Workflow output definition

main.nf

@@ -10,6 +10,7 @@
 */
 
 nextflow.enable.dsl = 2
+nextflow.preview.output = true
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -164,6 +165,11 @@ workflow {
  )
 }
 
+output {
+ directory params.outdir
+ mode params.publish_dir_mode
+}
+
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  THE END

modules/local/bedtools_genomecov/nextflow.config

@@ -3,9 +3,6 @@ if (!params.skip_alignment && !params.skip_bigwig) {
  process {
  withName: 'BEDTOOLS_GENOMECOV' {
  ext.args = '-split -du'
- publishDir = [
- enabled: false
- ]
  }
  }
 }

modules/local/deseq2_qc/main.nf

@@ -24,6 +24,16 @@ process DESEQ2_QC {
  path "size_factors" , optional:true, emit: size_factors
  path "versions.yml" , emit: versions
 
+ publish:
+ pdf >> 'deseq2'
+ rdata >> 'deseq2'
+ pca_txt >> 'deseq2'
+ pca_multiqc >> 'deseq2'
+ dists_txt >> 'deseq2'
+ dists_multiqc >> 'deseq2'
+ log >> 'deseq2'
+ size_factors >> 'deseq2'
+
  when:
  task.ext.when == null || task.ext.when
 

modules/local/dupradar/main.nf

@@ -17,6 +17,10 @@ process DUPRADAR {
  tuple val(meta), path("*_mqc.txt"), emit: multiqc
  path "versions.yml" , emit: versions
 
+ publish:
+ pdf >> 'dupradar/'
+ txt >> 'dupradar/'
+
  when:
  task.ext.when == null || task.ext.when
 

modules/local/multiqc_custom_biotype/main.nf

@@ -14,6 +14,9 @@ process MULTIQC_CUSTOM_BIOTYPE {
  tuple val(meta), path("*.tsv"), emit: tsv
  path "versions.yml" , emit: versions
 
+ publish:
+ tsv >> 'featurecounts/'
+
  when:
  task.ext.when == null || task.ext.when
 

nextflow.config

@@ -135,15 +135,6 @@ params {
 
 }
 
-// Default publishing logic for pipeline
-process {
- publishDir = [
- path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
- mode: params.publish_dir_mode,
- saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
- ]
-}
-
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
 

subworkflows/local/align_star/main.nf

@@ -62,6 +62,16 @@ workflow ALIGN_STAR {
  BAM_SORT_STATS_SAMTOOLS ( ch_orig_bam, fasta )
  ch_versions = ch_versions.mix(BAM_SORT_STATS_SAMTOOLS.out.versions)
 
+ publish:
+ ch_orig_bam >> (params.save_align_intermeds || params.save_umi_intermeds ? 'star_salmon/' : null)
+ ch_log_final >> 'star_salmon/log/'
+ ch_log_out >> 'star_salmon/log/'
+ ch_log_progress >> 'star_salmon/log/'
+ ch_bam_sorted >> (params.save_align_intermeds || params.save_umi_intermeds ? 'star_salmon/' : null)
+ ch_bam_transcript >> (params.save_align_intermeds || params.save_umi_intermeds ? 'star_salmon/' : null)
+ ch_fastq >> (params.save_unaligned ? 'star_salmon/unmapped/' : null)
+ ch_tab >> 'star_salmon/log/'
+
  emit:
  orig_bam = ch_orig_bam // channel: [ val(meta), bam ]
  log_final = ch_log_final // channel: [ val(meta), log_final ]

subworkflows/local/align_star/nextflow.config

@@ -15,25 +15,6 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {
  params.save_unaligned ? '--outReadsUnmapped Fastx' : '',
  params.extra_star_align_args ? params.extra_star_align_args.split("\\s(?=--)") : ''
  ].flatten().unique(false).join(' ').trim() }
- publishDir = [
- [
- path: { "${params.outdir}/${params.aligner}/log" },
- mode: params.publish_dir_mode,
- pattern: '*.{out,tab}'
- ],
- [
- path: { params.save_align_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
- mode: params.publish_dir_mode,
- pattern: '*.bam',
- saveAs: { params.save_align_intermeds ? it : null }
- ],
- [
- path: { params.save_unaligned ? "${params.outdir}/${params.aligner}/unmapped" : params.outdir },
- mode: params.publish_dir_mode,
- pattern: '*.fastq.gz',
- saveAs: { params.save_unaligned ? it : null }
- ]
- ]
  }
  }
 }