Workflow output definition

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

@@ -135,15 +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/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

@@ -343,3 +343,28 @@ workflow PREPARE_GENOME {
     kallisto_index   = ch_kallisto_index         // channel: [ meta, path(kallisto/index/) ]
     versions         = ch_versions.ifEmpty(null) // channel: [ versions.yml ]
 }
+
+output {
+    directory params.outdir, mode: params.publish_dir_mode, enabled: params.save_reference
+
+    'genome' {
+        from PREPARE_GENOME.out.fasta
+        from PREPARE_GENOME.out.gtf
+        // from PREPARE_GENOME.out.gff
+        // from PREPARE_GENOME.out.add_fasta
+        from PREPARE_GENOME.out.gene_bed
+        from PREPARE_GENOME.out.transcript_fasta
+        from PREPARE_GENOME.out.fai
+        // from PREPARE_GENOME.out.sizes
+    }
+
+    'genome/index' {
+        from PREPARE_GENOME.out.splicesites
+        from PREPARE_GENOME.out.bbsplit_index
+        from PREPARE_GENOME.out.star_index
+        from PREPARE_GENOME.out.rsem_index
+        from PREPARE_GENOME.out.hisat2_index
+        from PREPARE_GENOME.out.salmon_index
+        from PREPARE_GENOME.out.kallisto_index
+    }
+}

subworkflows/local/prepare_genome/nextflow.config

@@ -1,114 +1,36 @@
 process {
-    withName: 'GUNZIP_.*|MAKE_TRANSCRIPTS_FASTA' {
-        publishDir = [
-            path: { params.save_reference ? "${params.outdir}/genome" : params.outdir },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
-        ]
-    }
-
     withName: 'UNTAR_.*' {
         ext.args2 = '--no-same-owner'
     }
 
-    withName: 'UNTAR_.*|STAR_GENOMEGENERATE|STAR_GENOMEGENERATE_IGENOMES|HISAT2_BUILD' {
-        publishDir = [
-            path: { params.save_reference ? "${params.outdir}/genome/index" : params.outdir },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
-        ]
-    }
-
     withName: 'GFFREAD' {
         ext.args   = '--keep-exon-attrs -F -T'
-        publishDir = [
-            path: { params.save_reference ? "${params.outdir}/genome" : params.outdir },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
-        ]
-    }
-
-    withName: 'HISAT2_EXTRACTSPLICESITES' {
-        publishDir = [
-            path: { params.save_reference ? "${params.outdir}/genome/index" : params.outdir },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
-        ]
     }
 
     withName: 'SALMON_INDEX' {
         ext.args   = { [
                 params.gencode ? '--gencode' : '',
                 params.pseudo_aligner_kmer_size ? "-k ${params.pseudo_aligner_kmer_size}": ''
         ].join(' ').trim() }
-        publishDir = [
-            path: { params.save_reference ? "${params.outdir}/genome/index" : params.outdir },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
-        ]
     }
 
     withName: 'KALLISTO_INDEX' {
         ext.args   = params.pseudo_aligner_kmer_size ? "-k ${params.pseudo_aligner_kmer_size}" : ''
-        publishDir = [
-            path: { params.save_reference ? "${params.outdir}/genome/index" : params.outdir },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
-        ]
     }
 
     withName: 'RSEM_PREPAREREFERENCE_GENOME' {
         ext.args   = '--star'
-        publishDir = [
-            path: { params.save_reference ? "${params.outdir}/genome/index" : params.outdir },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
-        ]
-    }
-
-    withName: 'GTF2BED' {
-        publishDir = [
-            path: { params.save_reference ? "${params.outdir}/genome" : params.outdir },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
-        ]
-    }
-
-    withName: 'CAT_ADDITIONAL_FASTA|PREPROCESS_TRANSCRIPTS_FASTA_GENCODE' {
-        publishDir = [
-            path: { params.save_reference ? "${params.outdir}/genome" : params.outdir },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
-        ]
     }
 
     withName: 'GTF_FILTER' {
         ext.args   = { params.skip_gtf_transcript_filter ?: '--skip_transcript_id_check' }
-        publishDir = [
-            path: { params.save_reference ? "${params.outdir}/genome" : params.outdir },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
-        ]
-    }
-
-    withName: 'CUSTOM_GETCHROMSIZES' {
-        publishDir = [
-            path: { params.save_reference ? "${params.outdir}/genome" : params.outdir },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
-        ]
     }
 }
 
 if (!params.skip_bbsplit && params.bbsplit_fasta_list) {
     process {
         withName: 'PREPARE_GENOME:BBMAP_BBSPLIT' {
             ext.args   = 'build=1'
-            publishDir = [
-                path: { params.save_reference ? "${params.outdir}/genome/index" : params.outdir },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
-            ]
         }
     }
 }