From 36bb93c1215928479a8edef0bd3ca93b8e12f417 Mon Sep 17 00:00:00 2001
From: elabaron <emmanuel.labaronne@ens-lyon.fr>
Date: Thu, 16 Jul 2020 17:19:54 +0200
Subject: [PATCH] fix beug for psmn
---
src/RNAseq.config | 15 +++++++++++++--
src/RNAseq.nf | 17 +++++++++++++----
src/RNAseq_illumina.nf | 32 +++++++++++++++++++++++++++++++-
src/norm_coverage.sh | 29 +++++++++++++++++++----------
4 files changed, 76 insertions(+), 17 deletions(-)
diff --git a/src/RNAseq.config b/src/RNAseq.config
index 33593dc0..cc96d3ab 100644
--- a/src/RNAseq.config
+++ b/src/RNAseq.config
@@ -27,6 +27,7 @@ profiles {
clusterOptions = "-cwd -V"
memory = "20GB"
cpus = 16
+ penv = 'openmp16'
time = "12h"
queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
penv = 'openmp16'
@@ -42,8 +43,7 @@ profiles {
queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
}
withName: counting {
- beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "htseq/0.11.2"
+ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules; module purge; module load htseq/0.11.2"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
@@ -51,6 +51,17 @@ profiles {
time = "12h"
queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
}
+ withName: coverage{
+ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+ module = "deeptools/3.0.2"
+ executor = "sge"
+ clusterOptions = "-cwd -V"
+ cpus = 16
+ memory = "30GB"
+ time = "24h"
+ penv = 'openmp16'
+ queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
+ }
}
}
docker {
diff --git a/src/RNAseq.nf b/src/RNAseq.nf
index 791d4b0a..bb673adc 100644
--- a/src/RNAseq.nf
+++ b/src/RNAseq.nf
@@ -4,6 +4,10 @@
params.fastq_raw = "data/demultiplexed/*{_R1,_R2}.fastq.gz"
params.output = "results"
+params.script_cov = "src/norm_coverage.sh"
+
+log.info "script for coverage : ${script_cov}"
+
Channel
.fromFilePairs(params.fastq_raw)
@@ -27,8 +31,7 @@ process trimming {
script:
"""
- cutadapt -a AGATCGGAAGAGC -A AGATCGGAAGAGC \
- --minimum-length 50 \
+ cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT \
-o ${file_id}_cut_R1.fastq.gz -p ${file_id}_tmp_R2.fastq.gz \
${reads[0]} ${reads[1]} > ${file_id}_report.txt
@@ -129,7 +132,7 @@ samtools index ${file_id}_sorted.bam
"""
}
-sorted_bam_files.into{sorted_bam_htseq, sorted_bam_coverage}
+sorted_bam_files.into{sorted_bam_htseq; sorted_bam_coverage}
/* HTseq */
@@ -190,19 +193,25 @@ htseq-count ${bam[0]} ${gtf} \
"""
}
+Channel
+ .fromFilePairs(params.script_cov)
+ .ifEmpty { error "Cannot find any file matching: ${params.script_cov}" }
+ .set {script_channel}
+
process coverage {
tag "$file_id"
publishDir "${params.output}/05_coverage/", mode: 'copy'
input:
set file_id, file(bam) from sorted_bam_coverage
+ set script from script_channel.collect()
output:
file "*.bw" into coverage_files
script:
"""
-bash src/norm_coverage.sh -b ${bam} \
+bash ${script} -b ${bam} \
-o {file_id}.bw \
--binSize 1 \
-p ${cpus} 8
diff --git a/src/RNAseq_illumina.nf b/src/RNAseq_illumina.nf
index b1e93381..8c70bd89 100644
--- a/src/RNAseq_illumina.nf
+++ b/src/RNAseq_illumina.nf
@@ -4,6 +4,10 @@
params.fastq_raw = "data/demultiplexed/*{_R1,_R2}.fastq.gz"
params.output = "results"
+params.script_cov = "src/norm_coverage.sh"
+
+log.info "script for coverage : ${params.script_cov}"
+
Channel
.fromFilePairs(params.fastq_raw)
@@ -127,6 +131,7 @@ samtools index ${file_id}_sorted.bam
"""
}
+sorted_bam_files.into{sorted_bam_htseq; sorted_bam_coverage}
/* HTseq */
@@ -134,7 +139,7 @@ process sort_bam {
tag "$file_id"
input:
- set file_id, file(bam) from sorted_bam_files
+ set file_id, file(bam) from sorted_bam_htseq
output:
set file_id, "*_htseq.bam" into sorted_bam_files_2
@@ -186,3 +191,28 @@ htseq-count ${bam[0]} ${gtf} \
"""
}
+
+Channel
+ .fromPath(params.script_cov)
+ .ifEmpty { error "Cannot find any file matching: ${params.script_cov}" }
+ .set {script_channel}
+
+process coverage {
+ tag "$file_id"
+ publishDir "${params.output}/05_coverage/", mode: 'copy'
+
+ input:
+ set file_id, file(bam) from sorted_bam_coverage
+ set script from script_channel.collect()
+
+ output:
+ file "*.bw" into coverage_files
+
+ script:
+"""
+bash ${script} -b ${bam[0]} \
+ -o ${file_id}.bw \
+ --binSize 1 \
+ -p ${task.cpus}
+"""
+}
diff --git a/src/norm_coverage.sh b/src/norm_coverage.sh
index 8dcf4c83..b5485369 100644
--- a/src/norm_coverage.sh
+++ b/src/norm_coverage.sh
@@ -2,33 +2,42 @@
set -e
-usage() { echo "Usage: $0 -b <bamfile.bam> -o <outputName> --binSize <int> -p <CPUs>" 1>&2; exit 1; }
+usage() { echo "Usage: $0 -b <bamfile.bam> -o <outputName> -s <binSize> -p <CPUs>" 1>&2; exit 1; }
cpus=4
binSize=1
-while getopts "b:o:binSize:p:" arg; do
+while getopts "hb:o:s:p:" arg; do
case $arg in
- -h)
- echo "usage"
+ h)
+ usage
;;
- -b)
+ b)
bam=$OPTARG
;;
- -o)
+ o)
output=$OPTARG
;;
- --binSize)
+ s)
binSize=$OPTARG
;;
- -p)
+ p)
cpus=$OPTARG
;;
+ \?)
+ echo "$OPTARG : invalid option"
+ usage
+ ;;
+ :)
+ echo "$OPTARG requiert an argument"
+ usage
+ ;;
+
esac
done
hg38=$(samtools view ${bam} | awk '{print $1}' | sort | uniq | wc -l)
factor=$(echo "1000000/($hg38)" | bc -l)
echo "hg38 counts : $hg38"
-echo "scaling factor : $factor\n"
-bamCoverage -p ${cpus} --scaleFactor ${factor} --binSize ${binSize} -b ${bam} -o ${output}
+echo "scaling factor : $factor"
+echo "bamCoverage -p ${cpus} --scaleFactor ${factor} --binSize ${binSize} -b ${bam} -o ${output}"
--
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