From d0c2a2b42f13c8ec4761e1841f50f7125d735a1f Mon Sep 17 00:00:00 2001
From: elabaron <emmanuel.labaronne@ens-lyon.fr>
Date: Wed, 19 Feb 2020 16:40:11 +0100
Subject: [PATCH] fix beugs in RNAseq pipeline
---
src/RNAseq.config | 2 +-
src/RNAseq.nf | 12 ++++++------
2 files changed, 7 insertions(+), 7 deletions(-)
diff --git a/src/RNAseq.config b/src/RNAseq.config
index 57e50ce5..33976912 100644
--- a/src/RNAseq.config
+++ b/src/RNAseq.config
@@ -3,7 +3,7 @@ profiles {
process{
withName: trimming {
beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/cutadapt_2.1"
+ conda = "$baseDir/.conda_envs/cutadapt_2.4"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/RNAseq.nf b/src/RNAseq.nf
index f153c932..911314d5 100644
--- a/src/RNAseq.nf
+++ b/src/RNAseq.nf
@@ -27,11 +27,11 @@ process trimming {
script:
"""
cutadapt -a AGATCGGAAGAGC -A AGATCGGAAGAGC \
- -o ${pair_id}_cut_R1.fastq.gz -p ${pair_id}_tmp_R2.fastq.gz \
- ${reads[0]} ${reads[1]} > ${pair_id}_report.txt
+ -o ${file_id}_cut_R1.fastq.gz -p ${file_id}_tmp_R2.fastq.gz \
+ ${reads[0]} ${reads[1]} > ${file_id}_report.txt
- cutadapt -u -14 -o ${pair_id}_cut_R2.fastq.gz ${pair_id}_tmp_R2.fastq.gz \
- > ${pair_id}_cut_report.txt
+ cutadapt -u -14 -o ${file_id}_cut_R2.fastq.gz ${file_id}_tmp_R2.fastq.gz \
+ > ${file_id}_cut_report.txt
"""
}
@@ -82,13 +82,13 @@ log.info "index : ${params.index_hg38}"
Channel
.fromPath ( params.index_hg38 )
.ifEmpty { error "Cannot find any hg38 index files matching: ${params.index_hg38}" }
- .set { index_file_hg38 }--paired
+ .set { index_file_hg38 }
process hisat2_human {
tag "$file_id"
input:
- set file_id, file(fastq_filtred) from rRNA_removed_reads
+ set file_id, file(fastq_filtred) from rRNA_removed_files
file index from index_file_hg38.toList()
output:
--
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