Remove prepare_genome.config and rnaseq nextflow.config, consolidate module configs in modules.config

Author: maxulysse

conf/modules.config

@@ -11,7 +11,20 @@
 */
 
 process {
+    withName: 'BUILD_INTERVALS' {
+        ext.args   = { "-v FS='\t' -v OFS='\t' '{ print \$1, \"0\", \$2 }'" }
+        ext.suffix = { "bed" }
+    }
+    withName: 'GFFREAD' {
+        ext.args   = '--keep-exon-attrs -F -T'
+    }
+    withName: 'KALLISTO_INDEX' {
+        ext.args   = { params.kallisto_make_unique ? '--make-unique' : '' }
+    }
     withName: 'MULTIQC' {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
     }
+    withName: 'RSEM_PREPAREREFERENCE_GENOME' {
+        ext.args   = '--star'
+    }
 }

conf/prepare_genome.config

@@ -287,9 +287,7 @@ plugins {
 }
 
 validation {
-    defaultIgnoreParams = ["genomes"]
     monochromeLogs = params.monochrome_logs
 }
 // Load modules.config for DSL2 module specific options
 includeConfig 'conf/modules.config'
-includeConfig 'conf/prepare_genome.config'