From c82cceba4141c2a85125a4d77977e98076564210 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 2 Aug 2018 17:19:47 +0200
Subject: [PATCH] UrQt: nf add file_id var for single-end like for paired-end
---
src/nf_modules/UrQt/tests/trimming_single.nf | 11 +++++-----
src/nf_modules/UrQt/urqt.nf | 22 +++++++++-----------
2 files changed, 16 insertions(+), 17 deletions(-)
diff --git a/src/nf_modules/UrQt/tests/trimming_single.nf b/src/nf_modules/UrQt/tests/trimming_single.nf
index 3160f3b..5eb1e84 100644
--- a/src/nf_modules/UrQt/tests/trimming_single.nf
+++ b/src/nf_modules/UrQt/tests/trimming_single.nf
@@ -5,24 +5,25 @@ log.info "fastq files : ${params.fastq}"
Channel
.fromPath( params.fastq )
.ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
+ .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
.set { fastq_files }
process trimming {
- tag "$reads.baseName"
+ tag "$file_id"
cpus 4
input:
- file reads from fastq_files
+ set file_id, file(reads) from fastq_files
output:
- file "*_trim.fastq.gz" into fastq_files_trim
+ set file_id, "*_trim.fastq.gz" into fastq_files_trim
script:
"""
UrQt --t 20 --m ${task.cpus} --gz \
--in ${reads} \
- --out ${reads.baseName}_trim.fastq.gz \
- > ${reads.baseName}_trimming_report.txt
+ --out ${file_id}_trim.fastq.gz \
+ > ${file_id}_trimming_report.txt
"""
}
diff --git a/src/nf_modules/UrQt/urqt.nf b/src/nf_modules/UrQt/urqt.nf
index d240336..3a0e7d8 100644
--- a/src/nf_modules/UrQt/urqt.nf
+++ b/src/nf_modules/UrQt/urqt.nf
@@ -49,26 +49,24 @@ log.info "fastq files : ${params.fastq}"
Channel
.fromPath( params.fastq )
.ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
+ .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
.set { fastq_files }
process trimming {
- tag "$reads.baseName"
+ tag "$file_id"
cpus 4
- publishDir "results/fastq/trimming/", mode: 'copy'
input:
- file reads from fastq_files
+ set file_id, file(reads) from fastq_files
output:
- file "*_trim.fastq.gz" into fastq_files_trim
+ set file_id, "*_trim.fastq.gz" into fastq_files_trim
script:
-"""
-
-UrQt --t 20 --m ${task.cpus} --gz \
---in ${reads} \
---out ${reads.baseName}_trim.fastq.gz \
-> ${reads.baseName}_trimming_report.txt
-"""
+ """
+ UrQt --t 20 --m ${task.cpus} --gz \
+ --in ${reads} \
+ --out ${file_id}_trim.fastq.gz \
+ > ${file_id}_trimming_report.txt
+ """
}
-
--
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