FastQ namming using NGL api

• Name of fastq with info from NGL databases

  • Uniformity with ng6 file names (new pipeline option)
  • Add files to readsets
  • Move MD5SUM process from CORE_PIPELINE to ILLUMINA_QC workflow

  ref: #91 (closed)

conf/base.config

@@ -125,12 +125,15 @@ process {
 	withLabel: bwa {
 		module = toolsModuleHash['BWA']
 		cpus = { checkMax( 6 * task.attempt, 'cpus' ) }
-	    memory = { checkMax( 8.GB * task.attempt, 'memory' ) }
+	    memory = { checkMax( 16.GB * task.attempt, 'memory' ) }
 	    time = { checkMax( 3.d * task.attempt, 'time' ) }
 
 		publishDir = [
 			path: "${params.outdir}/alignment/bwa",
-			mode: 'copy'
+			mode: {
+				if (params.DTM_mode) 'symlink'
+				else 'copy'
+			}
 		]
 	}
 
@@ -207,6 +210,13 @@ process {
 
 	}
 
+	withName: FILE_RENAME {
+		ext.args = [
+			params.run_date ? "--date " +  params.run_date : '',
+			params.ng6_name ? "--ng6_like" : '',
+		].join(' ')
+	}
+
 	// ----- WithLabel
 	withLabel: littleJob {
 		executor = 'local'
@@ -216,7 +226,7 @@ process {
 		module = toolsModuleHash['SAMTOOLS']
 		cpus = { checkMax( 6 * task.attempt, 'cpus' ) }
 	    memory = { checkMax( 8.GB * task.attempt, 'memory' ) }
-	    time = { checkMax( 3.h * task.attempt, 'time' ) }
+	    time = { checkMax( 24.h * task.attempt, 'time' ) }
 	}
 
 	withLabel: alignment {