From f9a6c22f504050ec3e6ea63d4d9ddfab784ad5d3 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 2 Aug 2018 17:32:41 +0200
Subject: [PATCH] Bowtie: nf add file_id var for single-end like for paired-end
---
src/nf_modules/Bowtie/bowtie.nf | 35 ++++++++-----------
src/nf_modules/Bowtie/tests/mapping_single.nf | 13 +++----
2 files changed, 22 insertions(+), 26 deletions(-)
diff --git a/src/nf_modules/Bowtie/bowtie.nf b/src/nf_modules/Bowtie/bowtie.nf
index ff7ad04..0344760 100644
--- a/src/nf_modules/Bowtie/bowtie.nf
+++ b/src/nf_modules/Bowtie/bowtie.nf
@@ -96,14 +96,18 @@ fi
/*
* for single-end data
*/
-params.fastq = "$baseDir/data/fastq/*.fastq"
+params.mean = 200
+params.sd = 100
log.info "fastq files : ${params.fastq}"
log.info "index files : ${params.index}"
+log.info "mean read size: ${params.mean}"
+log.info "sd read size: ${params.sd}"
Channel
.fromPath( params.fastq )
.ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
+ .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
.set { fastq_files }
Channel
.fromPath( params.index )
@@ -111,33 +115,24 @@ Channel
.set { index_files }
process mapping_fastq {
- tag "$reads.baseName"
+ tag "$file_id"
cpus 4
- publishDir "results/mapping/bams/", mode: 'copy'
+ 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:
- file "*.bam" into bam_files
- file "*_report.txt" into mapping_report
+ file "*" into count_files
script:
-index_id = index[0]
-for (index_file in index) {
- if (index_file =~ /.*\.1\.ebwt/ && !(index_file =~ /.*\.rev\.1\.ebwt/)) {
- index_id = ( index_file =~ /(.*)\.1\.ebwt/)[0][1]
- }
-}
"""
-bowtie --best -v 3 -k 1 --sam -p ${task.cpus} ${index_id} \
--q ${reads} 2> \
-${reads.baseName}_bowtie_report.txt | \
-samtools view -Sb - > ${reads.baseName}.bam
-
-if grep -q "Error" ${reads.baseName}_bowtie_report.txt; then
- exit 1
-fi
+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/Bowtie/tests/mapping_single.nf b/src/nf_modules/Bowtie/tests/mapping_single.nf
index ad94f5b..6697681 100644
--- a/src/nf_modules/Bowtie/tests/mapping_single.nf
+++ b/src/nf_modules/Bowtie/tests/mapping_single.nf
@@ -6,6 +6,7 @@ log.info "index files : ${params.index}"
Channel
.fromPath( params.fastq )
.ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
+ .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
.set { fastq_files }
Channel
.fromPath( params.index )
@@ -13,16 +14,16 @@ Channel
.set { index_files }
process mapping_fastq {
- tag "$reads.baseName"
+ tag "$file_id"
cpus 4
publishDir "results/mapping/bams/", mode: 'copy'
input:
- file reads from fastq_files
+ set file_id, file(reads) from fastq_files
file index from index_files.collect()
output:
- file "*.bam" into bam_files
+ set file_id, "*.bam" into bam_files
file "*_report.txt" into mapping_report
script:
@@ -35,10 +36,10 @@ for (index_file in index) {
"""
bowtie --best -v 3 -k 1 --sam -p ${task.cpus} ${index_id} \
-q ${reads} 2> \
-${reads.baseName}_bowtie_report.txt | \
-samtools view -Sb - > ${reads.baseName}.bam
+${file_id}_bowtie_report.txt | \
+samtools view -Sb - > ${file_id}.bam
-if grep -q "Error" ${reads.baseName}_bowtie_report.txt; then
+if grep -q "Error" ${file_id}_bowtie_report.txt; then
exit 1
fi
"""
--
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