_schema.json +++ b/target/nextflow/workflows/quality_control/nextflow_schema.json @@ -665,26 +665,6 @@ } - , - "mqc_yml": { - "type": - "string", - "description": "Type: `file`. Software versions", - "help_text": "Type: `file`. Software versions" - - } - - - , - "workflow_summary": { - "type": - "string", - "description": "Type: `file`. ", - "help_text": "Type: `file`. " - - } - - , "passed_trimmed_reads": { "type": @@ -805,6 +785,16 @@ } + , + "rsem_multiqc": { + "type": + "string", + "description": "Type: `file`. ", + "help_text": "Type: `file`. " + + } + + , "genome_bam_stats": { "type": @@ -1283,17 +1273,6 @@ } - , - "multiqc_versions": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.multiqc_versions.multiqc_versions`. ", - "help_text": "Type: `file`, default: `$id.$key.multiqc_versions.multiqc_versions`. " - , - "default": "$id.$key.multiqc_versions.multiqc_versions" - } - - , "featurecounts": { "type": diff --git a/target/nextflow/workflows/rnaseq/.config.vsh.yaml b/target/nextflow/workflows/rnaseq/.config.vsh.yaml index 83ccd40..c1ebddd 100644 --- a/target/nextflow/workflows/rnaseq/.config.vsh.yaml +++ b/target/nextflow/workflows/rnaseq/.config.vsh.yaml @@ -1172,7 +1172,18 @@ argument_groups: name: "--salmon_quant_results" info: null default: - - "Salmon/$id" + - "STAR_Salmon/$id" + must_exist: true + create_parent: true + required: false + direction: "output" + multiple: false + multiple_sep: ";" + - type: "file" + name: "--pseudo_quant_results" + info: null + default: + - "Pseudo_align_quant/$id" must_exist: true create_parent: true required: false @@ -2095,8 +2106,8 @@ build_info: output: "target/nextflow/workflows/rnaseq" executable: "target/nextflow/workflows/rnaseq/main.nf" viash_version: "0.9.0" - git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df" - git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" + git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/workflows/prepare_genome" - "target/nextflow/cat_fastq" diff --git a/target/nextflow/workflows/rnaseq/main.nf b/target/nextflow/workflows/rnaseq/main.nf index d917e2b..5cd47fd 100644 --- a/target/nextflow/workflows/rnaseq/main.nf +++ b/target/nextflow/workflows/rnaseq/main.nf @@ -4158,7 +4158,20 @@ meta = [ "type" : "file", "name" : "--salmon_quant_results", "default" : [ - "Salmon/$id" + "STAR_Salmon/$id" + ], + "must_exist" : true, + "create_parent" : true, + "required" : false, + "direction" : "output", + "multiple" : false, + "multiple_sep" : ";" + }, + { + "type" : "file", + "name" : "--pseudo_quant_results", + "default" : [ + "Pseudo_align_quant/$id" ], "must_exist" : true, "create_parent" : true, @@ -4876,7 +4889,7 @@ meta = [ }, { "type" : "file", - "name" : "--dupradar_output_duprate_exp_densplot", + "name" : "--duprada''' + '''r_output_duprate_exp_densplot", "description" : "path to output file (pdf) of 2D density scatter plot of duplicate tag counts", "default" : [ "dupradar/scatter_plot/$id.duprate_exp_densityplot.pdf" @@ -4884,7 +4897,7 @@ meta = [ "must_exist" : true, "create_parent" : true, "required" : false, - "direction" : ''' + '''"output", + "direction" : "output", "multiple" : false, "multiple_sep" : ";" }, @@ -5257,8 +5270,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/rnaseq", "viash_version" : "0.9.0", - "git_commit" : "b291665ddc01d0f8072d9d3d7b4aa9932afb84df", - "git_remote" : "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq" + "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", + "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", @@ -5531,6 +5544,8 @@ workflow run_wf { toState: [ "star_alignment": "star_alignment", "star_multiqc": "star_multiqc", + "rsem_multiqc": "rsem_multiqc", + "salmon_multiqc": "salmon_multiqc", "genome_bam_sorted": "genome_bam_sorted", "genome_bam_index": "genome_bam_index", "genome_bam_stats": "genome_bam_stats", @@ -5556,7 +5571,7 @@ workflow run_wf { def passed_mapping = (percent_mapped >= state.min_mapped_reads) ? true : false [ id, state + [percent_mapped: percent_mapped, passed_mapping: passed_mapping] ] } - + // Pseudo-alignment and quantification | pseudo_alignment_and_quant.run ( runIf: { id, state -> !state.skip_pseudo_alignment && state.passed_trimmed_reads }, @@ -5648,18 +5663,23 @@ workflow run_wf { "skip_align": "skip_alignment", "skip_pseudo_align": "skip_pseudo_alignment", "gtf": "gtf", + "num_trimmed_reads": "num_trimmed_reads", + "passed_trimmed_reads": "passed_trimmed_reads", + "passed_mapping": "passed_mapping", + "percent_mapped": "percent_mapped", "genome_bam": "genome_bam_sorted", "genome_bam_index": "genome_bam_index", - "quant_out_dir": "quant_out_dir", + "salmon_multiqc": "salmon_multiqc", "quant_results_file": "quant_results_file", + "rsem_multiqc": "rsem_multiqc", "rsem_counts_gene": "rsem_counts_gene", "rsem_counts_transcripts": "rsem_counts_transcripts", + "pseudo_multiqc": "pseudo_multiqc", "pseudo_quant_out_dir": "pseudo_quant_out_dir", "pseudo_salmon_quant_results_file": "pseudo_salmon_quant_results_file", "pseudo_kallisto_quant_results_file": "pseudo_kallisto_quant_results_file", "aligner": "aligner", "pseudo_aligner": "pseudo_aligner", - "pseudo_multiqc": "pseudo_multiqc", "gene_bed": "gene_bed", "extra_preseq_args": "extra_preseq_args", "extra_featurecounts_args": "extra_featurecounts_args", @@ -5687,11 +5707,7 @@ workflow run_wf { "genome_bam_flagstat": "genome_bam_flagstat", "genome_bam_idxstats": "genome_bam_idxstats", "markduplicates_multiqc": "markduplicates_metrics", - "rseqc_modules": "rseqc_modules", - "num_trimmed_reads": "num_trimmed_reads", - "passed_trimmed_reads": "passed_trimmed_reads", - "passed_mapping": "passed_mapping", - "percent_mapped": "percent_mapped" + "rseqc_modules": "rseqc_modules" ], toState: [ "preseq_output": "preseq_output", @@ -5737,7 +5753,7 @@ workflow run_wf { "counts_gene_scaled": "counts_gene_scaled", "tpm_transcript": "tpm_transcript", "counts_transcript": "counts_transcript", - "salmon_merged_summarizedexperiment": "salmon_merged_summarizedexperiment", + "qunat_merged_summarizedexperiment": "quant_merged_summarizedexperiment", "deseq2_output": "deseq2_output", "multiqc_report": "multiqc_report", "multiqc_data": "multiqc_data", @@ -5784,7 +5800,8 @@ workflow run_wf { "transcriptome_bam_stats": "transcriptome_bam_stats", "transcriptome_bam_flagstat": "transcriptome_bam_flagstat", "transcriptome_bam_idxstats": "transcriptome_bam_idxstats", - "salmon_quant_results": "salmon_quant_results", + "salmon_quant_results": "quant_out_dir", + "pseudo_quant_results": "pseudo_quant_out_dir", "stringtie_transcript_gtf": "stringtie_transcript_gtf", "stringtie_coverage_gtf": "stringtie_coverage_gtf", "stringtie_abundance": "stringtie_abundance", @@ -5850,8 +5867,7 @@ workflow run_wf { "deseq2_output_pseudo": "deseq2_output_pseudo", "multiqc_report": "multiqc_report", "multiqc_data": "multiqc_data", - "multiqc_plots": "multiqc_plots", - "multiqc_versions": "multiqc_versions" + "multiqc_plots": "multiqc_plots" ] ) @@ -5930,7 +5946,7 @@ def getFastpReadsAfterFiltering(json_file) { } // -// Function that parses and returns the alignment rate from the STAR log output +// Function that parses and returns the alignment rate from the STAR log outputs // def getStarPercentMapped(align_log) { def percent_aligned = 0 diff --git a/target/nextflow/workflows/rnaseq/nextflow_schema.json b/target/nextflow/workflows/rnaseq/nextflow_schema.json index 6d66d1f..c646b4e 100644 --- a/target/nextflow/workflows/rnaseq/nextflow_schema.json +++ b/target/nextflow/workflows/rnaseq/nextflow_schema.json @@ -1360,6 +1360,17 @@ } + , + "pseudo_quant_results": { + "type": + "string", + "description": "Type: `file`, default: `$id.$key.pseudo_quant_results.pseudo_quant_results`. ", + "help_text": "Type: `file`, default: `$id.$key.pseudo_quant_results.pseudo_quant_results`. " + , + "default": "$id.$key.pseudo_quant_results.pseudo_quant_results" + } + + , "rsem_counts_gene": { "type":