Merge remote-tracking branch 'upstream/dev' into updates

Author: JoseEspinosa

main.nf

@@ -11,18 +11,6 @@
 
 nextflow.enable.dsl = 2
 
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-include { CHIPSEQ                 } from './workflows/chipseq'
-include { PREPARE_GENOME          } from './subworkflows/local/prepare_genome'
-include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_chipseq_pipeline'
-include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_chipseq_pipeline'
-include { getGenomeAttribute      } from './subworkflows/local/utils_nfcore_chipseq_pipeline'
-include { getMacsGsize            } from './subworkflows/local/utils_nfcore_chipseq_pipeline'
-
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     GENOME PARAMETER VALUES
@@ -40,6 +28,18 @@ params.gene_bed      = getGenomeAttribute('gene_bed')
 params.blacklist     = getGenomeAttribute('blacklist')
 params.macs_gsize    = getMacsGsize(params)
 
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+include { CHIPSEQ                 } from './workflows/chipseq'
+include { PREPARE_GENOME          } from './subworkflows/local/prepare_genome'
+include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_chipseq_pipeline'
+include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_chipseq_pipeline'
+// include { getGenomeAttribute      } from './subworkflows/local/utils_nfcore_chipseq_pipeline'
+// include { getMacsGsize            } from './subworkflows/local/utils_nfcore_chipseq_pipeline'
+
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     NAMED WORKFLOWS FOR PIPELINE
@@ -137,6 +137,39 @@ workflow {
     )
 }
 
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    FUNCTIONS
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+//
+// Get attribute from genome config file e.g. fasta
+//
+def getGenomeAttribute(attribute) {
+    if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) {
+        if (params.genomes[ params.genome ].containsKey(attribute)) {
+            return params.genomes[ params.genome ][ attribute ]
+        }
+    }
+    return null
+}
+
+//
+// Get macs genome size (macs_gsize)
+//
+def getMacsGsize(params) {
+    def val = null
+    if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) {
+        if (params.genomes[ params.genome ].containsKey('macs_gsize')) {
+            if (params.genomes[ params.genome ][ 'macs_gsize' ].containsKey(params.read_length.toString())) {
+                val = params.genomes[ params.genome ][ 'macs_gsize' ][ params.read_length.toString() ]
+            }
+        }
+    }
+    return val
+}
+
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     THE END

subworkflows/local/prepare_genome.nf

@@ -146,7 +146,7 @@ workflow PREPARE_GENOME {
                 ch_bwa_index = UNTAR_BWA_INDEX ( [ [:], bwa_index ] ).untar
                 ch_versions  = ch_versions.mix(UNTAR_BWA_INDEX.out.versions)
             } else {
-                ch_bwa_index = file(bwa_index)
+                ch_bwa_index = [ [:], file(bwa_index) ]
             }
         } else {
             ch_bwa_index = BWA_INDEX ( ch_fasta.map { [ [:], it ] } ).index

subworkflows/local/utils_nfcore_chipseq_pipeline/main.nf

@@ -149,18 +149,6 @@ def validateInputParameters() {
     }
 }
 
-//
-// Get attribute from genome config file e.g. fasta
-//
-def getGenomeAttribute(attribute) {
-    if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) {
-        if (params.genomes[ params.genome ].containsKey(attribute)) {
-            return params.genomes[ params.genome ][ attribute ]
-        }
-    }
-    return null
-}
-
 //
 // Exit pipeline if incorrect --genome key provided
 //
@@ -175,21 +163,6 @@ def genomeExistsError() {
     }
 }
 
-//
-// Get macs genome size (macs_gsize)
-//
-def getMacsGsize(params) {
-    def val = null
-    if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) {
-        if (params.genomes[ params.genome ].containsKey('macs_gsize')) {
-            if (params.genomes[ params.genome ][ 'macs_gsize' ].containsKey(params.read_length.toString())) {
-                val = params.genomes[ params.genome ][ 'macs_gsize' ][ params.read_length.toString() ]
-            }
-        }
-    }
-    return val
-}
-
 //
 // Generate methods description for MultiQC
 //