From 6ccc5fa2b70f955c962037efc7f1825baf6ec5fe Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 25 Jul 2018 14:33:01 +0200
Subject: [PATCH] FastQC.nf: add paired process
---
src/nf_modules/FastQC/fastqc.config | 4 +--
src/nf_modules/FastQC/fastqc.nf | 47 ++++++++++++++++++++++++++---
2 files changed, 44 insertions(+), 7 deletions(-)
diff --git a/src/nf_modules/FastQC/fastqc.config b/src/nf_modules/FastQC/fastqc.config
index db3b027..a658984 100644
--- a/src/nf_modules/FastQC/fastqc.config
+++ b/src/nf_modules/FastQC/fastqc.config
@@ -3,14 +3,14 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- $fastqc {
+ $fastqc_fastq {
container = "fastqc:0.11.5"
}
}
}
sge {
process{
- $fastqc {
+ $fastqc_fastq {
beforeScript = "module purge; module load FastQC/0.11.5"
executor = "sge"
cpus = 1
diff --git a/src/nf_modules/FastQC/fastqc.nf b/src/nf_modules/FastQC/fastqc.nf
index abe18a4..6ab4140 100644
--- a/src/nf_modules/FastQC/fastqc.nf
+++ b/src/nf_modules/FastQC/fastqc.nf
@@ -5,7 +5,13 @@
*/
/* fastQC */
-params.fastq = ""
+
+
+/*
+* for single-end data
+*/
+
+params.fastq = "$baseDir/data/fastq/*.fastq"
log.info "fastq files : ${params.fastq}"
@@ -14,20 +20,51 @@ Channel
.ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
.set { fastq_files }
-process fastqc {
+process fastqc_fastq {
tag "$fastq.baseName"
- publishDir "results/fastqc/", mode: 'copy'
+ publishDir "results/fastq/fastqc/", mode: 'copy'
+ cpus = 1
input:
file fastq from fastq_files
output:
- file "*.htlm" into fastqc_repport
+ file "*.{zip,html}" into fastqc_repport
script:
"""
-fastqc -o ./ --noextract -f fastq ${fastq}
+fastqc --quiet --threads ${task.cpus} --outdir -f fastq ./ ${fastq}
"""
}
+/*
+* for paired-end data
+*/
+
+params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
+
+log.info "fastq files : ${params.fastq}"
+
+Channel
+ .fromFilePairs( params.fastq )
+ .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
+ .set { fastq_files }
+
+process fastqc_fastq {
+ tag "$pair_id"
+ publishDir "results/fastq/fastqc/", mode: 'copy'
+
+ input:
+ set pair_id, file(reads) from fastq_files
+
+ output:
+ file "*.{zip,html}" into fastqc_repport
+
+ script:
+"""
+fastqc --quiet --threads ${task.cpus} --outdir -f fastq ./ \
+${fastq[0]} ${fastq[1]}
+"""
+}
+
--
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