From 7ed402cc70cb45812006bd7d8476bdf8a7db1469 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 2 Aug 2018 17:06:00 +0200
Subject: [PATCH] RSEM: nf add file_id var in single-end like for paired-end
---
src/nf_modules/RSEM/rsem.nf | 11 ++++++-----
src/nf_modules/RSEM/tests/quantification_single.nf | 7 ++++---
2 files changed, 10 insertions(+), 8 deletions(-)
diff --git a/src/nf_modules/RSEM/rsem.nf b/src/nf_modules/RSEM/rsem.nf
index 9a14cc8..aa2fc95 100644
--- a/src/nf_modules/RSEM/rsem.nf
+++ b/src/nf_modules/RSEM/rsem.nf
@@ -96,7 +96,7 @@ rsem-calculate-expression --bowtie2 \
params.fastq = "$baseDir/data/fastq/*.fastq"
params.index = "$baseDir/data/index/*.index*"
-params.mean = 300
+params.mean = 125
params.sd = 100
log.info "fastq files : ${params.fastq}"
@@ -107,6 +107,7 @@ log.info "sd read size: ${params.sd}"
Channel
.fromPath( params.fastq )
.ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
+ .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
.set { fastq_files }
Channel
.fromPath( params.index )
@@ -114,12 +115,12 @@ Channel
.set { index_files }
process mapping_fastq {
- tag "$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:
@@ -133,7 +134,7 @@ rsem-calculate-expression --bowtie2 \
--bowtie2-sensitivity-level "very_sensitive" \
--fragment-length-mean ${params.mean} --fragment-length-sd ${params.sd} \
--output-genome-bam -p ${task.cpus} \
-${reads} ${index_name} ${tagname} > ${tagname}_rsem_bowtie2_report.txt
+${reads} ${index_name} ${file_id} \
+> ${reads.baseName}_rsem_bowtie2_report.txt
"""
}
-
diff --git a/src/nf_modules/RSEM/tests/quantification_single.nf b/src/nf_modules/RSEM/tests/quantification_single.nf
index 63b2a40..47e0047 100644
--- a/src/nf_modules/RSEM/tests/quantification_single.nf
+++ b/src/nf_modules/RSEM/tests/quantification_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:
@@ -37,7 +38,7 @@ rsem-calculate-expression --bowtie2 \
--bowtie2-sensitivity-level "very_sensitive" \
--fragment-length-mean ${params.mean} --fragment-length-sd ${params.sd} \
--output-genome-bam -p ${task.cpus} \
-${reads} ${index_name} ${reads.baseName} \
+${reads} ${index_name} ${file_id} \
> ${reads.baseName}_rsem_bowtie2_report.txt
"""
}
--
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