Commit d5ba8a06 authored by Gervaise Henry's avatar Gervaise Henry 🤠
Browse files

Split version file gen to separate process, run single version/multiqc process

parent 42d035c6
Pipeline #3635 passed with stages
in 1 minute and 29 seconds
...@@ -20,7 +20,7 @@ process { ...@@ -20,7 +20,7 @@ process {
executor = 'super' executor = 'super'
} }
withLabel:versions { withLabel:versions {
module = ['python/3.6.1-2-anaconda'] module = ['python/3.6.1-2-anaconda', 'cellranger/3.0.2', 'bcl2fastq/2.19.1', 'fastqc/0.11.5']
executor = 'local' executor = 'local'
} }
withLabel:multiqc { withLabel:multiqc {
......
...@@ -84,7 +84,6 @@ process mkfastq { ...@@ -84,7 +84,6 @@ process mkfastq {
file("**/outs/**/*.fastq.gz") into fastqPaths file("**/outs/**/*.fastq.gz") into fastqPaths
file("**/outs/fastq_path/Stats/Stats.json") into bqcPaths file("**/outs/fastq_path/Stats/Stats.json") into bqcPaths
file("version*.txt") into versionPaths_mkfastq
val "${bcl.baseName}" into bclName val "${bcl.baseName}" into bclName
script: script:
...@@ -92,7 +91,6 @@ process mkfastq { ...@@ -92,7 +91,6 @@ process mkfastq {
""" """
hostname hostname
ulimit -a ulimit -a
sh $baseDir/scripts/versions_mkfastq.sh
cellranger mkfastq --id="${bcl.baseName}" --run=$bcl --csv=$design -r \$SLURM_CPUS_ON_NODE -p \$SLURM_CPUS_ON_NODE -w \$SLURM_CPUS_ON_NODE cellranger mkfastq --id="${bcl.baseName}" --run=$bcl --csv=$design -r \$SLURM_CPUS_ON_NODE -p \$SLURM_CPUS_ON_NODE -w \$SLURM_CPUS_ON_NODE
""" """
} }
...@@ -110,7 +108,6 @@ process fastqc { ...@@ -110,7 +108,6 @@ process fastqc {
output: output:
file("*fastqc.zip") into fqcPaths file("*fastqc.zip") into fqcPaths
file("version*.txt") into versionPaths_fastqc
script: script:
...@@ -125,12 +122,10 @@ process fastqc { ...@@ -125,12 +122,10 @@ process fastqc {
process versions { process versions {
tag "$name" tag "$name"
publishDir "$outDir/misc/${task.process}/$name", mode: 'copy' publishDir "$outDir/misc/${task.process}/$name", mode: 'copy'
module 'python/3.6.1-2-anaconda' module 'python/3.6.1-2-anaconda:cellranger/3.0.2:bcl2fastq/2.19.1:fastqc/0.11.5'
input: input:
file versionPaths_mkfastq
file versionPaths_fastqc
output: output:
...@@ -142,14 +137,12 @@ process versions { ...@@ -142,14 +137,12 @@ process versions {
hostname hostname
ulimit -a ulimit -a
echo $workflow.nextflow.version > version_nextflow.txt echo $workflow.nextflow.version > version_nextflow.txt
sh $baseDir/scripts/versions_mkfastq.sh
bash $baseDir/scripts/versions_fastqc.sh
python3 $baseDir/scripts/generate_versions.py -f version_*.txt -o versions python3 $baseDir/scripts/generate_versions.py -f version_*.txt -o versions
""" """
} }
bqcPathsAll = Channel
.from(bqcPaths)
.collect()
process multiqc { process multiqc {
tag "$name" tag "$name"
queue 'super' queue 'super'
...@@ -158,8 +151,8 @@ process multiqc { ...@@ -158,8 +151,8 @@ process multiqc {
input: input:
file bqcPathsAll file bqc name "bqc/?/*" from bqcPaths.collect()
file fqcPaths file fqc name "fqc/?/*" from fqcPaths.collect()
file yamlPaths file yamlPaths
output: output:
......
...@@ -5,4 +5,3 @@ find . -name '*.fastq.gz' | awk '{printf("fastqc \"%s\"\n", $0)}' | parallel -j ...@@ -5,4 +5,3 @@ find . -name '*.fastq.gz' | awk '{printf("fastqc \"%s\"\n", $0)}' | parallel -j
#for i in `ls *.fastq.gz`; #for i in `ls *.fastq.gz`;
#do echo "fastqc ${i}"; #do echo "fastqc ${i}";
#done | parallel -j `grep -c ^processor /proc/cpuinfo` --verbose; #done | parallel -j `grep -c ^processor /proc/cpuinfo` --verbose;
fastqc --version | grep 'FastQC v' | sed -n -e 's/^FastQC v//p' > version_fastqc.txt
#!/bin/bash
fastqc --version | grep 'FastQC v' | sed -n -e 's/^FastQC v//p' > version_fastqc.txt
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment