From 9496c2dbc387360ed9e448d327e4876c2a178d2d Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 2 Aug 2018 17:03:29 +0200
Subject: [PATCH] FastQC: add id_file var for single-end like for paired-end
---
src/nf_modules/FastQC/fastqc.nf | 5 +++--
src/nf_modules/FastQC/tests/fastqc_single.nf | 5 +++--
2 files changed, 6 insertions(+), 4 deletions(-)
diff --git a/src/nf_modules/FastQC/fastqc.nf b/src/nf_modules/FastQC/fastqc.nf
index 2a725f4..6e90d45 100644
--- a/src/nf_modules/FastQC/fastqc.nf
+++ b/src/nf_modules/FastQC/fastqc.nf
@@ -18,15 +18,16 @@ log.info "fastq files : ${params.fastq}"
Channel
.fromPath( params.fastq )
.ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
+ .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
.set { fastq_files }
process fastqc_fastq {
- tag "$reads.baseName"
+ tag "$file_id"
publishDir "results/fastq/fastqc/", mode: 'copy'
cpus = 1
input:
- file reads from fastq_files
+ set file_id, file(reads) from fastq_files
output:
file "*.{zip,html}" into fastqc_report
diff --git a/src/nf_modules/FastQC/tests/fastqc_single.nf b/src/nf_modules/FastQC/tests/fastqc_single.nf
index 318d20c..4598416 100644
--- a/src/nf_modules/FastQC/tests/fastqc_single.nf
+++ b/src/nf_modules/FastQC/tests/fastqc_single.nf
@@ -5,15 +5,16 @@ log.info "fastq files : ${params.fastq}"
Channel
.fromPath( params.fastq )
.ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
+ .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
.set { fastq_files }
process fastqc_fastq {
- tag "$reads.baseName"
+ tag "$file_id"
publishDir "results/fastq/fastqc/", mode: 'copy'
cpus = 1
input:
- file reads from fastq_files
+ set file_id, file(reads) from fastq_files
output:
file "*.{zip,html}" into fastqc_report
--
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