From 2ce056071b081793783b7c880d012ea35f801b33 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 2 Aug 2018 17:27:31 +0200
Subject: [PATCH] Kallisto: nf add file_id var for single-end like for
paired-end
---
src/nf_modules/Kallisto/kallisto.nf | 16 +++++++++-------
src/nf_modules/Kallisto/tests/mapping_single.nf | 11 ++++++-----
2 files changed, 15 insertions(+), 12 deletions(-)
diff --git a/src/nf_modules/Kallisto/kallisto.nf b/src/nf_modules/Kallisto/kallisto.nf
index cd7b1ea..ae6b6b7 100644
--- a/src/nf_modules/Kallisto/kallisto.nf
+++ b/src/nf_modules/Kallisto/kallisto.nf
@@ -91,6 +91,7 @@ log.info "sd read size: ${params.sd}"
Channel
.fromPath( params.fastq )
.ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
+ .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
.set { fastq_files }
Channel
.fromPath( params.index )
@@ -98,12 +99,12 @@ Channel
.set { index_files }
process mapping_fastq {
- tag "$reads.baseName"
+ tag "$file_id"
cpus 4
publishDir "results/mapping/quantification/", mode: 'copy'
input:
- file reads from fastq_files
+ set file_id, file(reads) from fastq_files
file index from index_files.collect()
output:
@@ -111,11 +112,12 @@ process mapping_fastq {
script:
"""
-mkdir ${reads.baseName}
-kallisto quant -i ${index} -t ${task.cpus} --single
---bias --bootstrap-samples 100 -o ${reads.baseName} \
--l ${params.mean} -s ${params.sd} -o ./ \
-${reads} > ${reads.baseName}_kallisto_report.txt
+mkdir ${file_id}
+kallisto quant -i ${index} -t ${task.cpus} --single \
+--bias --bootstrap-samples 100 -o ${file_id} \
+-l ${params.mean} -s ${params.sd} \
+${reads} > ${file_id}_kallisto_report.txt
"""
}
+
diff --git a/src/nf_modules/Kallisto/tests/mapping_single.nf b/src/nf_modules/Kallisto/tests/mapping_single.nf
index 69e3a6f..cba5aff 100644
--- a/src/nf_modules/Kallisto/tests/mapping_single.nf
+++ b/src/nf_modules/Kallisto/tests/mapping_single.nf
@@ -11,6 +11,7 @@ log.info "sd read size: ${params.sd}"
Channel
.fromPath( params.fastq )
.ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
+ .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
.set { fastq_files }
Channel
.fromPath( params.index )
@@ -18,12 +19,12 @@ Channel
.set { index_files }
process mapping_fastq {
- tag "$reads.baseName"
+ tag "$file_id"
cpus 4
publishDir "results/mapping/quantification/", mode: 'copy'
input:
- file reads from fastq_files
+ set file_id, file(reads) from fastq_files
file index from index_files.collect()
output:
@@ -31,11 +32,11 @@ process mapping_fastq {
script:
"""
-mkdir ${reads.baseName}
+mkdir ${file_id}
kallisto quant -i ${index} -t ${task.cpus} --single \
---bias --bootstrap-samples 100 -o ${reads.baseName} \
+--bias --bootstrap-samples 100 -o ${file_id} \
-l ${params.mean} -s ${params.sd} \
-${reads} > ${reads.baseName}_kallisto_report.txt
+${reads} > ${file_id}_kallisto_report.txt
"""
}
--
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