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BICF
Astrocyte
cellranger_mkfastq
Commits
d5ba8a06
Commit
d5ba8a06
authored
Apr 25, 2019
by
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
Changes
4
Pipelines
1
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workflow/conf/biohpc.config
View file @
d5ba8a06
...
...
@@ -20,7 +20,7 @@ process {
executor
=
'super'
}
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'
}
withLabel
:
multiqc
{
...
...
workflow/main.nf
View file @
d5ba8a06
...
...
@@ -84,7 +84,6 @@ process mkfastq {
file("**/outs/**/*.fastq.gz") into fastqPaths
file("**/outs/fastq_path/Stats/Stats.json") into bqcPaths
file("version*.txt") into versionPaths_mkfastq
val "${bcl.baseName}" into bclName
script:
...
...
@@ -92,7 +91,6 @@ process mkfastq {
"""
hostname
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
"""
}
...
...
@@ -110,7 +108,6 @@ process fastqc {
output:
file("*fastqc.zip") into fqcPaths
file("version*.txt") into versionPaths_fastqc
script:
...
...
@@ -125,12 +122,10 @@ process fastqc {
process versions {
tag "$name"
publishDir "$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:
file versionPaths_mkfastq
file versionPaths_fastqc
output:
...
...
@@ -142,14 +137,12 @@ process versions {
hostname
ulimit -a
echo $workflow.nextflow.version > version_nextflow.txt
sh $baseDir/scripts/versions_mkfastq.sh
bash $baseDir/scripts/versions_fastqc.sh
python3 $baseDir/scripts/generate_versions.py -f version_*.txt -o versions
"""
}
bqcPathsAll = Channel
.from(bqcPaths)
.collect()
process multiqc {
tag "$name"
queue 'super'
...
...
@@ -158,8 +151,8 @@ process multiqc {
input:
file bqc
PathsAll
file fqc
Paths
file bqc
name "bqc/?/*" from bqcPaths.collect()
file fqc
name "fqc/?/*" from fqcPaths.collect()
file yamlPaths
output:
...
...
workflow/scripts/fastqc.sh
View file @
d5ba8a06
...
...
@@ -5,4 +5,3 @@ find . -name '*.fastq.gz' | awk '{printf("fastqc \"%s\"\n", $0)}' | parallel -j
#for i in `ls *.fastq.gz`;
#do echo "fastqc ${i}";
#done | parallel -j `grep -c ^processor /proc/cpuinfo` --verbose;
fastqc
--version
|
grep
'FastQC v'
|
sed
-n
-e
's/^FastQC v//p'
>
version_fastqc.txt
workflow/scripts/versions_fastqc.sh
0 → 100644
View file @
d5ba8a06
#!/bin/bash
fastqc
--version
|
grep
'FastQC v'
|
sed
-n
-e
's/^FastQC v//p'
>
version_fastqc.txt
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