From 2253e27e4d0557da6d7f4588b5c73ebc62d3041c Mon Sep 17 00:00:00 2001
From: jsabban <jules.sabban@inrae.fr>
Date: Tue, 12 Sep 2023 14:41:09 +0200
Subject: [PATCH] Replace zcat + gzip by cat in core_pipeline
Ref: #79
---
modules/local/module_core.nf | 13 +++----------
sub-workflows/local/core_pipeline.nf | 9 +++++----
2 files changed, 8 insertions(+), 14 deletions(-)
diff --git a/modules/local/module_core.nf b/modules/local/module_core.nf
index 7db960a..a874ffc 100644
--- a/modules/local/module_core.nf
+++ b/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 >> ${sample}_R2_001.fastq
- done
"""
}
diff --git a/sub-workflows/local/core_pipeline.nf b/sub-workflows/local/core_pipeline.nf
index d837b87..73c5fd8 100644
--- a/sub-workflows/local/core_pipeline.nf
+++ b/sub-workflows/local/core_pipeline.nf
@@ -17,7 +17,7 @@ include {
DUPLICATED_READS;
MERGE_LANES;
} from "$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
}
--
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