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Commit 435f1cb3 authored by Jules Sabban's avatar Jules Sabban
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Merge branch 'dev_Jules' into 'master'

Replace zcat + gzip by cat in core_pipeline

See merge request !13
parents 89916947 2253e27e
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1 merge request!13Replace zcat + gzip by cat in core_pipeline
Pipeline #122667 failed
......@@ -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 >> ${sample}_R2_001.fastq
done
"""
}
......
......@@ -17,7 +17,7 @@ include {
DUPLICATED_READS;
MERGE_LANES;
} from "$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
}
......
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