Merge branch 'dev_Jules' into 'master'

Replace zcat + gzip by cat in core_pipeline

See merge request !13

modules/local/module_core.nf

@@ -124,23 +124,16 @@ process MERGE_LANES {
 		tuple val(sample), path(reads)
 	
 	output:
-		tuple val(sample), path("*.fastq"), emit: fastq
+		tuple val(sample), path("*_R{1,2}_001.fastq.gz"), emit: fastq
 	
 	script:
 	def args = task.ext.args ?: ''
 	"""
 	#!/bin/bash
 
-	R1_files=\$(ls *R1*)
-	R2_files=\$(ls *R2*)
+	cat `ls *R1*` > ${sample}_R1_001.fastq.gz
+	cat `ls *R2*` > ${sample}_R2_001.fastq.gz
 
-	for file in \$R1_files; do
-		zcat \$file >> ${sample}_R1_001.fastq
-	done
-
-	for file in \$R2_files; do
-		zcat \$file >> ${sample}_R2_001.fastq
-	done
 	"""
 }
 

sub-workflows/local/core_pipeline.nf

@@ -17,7 +17,7 @@ include {
 	DUPLICATED_READS;
 	MERGE_LANES;
 } from "$baseDir/modules/local/module_core.nf"
-include { GUNZIP; GZIP		} from "${params.shared_modules}/gzip.nf"
+include { GUNZIP			} from "${params.shared_modules}/gzip.nf"
 include { SEQTK_SAMPLE 		} from "${params.shared_modules}/seqtk.nf"
 include { md5sum as MD5SUM	} from "${params.shared_modules}/md5sum.nf"
 //-------------------------------------------------
@@ -41,9 +41,10 @@ workflow CORE {
 				.groupTuple()
 			)
 
-			GZIP(MERGE_LANES.out.fastq)
-
-			ch_read = GZIP.out
+			ch_read = MERGE_LANES.out.fastq
+				.collect{it[1]}
+				.flatten()
+				.map{$it -> [$it.simpleName, $it]}
 		} else {
 			ch_read = ch_fastq
 		}