From efbe4d007c8db205bdd5638e3b3b57bbc70a0348 Mon Sep 17 00:00:00 2001 From: Sam Nicholls Date: Tue, 26 May 2026 20:12:38 +0000 Subject: [PATCH] Shorten workflow names for log --- main.nf | 60 +++++++++++++++++------------------ subworkflows/mods.nf | 2 +- subworkflows/transcriptome.nf | 2 +- 3 files changed, 32 insertions(+), 32 deletions(-) diff --git a/main.nf b/main.nf index ea3ab07..178a93a 100644 --- a/main.nf +++ b/main.nf @@ -6,9 +6,9 @@ nextflow.enable.dsl = 2 include { fastq_ingress; xam_ingress } from './lib/ingress' include { getParams; configure_igv } from './lib/common' include { prepare_reference } from './lib/reference' -include { transcriptome_analysis } from './subworkflows/transcriptome' +include { transcriptome } from './subworkflows/transcriptome' include { differential_expression } from './subworkflows/differential_expression' -include { mod_analysis } from './subworkflows/mods' +include { mods } from './subworkflows/mods' @@ -91,7 +91,7 @@ process publishResults { } -workflow pipeline { +workflow wf { take: reads sample_sheet @@ -101,13 +101,13 @@ workflow pipeline { software_versions = getVersions() workflow_params = getParams() - transcriptome = transcriptome_analysis(reads, ref_genome, ref_annotation, sample_sheet) - mods = mod_analysis(reads, ref_genome) + transcriptome_results = transcriptome(reads, ref_genome, ref_annotation, sample_sheet) + mod_results = mods(reads, ref_genome) if (params.de_analysis) { de_results = differential_expression( - transcriptome.joint_transcript_rds, - transcriptome.joint_gene_rds, + transcriptome_results.joint_transcript_rds, + transcriptome_results.joint_gene_rds, sample_sheet ) de_dir = de_results.dir @@ -128,12 +128,12 @@ workflow pipeline { ] } - sample_dirs_for_report = transcriptome.sample_dirs + sample_dirs_for_report = transcriptome_results.sample_dirs .map { meta, sample_dir -> sample_dir } .collect() - sqanti_dirs_for_report = transcriptome.joint_sqanti_dir - .concat(transcriptome.sample_sqanti_dirs.map { meta, sqanti_dir -> sqanti_dir }) + sqanti_dirs_for_report = transcriptome_results.joint_sqanti_dir + .concat(transcriptome_results.sample_sqanti_dirs.map { meta, sqanti_dir -> sqanti_dir }) .ifEmpty(OPTIONAL_FILE) .collect() @@ -153,33 +153,33 @@ workflow pipeline { report_input, software_versions, workflow_params, - transcriptome.joint_dir.ifEmpty(OPTIONAL_FILE), + transcriptome_results.joint_dir.ifEmpty(OPTIONAL_FILE), sample_dirs_for_report, sqanti_dirs_for_report, de_dir, - transcriptome.annotation_reference_summary, + transcriptome_results.annotation_reference_summary, workflow.manifest.version ) results = Channel.empty() .concat(report.report.map { [it, null] }) .concat(workflow_params.map { [it, null] }) - .concat(transcriptome.annotation_reference_summary.map { [it, "cohort/reference"] }) - .concat(transcriptome.unstranded_annotation.map { [it, "cohort/reference"] }) - .concat(transcriptome.joint_gtf.map { [it, "cohort"] }) - .concat(transcriptome.joint_fasta.map { [it, "cohort"] }) - .concat(transcriptome.joint_transcript_counts.map { [it, "cohort"] }) - .concat(transcriptome.joint_gene_counts.map { [it, "cohort"] }) - .concat(transcriptome.joint_transcript_rds.map { [it, "cohort"] }) - .concat(transcriptome.joint_gene_rds.map { [it, "cohort"] }) - .concat(transcriptome.joint_metadata.map { [it, "cohort"] }) - .concat(transcriptome.sample_gtf.map { meta, gtf -> [gtf, "samples/${meta.alias}"] }) - .concat(transcriptome.sample_fastas.map { meta, fasta -> [fasta, "samples/${meta.alias}"] }) - .concat(transcriptome.sample_transcript_counts.map { meta, counts -> [counts, "samples/${meta.alias}"] }) - .concat(transcriptome.sample_gene_counts.map { meta, counts -> [counts, "samples/${meta.alias}"] }) - .concat(transcriptome.sample_transcript_rds.map { meta, rds -> [rds, "samples/${meta.alias}"] }) - .concat(transcriptome.sample_gene_rds.map { meta, rds -> [rds, "samples/${meta.alias}"] }) - .concat(transcriptome.sample_metadata.map { meta, metadata -> [metadata, "samples/${meta.alias}"] }) + .concat(transcriptome_results.annotation_reference_summary.map { [it, "cohort/reference"] }) + .concat(transcriptome_results.unstranded_annotation.map { [it, "cohort/reference"] }) + .concat(transcriptome_results.joint_gtf.map { [it, "cohort"] }) + .concat(transcriptome_results.joint_fasta.map { [it, "cohort"] }) + .concat(transcriptome_results.joint_transcript_counts.map { [it, "cohort"] }) + .concat(transcriptome_results.joint_gene_counts.map { [it, "cohort"] }) + .concat(transcriptome_results.joint_transcript_rds.map { [it, "cohort"] }) + .concat(transcriptome_results.joint_gene_rds.map { [it, "cohort"] }) + .concat(transcriptome_results.joint_metadata.map { [it, "cohort"] }) + .concat(transcriptome_results.sample_gtf.map { meta, gtf -> [gtf, "samples/${meta.alias}"] }) + .concat(transcriptome_results.sample_fastas.map { meta, fasta -> [fasta, "samples/${meta.alias}"] }) + .concat(transcriptome_results.sample_transcript_counts.map { meta, counts -> [counts, "samples/${meta.alias}"] }) + .concat(transcriptome_results.sample_gene_counts.map { meta, counts -> [counts, "samples/${meta.alias}"] }) + .concat(transcriptome_results.sample_transcript_rds.map { meta, rds -> [rds, "samples/${meta.alias}"] }) + .concat(transcriptome_results.sample_gene_rds.map { meta, rds -> [rds, "samples/${meta.alias}"] }) + .concat(transcriptome_results.sample_metadata.map { meta, metadata -> [metadata, "samples/${meta.alias}"] }) .concat(generated_alignment_outputs) if (params.de_analysis) { @@ -187,7 +187,7 @@ workflow pipeline { } emit: results = results - bigwigs = mods.bigwig + bigwigs = mod_results.bigwig } @@ -264,7 +264,7 @@ workflow { processed_samples = analysis_samples - pipeline_run = pipeline(processed_samples, sample_sheet, ref_genome, ref_annotation) + pipeline_run = wf(processed_samples, sample_sheet, ref_genome, ref_annotation) results = pipeline_run.results reference_basename = file(params.ref_genome).getName() diff --git a/subworkflows/mods.nf b/subworkflows/mods.nf index 8e8f67b..d7fbcda 100644 --- a/subworkflows/mods.nf +++ b/subworkflows/mods.nf @@ -126,7 +126,7 @@ process inferModkitBases { """ } -workflow mod_analysis { +workflow mods { take: xams ref_genome diff --git a/subworkflows/transcriptome.nf b/subworkflows/transcriptome.nf index 7500635..358350e 100644 --- a/subworkflows/transcriptome.nf +++ b/subworkflows/transcriptome.nf @@ -208,7 +208,7 @@ process runPerSampleSqanti { } -workflow transcriptome_analysis { +workflow transcriptome { take: alignments ref_genome