Preview: Record types

conf/modules/bedtools_intersect.config

@@ -3,12 +3,5 @@ process {
         ext.args   = ''
         ext.prefix = { "${intervals1.baseName}" }
         ext.suffix = 'targeted.bedGraph'
-        publishDir = [
-            [
-                path: { params.aligner == 'bismark' ? "${params.outdir}/bismark/methylation_calls/bedGraph" : "${params.outdir}/methyldackel" },
-                mode: params.publish_dir_mode,
-                pattern: "*targeted.bedGraph"
-            ]
-        ]
     }
 }

conf/modules/bismark_align.config

@@ -15,24 +15,5 @@ process {
                     )
                 )
             ].join(' ').trim() }
-            publishDir = [
-                [
-                    path: { "${params.outdir}/${params.aligner}/alignments/unmapped" },
-                    mode: params.publish_dir_mode,
-                    pattern: "*.fq.gz",
-                    enabled: params.unmapped
-                ],
-                [
-                    path: { "${params.outdir}/${params.aligner}/alignments" },
-                    mode: params.publish_dir_mode,
-                    pattern: "*.bam",
-                    enabled: (params.save_align_intermeds || params.skip_deduplication || params.rrbs)
-                ],
-                [
-                    path: { "${params.outdir}/${params.aligner}/alignments/logs" },
-                    mode: params.publish_dir_mode,
-                    pattern: "*.txt"
-                ]
-            ]
         }
 }

conf/modules/bismark_coverage2cytosine.config

@@ -1,22 +1,5 @@
 process {
     withName: BISMARK_COVERAGE2CYTOSINE {
         ext.args = params.nomeseq ? '--nome-seq' : ''
-        publishDir = [
-            [
-                path: { "${params.outdir}/bismark/coverage2cytosine/summaries" },
-                mode: params.publish_dir_mode,
-                pattern: "*_summary.txt"
-            ],
-            [
-                path: { "${params.outdir}/bismark/coverage2cytosine/reports" },
-                mode: params.publish_dir_mode,
-                pattern: "*_report.txt.gz"
-            ],
-            [
-                path: { "${params.outdir}/bismark/coverage2cytosine/coverage" },
-                mode: params.publish_dir_mode,
-                pattern: "*cov.gz"
-            ]
-        ]
     }
 }

conf/modules/bismark_deduplicate.config

@@ -1,12 +1,5 @@
 process {
     withName: BISMARK_DEDUPLICATE {
         ext.args = ''
-        publishDir = [
-            [
-                path: { "${params.outdir}/${params.aligner}/deduplicated/logs" },
-                mode: params.publish_dir_mode,
-                pattern: "*.txt"
-            ]
-        ]
     }
 }

conf/modules/bismark_genomepreparation.config

@@ -4,11 +4,5 @@ process {
             (params.aligner == 'bismark_hisat') ? ' --hisat2' : ' --bowtie2',
             params.slamseq ? ' --slam' : ''
         ].join(' ').trim()
-        publishDir = [
-            path: { "${params.outdir}/${params.aligner}/reference_genome" },
-            saveAs: { it =~ /.*\.yml/ ? null : it },
-            mode: params.publish_dir_mode,
-            enabled: params.save_reference
-        ]
     }
 }

conf/modules/bismark_methylationextractor.config

@@ -10,32 +10,5 @@ process {
             meta.single_end ? '' : (params.ignore_r2        > 0 ? "--ignore_r2 ${params.ignore_r2}"       : ""),
             meta.single_end ? '' : (params.ignore_3prime_r2 > 0 ? "--ignore_3prime_r2 ${params.ignore_3prime_r2}": "")
         ].join(' ').trim() }
-        publishDir = [
-            [
-                path: { "${params.outdir}/${params.aligner}/methylation_calls/mbias" },
-                mode: params.publish_dir_mode,
-                pattern: "*M-bias.txt"
-            ],
-            [
-                path: { "${params.outdir}/${params.aligner}/methylation_calls/methylation_coverage" },
-                mode: params.publish_dir_mode,
-                pattern: "*cov.gz"
-            ],
-            [
-                path: { "${params.outdir}/${params.aligner}/methylation_calls/bedGraph" },
-                mode: params.publish_dir_mode,
-                pattern: "*bedGraph.gz"
-            ],
-            [
-                path: { "${params.outdir}/${params.aligner}/methylation_calls/splitting_report" },
-                mode: params.publish_dir_mode,
-                pattern: "*splitting_report.txt"
-            ],
-            [
-                path: { "${params.outdir}/${params.aligner}/methylation_calls/methylation_calls" },
-                mode: params.publish_dir_mode,
-                pattern: "*txt.gz"
-            ]
-        ]
     }
 }

conf/modules/bismark_report.config

@@ -1,10 +1,5 @@
 process {
     withName: BISMARK_REPORT {
         ext.args = ''
-        publishDir = [
-            path: "${params.outdir}/${params.aligner}/reports",
-            mode: params.publish_dir_mode,
-            pattern: "*.html"
-        ]
     }
 }

conf/modules/bismark_summary.config

@@ -1,10 +1,5 @@
 process {
     withName: BISMARK_SUMMARY {
         ext.args = ''
-        publishDir = [
-            path: "${params.outdir}/${params.aligner}/summary",
-            mode: params.publish_dir_mode,
-            pattern: "*.{html,txt}"
-        ]
     }
 }

conf/modules/bwameth_align.config

@@ -2,11 +2,5 @@ process {
     withName: BWAMETH_ALIGN {
         cache = 'lenient' // This is set because in the module command the index files are touched so as to have bwameth not complain
         ext.args = ''
-        publishDir = [
-                path: { "${params.outdir}/${params.aligner}/alignments" },
-                pattern: "*.bam",
-                mode: params.publish_dir_mode,
-                enabled: params.save_align_intermeds
-        ]
     }
 }

conf/modules/bwameth_index.config

@@ -1,11 +1,5 @@
 process {
     withName: BWAMETH_INDEX {
         ext.args = ''
-        publishDir = [
-            path: { "${params.outdir}/${params.aligner}/reference_genome" },
-            mode: params.publish_dir_mode,
-            saveAs: { it.equals('versions.yml') ? null : it.tokenize("/").last() },
-            enabled: params.save_reference
-        ]
     }
 }

conf/modules/fastqc.config

@@ -1,17 +1,5 @@
 process {
     withName: FASTQC {
         ext.args = '--quiet'
-        publishDir = [
-            [
-                path: { "${params.outdir}/fastqc" },
-                mode: params.publish_dir_mode,
-                pattern: "*.html"
-            ],
-            [
-                path: { "${params.outdir}/fastqc/zips" },
-                mode: params.publish_dir_mode,
-                pattern: "*.zip"
-            ]
-        ]
     }
 }

conf/modules/methyldackel_extract.config

@@ -7,17 +7,5 @@ process {
             params.methyl_kit ? " --methylKit" : '',
             params.min_depth > 0 ? " --minDepth ${params.min_depth}" : ''
         ].join(" ").trim()
-        publishDir = [
-            [
-                path: { "${params.outdir}/methyldackel" },
-                mode: params.publish_dir_mode,
-                pattern: "*.bedGraph"
-            ],
-            [
-                path: { "${params.outdir}/methyldackel" },
-                mode: params.publish_dir_mode,
-                pattern: "*.methylKit"
-            ]
-        ]
     }
 }

conf/modules/methyldackel_mbias.config

@@ -4,12 +4,5 @@ process {
             params.all_contexts ? ' --CHG --CHH' : '',
             params.ignore_flags ? " --ignoreFlags" : ''
         ].join(" ").trim()
-        publishDir = [
-            [
-                path: { "${params.outdir}/methyldackel/mbias" },
-                mode: params.publish_dir_mode,
-                pattern: "*mbias.txt"
-            ]
-        ]
     }
 }

conf/modules/multiqc.config

@@ -1,10 +1,5 @@
 process {
     withName: 'MULTIQC' {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
-        publishDir = [
-            path: { "${params.outdir}/multiqc/${params.aligner}" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
     }
 }

conf/modules/parabricks_fq2bammeth.config

@@ -2,11 +2,5 @@ process {
     withName: PARABRICKS_FQ2BAMMETH {
         cache = 'lenient' // This is set because in the module command the index files are touched so as to have bwameth not complain
         ext.args = '--low-memory'
-        publishDir = [
-                path: { "${params.outdir}/${params.aligner}/alignments" },
-                pattern: "*.bam",
-                mode: params.publish_dir_mode,
-                enabled: params.save_align_intermeds
-        ]
     }
 }

conf/modules/picard_bedtointervallist.config

@@ -1,10 +1,5 @@
 process {
     withName: PICARD_BEDTOINTERVALLIST {
         ext.args = ""
-        publishDir = [
-            path: { "${params.outdir}/enrichment_metrics" },
-            mode: params.publish_dir_mode,
-            pattern: "*.intervallist"
-        ]
     }
 }

conf/modules/picard_collecthsmetrics.config

@@ -1,10 +1,5 @@
 process {
     withName: PICARD_COLLECTHSMETRICS {
         ext.args = "--MINIMUM_MAPPING_QUALITY 20 --COVERAGE_CAP 1000  --NEAR_DISTANCE 500"
-        publishDir = [
-            path: { "${params.outdir}/enrichment_metrics" },
-            mode: params.publish_dir_mode,
-            pattern: "*_metrics"
-        ]
     }
 }

conf/modules/picard_createsequencedictionary.config

@@ -1,11 +1,5 @@
 process {
     withName: PICARD_CREATESEQUENCEDICTIONARY {
         ext.args = ""
-        publishDir = [
-            path: { "${params.outdir}/${params.aligner}/reference_genome" },
-            mode: params.publish_dir_mode,
-            enabled: params.save_reference,
-            pattern: "*.dict"
-        ]
     }
 }

conf/modules/picard_markduplicates.config

@@ -2,17 +2,5 @@ process {
     withName: PICARD_MARKDUPLICATES {
         ext.args = "--ASSUME_SORTED true --REMOVE_DUPLICATES false --VALIDATION_STRINGENCY LENIENT --PROGRAM_RECORD_ID 'null' --TMP_DIR tmp"
         ext.prefix = { "${meta.id}.markdup.sorted" }
-        publishDir = [
-            [
-                path: { "${params.outdir}/${params.aligner}/deduplicated/picard_metrics" },
-                pattern: "*.metrics.txt",
-                mode: params.publish_dir_mode
-            ],
-            [
-                path: { "${params.outdir}/${params.aligner}/deduplicated" },
-                pattern: "*.bam",
-                mode: params.publish_dir_mode
-            ]
-        ]
     }
 }

conf/modules/preseq_lcextrap.config

@@ -1,19 +1,5 @@
 process {
     withName: PRESEQ_LCEXTRAP {
         ext.args = " -verbose -bam"
-        publishDir = [
-            [
-                path: { "${params.outdir}/${params.aligner}/preseq" },
-                mode: params.publish_dir_mode,
-                pattern: "*.txt",
-                enabled: params.run_preseq
-            ],
-            [
-                path: { "${params.outdir}/${params.aligner}/preseq/log" },
-                mode: params.publish_dir_mode,
-                pattern: "*.log",
-                enabled: params.run_preseq
-            ]
-        ]
     }
 }

conf/modules/qualimap_bamqc.config

@@ -4,13 +4,5 @@ process {
             params.genome.toString().startsWith('GRCh') ? '-gd HUMAN' : '',
             params.genome.toString().startsWith('GRCm') ? '-gd MOUSE' : ''
         ].join(" ").trim()
-        publishDir = [
-            [
-                path: { "${params.outdir}/${params.aligner}/qualimap/bamqc/" },
-                mode: params.publish_dir_mode,
-                pattern: "*",
-                enabled: params.run_qualimap
-            ]
-        ]
     }
 }

conf/modules/samtools_faidx.config

@@ -1,11 +1,5 @@
 process {
     withName: SAMTOOLS_FAIDX {
         ext.args = ""
-        publishDir = [
-            path: { "${params.outdir}/${params.aligner}/reference_genome" },
-            mode: params.publish_dir_mode,
-            enabled: params.save_reference,
-            pattern: "*.fai"
-        ]
     }
 }

conf/modules/samtools_flagstat.config

@@ -1,11 +1,4 @@
 process {
     withName: SAMTOOLS_FLAGSTAT {
-        publishDir = [
-            [
-                path: { "${params.outdir}/${params.aligner}/alignments/samtools_stats/" },
-                mode: params.publish_dir_mode,
-                pattern: "*.flagstat"
-            ]
-        ]
     }
 }

conf/modules/samtools_index.config

@@ -1,19 +1,5 @@
 process {
     withName: SAMTOOLS_INDEX {
         ext.prefix = ""
-        publishDir = [
-            [
-                path: { "${params.outdir}/${params.aligner}/deduplicated/" },
-                mode: params.publish_dir_mode,
-                pattern: "*.bai",
-                enabled: !params.skip_deduplication
-            ],
-            [
-                path: { "${params.outdir}/${params.aligner}/alignments/" },
-                mode: params.publish_dir_mode,
-                pattern: "*.bai",
-                enabled: params.skip_deduplication
-            ]
-        ]
     }
 }