kfukuta/wf-transcriptomes-v202
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Shorten workflow names for log

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This commit is contained in:
Sam Nicholls 2026-05-26 20:12:38 +00:00
parent e95b51016a
commit efbe4d007c
3 changed files with 32 additions and 32 deletions
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60
main.nf
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@ -6,9 +6,9 @@ nextflow.enable.dsl = 2
include { fastq_ingress; xam_ingress } from './lib/ingress' include { fastq_ingress; xam_ingress } from './lib/ingress'
include { getParams; configure_igv } from './lib/common' include { getParams; configure_igv } from './lib/common'
include { prepare_reference } from './lib/reference' 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 { 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: take:
reads reads
sample_sheet sample_sheet
@ -101,13 +101,13 @@ workflow pipeline {
software_versions = getVersions() software_versions = getVersions()
workflow_params = getParams() workflow_params = getParams()
transcriptome = transcriptome_analysis(reads, ref_genome, ref_annotation, sample_sheet) transcriptome_results = transcriptome(reads, ref_genome, ref_annotation, sample_sheet)
mods = mod_analysis(reads, ref_genome) mod_results = mods(reads, ref_genome)
if (params.de_analysis) { if (params.de_analysis) {
de_results = differential_expression( de_results = differential_expression(
transcriptome.joint_transcript_rds, transcriptome_results.joint_transcript_rds,
transcriptome.joint_gene_rds, transcriptome_results.joint_gene_rds,
sample_sheet sample_sheet
) )
de_dir = de_results.dir 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 } .map { meta, sample_dir -> sample_dir }
.collect() .collect()
sqanti_dirs_for_report = transcriptome.joint_sqanti_dir sqanti_dirs_for_report = transcriptome_results.joint_sqanti_dir
.concat(transcriptome.sample_sqanti_dirs.map { meta, sqanti_dir -> sqanti_dir }) .concat(transcriptome_results.sample_sqanti_dirs.map { meta, sqanti_dir -> sqanti_dir })
.ifEmpty(OPTIONAL_FILE) .ifEmpty(OPTIONAL_FILE)
.collect() .collect()
@ -153,33 +153,33 @@ workflow pipeline {
report_input, report_input,
software_versions, software_versions,
workflow_params, workflow_params,
transcriptome.joint_dir.ifEmpty(OPTIONAL_FILE), transcriptome_results.joint_dir.ifEmpty(OPTIONAL_FILE),
sample_dirs_for_report, sample_dirs_for_report,
sqanti_dirs_for_report, sqanti_dirs_for_report,
de_dir, de_dir,
transcriptome.annotation_reference_summary, transcriptome_results.annotation_reference_summary,
workflow.manifest.version workflow.manifest.version
) )
results = Channel.empty() results = Channel.empty()
.concat(report.report.map { [it, null] }) .concat(report.report.map { [it, null] })
.concat(workflow_params.map { [it, null] }) .concat(workflow_params.map { [it, null] })
.concat(transcriptome.annotation_reference_summary.map { [it, "cohort/reference"] }) .concat(transcriptome_results.annotation_reference_summary.map { [it, "cohort/reference"] })
.concat(transcriptome.unstranded_annotation.map { [it, "cohort/reference"] }) .concat(transcriptome_results.unstranded_annotation.map { [it, "cohort/reference"] })
.concat(transcriptome.joint_gtf.map { [it, "cohort"] }) .concat(transcriptome_results.joint_gtf.map { [it, "cohort"] })
.concat(transcriptome.joint_fasta.map { [it, "cohort"] }) .concat(transcriptome_results.joint_fasta.map { [it, "cohort"] })
.concat(transcriptome.joint_transcript_counts.map { [it, "cohort"] }) .concat(transcriptome_results.joint_transcript_counts.map { [it, "cohort"] })
.concat(transcriptome.joint_gene_counts.map { [it, "cohort"] }) .concat(transcriptome_results.joint_gene_counts.map { [it, "cohort"] })
.concat(transcriptome.joint_transcript_rds.map { [it, "cohort"] }) .concat(transcriptome_results.joint_transcript_rds.map { [it, "cohort"] })
.concat(transcriptome.joint_gene_rds.map { [it, "cohort"] }) .concat(transcriptome_results.joint_gene_rds.map { [it, "cohort"] })
.concat(transcriptome.joint_metadata.map { [it, "cohort"] }) .concat(transcriptome_results.joint_metadata.map { [it, "cohort"] })
.concat(transcriptome.sample_gtf.map { meta, gtf -> [gtf, "samples/${meta.alias}"] }) .concat(transcriptome_results.sample_gtf.map { meta, gtf -> [gtf, "samples/${meta.alias}"] })
.concat(transcriptome.sample_fastas.map { meta, fasta -> [fasta, "samples/${meta.alias}"] }) .concat(transcriptome_results.sample_fastas.map { meta, fasta -> [fasta, "samples/${meta.alias}"] })
.concat(transcriptome.sample_transcript_counts.map { meta, counts -> [counts, "samples/${meta.alias}"] }) .concat(transcriptome_results.sample_transcript_counts.map { meta, counts -> [counts, "samples/${meta.alias}"] })
.concat(transcriptome.sample_gene_counts.map { meta, counts -> [counts, "samples/${meta.alias}"] }) .concat(transcriptome_results.sample_gene_counts.map { meta, counts -> [counts, "samples/${meta.alias}"] })
.concat(transcriptome.sample_transcript_rds.map { meta, rds -> [rds, "samples/${meta.alias}"] }) .concat(transcriptome_results.sample_transcript_rds.map { meta, rds -> [rds, "samples/${meta.alias}"] })
.concat(transcriptome.sample_gene_rds.map { meta, rds -> [rds, "samples/${meta.alias}"] }) .concat(transcriptome_results.sample_gene_rds.map { meta, rds -> [rds, "samples/${meta.alias}"] })
.concat(transcriptome.sample_metadata.map { meta, metadata -> [metadata, "samples/${meta.alias}"] }) .concat(transcriptome_results.sample_metadata.map { meta, metadata -> [metadata, "samples/${meta.alias}"] })
.concat(generated_alignment_outputs) .concat(generated_alignment_outputs)
if (params.de_analysis) { if (params.de_analysis) {
@ -187,7 +187,7 @@ workflow pipeline {
} }
emit: emit:
results = results results = results
bigwigs = mods.bigwig bigwigs = mod_results.bigwig
} }
@ -264,7 +264,7 @@ workflow {
processed_samples = analysis_samples 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 results = pipeline_run.results
reference_basename = file(params.ref_genome).getName() reference_basename = file(params.ref_genome).getName()

2
subworkflows/mods.nf
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@ -126,7 +126,7 @@ process inferModkitBases {
""" """
} }
workflow mod_analysis { workflow mods {
take: take:
xams xams
ref_genome ref_genome

2
subworkflows/transcriptome.nf
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@ -208,7 +208,7 @@ process runPerSampleSqanti {
} }
workflow transcriptome_analysis { workflow transcriptome {
take: take:
alignments alignments
ref_genome ref_genome