Workflow output definition

main.nf

@@ -10,6 +10,7 @@
 */
 
 nextflow.enable.dsl = 2
+nextflow.preview.output = true
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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
-            ]
         }
     }
 }

nextflow.config

@@ -135,14 +135,8 @@ 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 }
-    ]
-}
+outputDir = params.outdir
+workflow.output.mode = params.publish_dir_mode
 
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'

subworkflows/local/align_star/main.nf

@@ -80,4 +80,14 @@ workflow ALIGN_STAR {
     idxstats       = BAM_SORT_STATS_SAMTOOLS.out.idxstats // channel: [ val(meta), [ idxstats ] ]
 
     versions       = ch_versions                    // channel: [ versions.yml ]
+
+    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'
 }

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 }
-                ]
-            ]
         }
     }
 }

subworkflows/local/prepare_genome/main.nf

@@ -76,6 +76,7 @@ workflow PREPARE_GENOME {
     //
     if (gtf || gff) {
         if (gtf) {
+            ch_gff = Channel.empty()
             if (gtf.endsWith('.gz')) {
                 ch_gtf      = GUNZIP_GTF ( [ [:], gtf ] ).gunzip.map { it[1] }
                 ch_versions = ch_versions.mix(GUNZIP_GTF.out.versions)
@@ -327,6 +328,30 @@ workflow PREPARE_GENOME {
         }
     }
 
+    //
+    // Collect channels for publishing
+    //
+    ch_genome = Channel.empty().mix(
+        ch_fasta,
+        ch_gtf,
+        ch_gff,
+        ch_add_fasta,
+        ch_gene_bed,
+        ch_transcript_fasta,
+        ch_fai,
+        ch_chrom_sizes,
+    )
+
+    ch_genome_index = Channel.empty().mix(
+        ch_splicesites,
+        ch_bbsplit_index,
+        ch_star_index,
+        ch_rsem_index,
+        ch_hisat2_index,
+        ch_salmon_index,
+        ch_kallisto_index,
+    )
+
     emit:
     fasta            = ch_fasta                  // channel: path(genome.fasta)
     gtf              = ch_gtf                    // channel: path(genome.gtf)
@@ -342,4 +367,8 @@ workflow PREPARE_GENOME {
     salmon_index     = ch_salmon_index           // channel: path(salmon/index/)
     kallisto_index   = ch_kallisto_index         // channel: [ meta, path(kallisto/index/) ]
     versions         = ch_versions.ifEmpty(null) // channel: [ versions.yml ]
+
+    publish:
+    ch_genome       >> (params.save_reference ? 'genome' : null)
+    ch_genome_index >> (params.save_reference ? 'genome/index' : null)
 }