Merge pull request #469 from nf-core/conf-modules-configs

Conf modules configs

modules/nf-core/bismark/align/nextflow.config → conf/modules/bismark_align.config

@@ -35,4 +35,4 @@ process {
                 ]
             ]
         }
-}
+}

modules/nf-core/bismark/coverage2cytosine/nextflow.config → conf/modules/bismark_coverage2cytosine.config

@@ -19,4 +19,4 @@ process {
             ]
         ]
     }
-}
+}

modules/nf-core/bismark/deduplicate/nextflow.config → conf/modules/bismark_deduplicate.config

@@ -9,4 +9,4 @@ process {
             ]
         ]
     }
-}
+}

modules/nf-core/bismark/genomepreparation/nextflow.config → conf/modules/bismark_genomepreparation.config

@@ -11,4 +11,4 @@ process {
             enabled: params.save_reference
         ]
     }
-}
+}

modules/nf-core/bismark/methylationextractor/nextflow.config → conf/modules/bismark_methylationextractor.config

@@ -38,4 +38,4 @@ process {
             ]
         ]
     }
-}
+}

modules/nf-core/bismark/report/nextflow.config → conf/modules/bismark_report.config

@@ -7,4 +7,4 @@ process {
             pattern: "*.html"
         ]
     }
-}
+}

modules/nf-core/bismark/summary/nextflow.config → conf/modules/bismark_summary.config

@@ -7,4 +7,4 @@ process {
             pattern: "*.{html,txt}"
         ]
     }
-}
+}

modules/nf-core/bwameth/align/nextflow.config → conf/modules/bwameth_align.config

@@ -8,4 +8,4 @@ process {
                 enabled: params.save_align_intermeds
         ]
     }
-}
+}

modules/nf-core/bwameth/index/nextflow.config → conf/modules/bwameth_index.config

@@ -8,4 +8,4 @@ process {
             enabled: params.save_reference
         ]
     }
-}
+}

modules/nf-core/fastqc/nextflow.config → conf/modules/fastqc.config

@@ -14,4 +14,4 @@ process {
             ]
         ]
     }
-}
+}

modules/nf-core/methyldackel/extract/nextflow.config → conf/modules/methyldackel_extract.config

@@ -19,4 +19,4 @@ process {
             ]
         ]
     }
-}
+}

modules/nf-core/methyldackel/mbias/nextflow.config → conf/modules/methyldackel_mbias.config

@@ -12,4 +12,4 @@ process {
             ]
         ]
     }
-}
+}

modules/nf-core/multiqc/nextflow.config → conf/modules/multiqc.config

@@ -7,4 +7,4 @@ process {
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
-}
+}

modules/nf-core/picard/markduplicates/nextflow.config → conf/modules/picard_markduplicates.config

@@ -15,4 +15,4 @@ process {
             ]
         ]
     }
-}
+}

modules/nf-core/preseq/lcextrap/nextflow.config → conf/modules/preseq_lcextrap.config

@@ -14,4 +14,4 @@ process {
             ]
         ]
     }
-}
+}

modules/nf-core/qualimap/bamqc/nextflow.config → conf/modules/qualimap_bamqc.config

@@ -5,4 +5,4 @@ process {
             params.genome.toString().startsWith('GRCm') ? '-gd MOUSE' : ''
         ].join(" ").trim()
     }
-}
+}

modules/nf-core/samtools/faidx/nextflow.config → conf/modules/samtools_faidx.config

@@ -8,4 +8,4 @@ process {
             pattern: "*.fai"
         ]
     }
-}
+}

modules/nf-core/samtools/flagstat/nextflow.config → conf/modules/samtools_flagstat.config

@@ -8,4 +8,4 @@ process {
             ]
         ]
     }
-}
+}

modules/nf-core/samtools/index/nextflow.config → conf/modules/samtools_index.config

@@ -16,4 +16,4 @@ process {
             ]
         ]
     }
-}
+}

modules/nf-core/samtools/sort/nextflow.config → conf/modules/samtools_sort.config

@@ -27,4 +27,4 @@ process {
             ]
         ]
     }
-}
+}

modules/nf-core/samtools/stats/nextflow.config → conf/modules/samtools_stats.config

@@ -8,4 +8,4 @@ process {
             ]
         ]
     }
-}
+}

modules/nf-core/trimgalore/nextflow.config → conf/modules/trimgalore.config

@@ -87,4 +87,4 @@ process {
             ]
         ]
     }
-}
+}

subworkflows/local/bwameth/nextflow.config

@@ -1,12 +1,11 @@
 
-includeConfig "../../../modules/nf-core/bwameth/align/nextflow.config"
-includeConfig "../../../modules/nf-core/samtools/sort/nextflow.config"
-
-includeConfig "../../../modules/nf-core/samtools/flagstat/nextflow.config"
-includeConfig "../../../modules/nf-core/samtools/stats/nextflow.config"
-includeConfig "../../../modules/nf-core/picard/markduplicates/nextflow.config"
-includeConfig "../../../modules/nf-core/methyldackel/extract/nextflow.config"
-includeConfig "../../../modules/nf-core/methyldackel/mbias/nextflow.config"
+includeConfig "../../../conf/modules/bwameth_align.config"
+includeConfig "../../../conf/modules/samtools_sort.config"
+includeConfig "../../../conf/modules/samtools_flagstat.config"
+includeConfig "../../../conf/modules/samtools_stats.config"
+includeConfig "../../../conf/modules/picard_markduplicates.config"
+includeConfig "../../../conf/modules/methyldackel_extract.config"
+includeConfig "../../../conf/modules/methyldackel_mbias.config"
 
 process {
 

workflows/methylseq/nextflow.config

@@ -1,9 +1,9 @@
 // module configs
-includeConfig "../../modules/nf-core/fastqc/nextflow.config"
-includeConfig "../../modules/nf-core/trimgalore/nextflow.config"
-includeConfig "../../modules/nf-core/multiqc/nextflow.config"
-includeConfig "../../modules/nf-core/preseq/lcextrap/nextflow.config"
-includeConfig "../../modules/nf-core/qualimap/bamqc/nextflow.config"
+includeConfig "../../conf/modules/fastqc.config"
+includeConfig "../../conf/modules/trimgalore.config"
+includeConfig "../../conf/modules/multiqc.config"
+includeConfig "../../conf/modules/preseq_lcextrap.config"
+includeConfig "../../conf/modules/qualimap_bamqc.config"
 
 // subworkflow configs
 includeConfig "../../subworkflows/nf-core/fasta_index_bismark_bwameth/nextflow.config"