From d93c0b555826abc5c2a2ed06b6e42737122cce61 Mon Sep 17 00:00:00 2001
From: Emmanuel Labaronne <emmanuel.labaronne@ens-lyon.fr>
Date: Wed, 24 Mar 2021 14:27:40 +0100
Subject: [PATCH] correct typos in nf_modules scripts
---
src/nf_modules/hisat2/mapping_paired.config | 2 +-
src/nf_modules/hisat2/mapping_paired.nf | 32 ++++++++++++++-------
src/nf_modules/kallisto/indexing.config | 2 +-
src/nf_modules/kallisto/indexing.nf | 2 +-
src/nf_modules/kallisto/mapping_paired.nf | 4 ++-
5 files changed, 27 insertions(+), 15 deletions(-)
diff --git a/src/nf_modules/hisat2/mapping_paired.config b/src/nf_modules/hisat2/mapping_paired.config
index 964db521..8333a585 100644
--- a/src/nf_modules/hisat2/mapping_paired.config
+++ b/src/nf_modules/hisat2/mapping_paired.config
@@ -29,7 +29,7 @@ profiles {
memory = "20GB"
cpus = 32
time = "12h"
- queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C"
penv = "openmp32"
}
}
diff --git a/src/nf_modules/hisat2/mapping_paired.nf b/src/nf_modules/hisat2/mapping_paired.nf
index 28b37e00..323faf7c 100644
--- a/src/nf_modules/hisat2/mapping_paired.nf
+++ b/src/nf_modules/hisat2/mapping_paired.nf
@@ -1,5 +1,6 @@
params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
params.index = "$baseDir/data/index/*.index.*"
+params.output = "results/"
log.info "fastq files : ${params.fastq}"
log.info "index files : ${params.index}"
@@ -15,15 +16,15 @@ Channel
process mapping_fastq {
tag "$pair_id"
- publishDir "results/mapping/", mode: 'copy'
+ publishDir "${params.output}", mode: 'copy'
input:
- set pair_id, file(reads) from fastq_files
+ set pair_id, file(fastq_filtred) from fastq_files
file index from index_files.collect()
output:
file "*" into counts_files
- set pair_id, "*.bam" into bam_files
+ set pair_id, "*.{bam, bai}" into bam_files
file "*_report.txt" into mapping_report
script:
@@ -34,15 +35,24 @@ process mapping_fastq {
}
}
"""
-hisat2 -p ${task.cpus} \
- -x ${index_id} \
- -1 ${reads[0]} \
- -2 ${reads[1]} 2> \
-${pair_id}_hisat2_report.txt | \
-samtools view -Sb - > ${pair_id}.bam
-
-if grep -q "Error" ${pair_id}_hisat2_report.txt; then
+hisat2 -x ${index_id} \
+ -p ${task.cpus} \
+ -1 ${fastq_filtred[0]} \
+ -2 ${fastq_filtred[1]} \
+ --un-conc-gz ${pair_id}_notaligned_R%.fastq.gz \
+ --rna-strandness 'FR' \
+ --dta \
+ --no-softclip\
+ --trim3 1\
+ --trim5 1\
+ 2> ${pair_id}_report.txt \
+| samtools view -bS -F 4 - \
+| samtools sort -@ ${task.cpus} -o ${pair_id}.bam \
+&& samtools index ${pair_id}.bam
+
+if grep -q "ERR" ${pair_id}.txt; then
exit 1
fi
+
"""
}
diff --git a/src/nf_modules/kallisto/indexing.config b/src/nf_modules/kallisto/indexing.config
index 52d83cf2..b60183d3 100644
--- a/src/nf_modules/kallisto/indexing.config
+++ b/src/nf_modules/kallisto/indexing.config
@@ -3,7 +3,7 @@ profiles {
docker.temp = "auto"
docker.enabled = true
process {
- withName index_fasta {
+ withName: index_fasta {
container = "lbmc/kallisto:0.44.0"
cpus = 4
}
diff --git a/src/nf_modules/kallisto/indexing.nf b/src/nf_modules/kallisto/indexing.nf
index ea153569..ed3c282c 100644
--- a/src/nf_modules/kallisto/indexing.nf
+++ b/src/nf_modules/kallisto/indexing.nf
@@ -9,7 +9,7 @@ Channel
process index_fasta {
tag "$fasta.baseName"
- publishDir "results/mapping/index/", mode: 'copy'
+ publishDir "results/index/", mode: 'copy'
input:
file fasta from fasta_file
diff --git a/src/nf_modules/kallisto/mapping_paired.nf b/src/nf_modules/kallisto/mapping_paired.nf
index 455e70cd..65dfc151 100644
--- a/src/nf_modules/kallisto/mapping_paired.nf
+++ b/src/nf_modules/kallisto/mapping_paired.nf
@@ -1,8 +1,10 @@
params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
params.index = "$baseDir/data/index/*.index.*"
+params.output = "results/mapping/quantification/"
log.info "fastq files : ${params.fastq}"
log.info "index files : ${params.index}"
+log.info "output folder : ${params.output}"
Channel
.fromFilePairs( params.fastq )
@@ -15,7 +17,7 @@ Channel
process mapping_fastq {
tag "$reads"
- publishDir "results/mapping/quantification/", mode: 'copy'
+ publishDir "${params.output}", mode: 'copy'
input:
set pair_id, file(reads) from fastq_files
--
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