Commit 42d035c6 authored by Gervaise Henry's avatar Gervaise Henry 🤠
Browse files

Run multiple mkfastq if multiple bcls

parent de4aab57
Pipeline #3633 passed with stages
in 1 minute and 39 seconds
......@@ -53,7 +53,7 @@ process untarBCL {
output:
file("*") into bclPaths
file("*") into bclPaths mode flatten
script:
......@@ -62,12 +62,13 @@ process untarBCL {
ulimit -a
name=`echo ${tar} | rev | cut -f1 -d '.' | rev`;
if [ "\${name}" == "gz" ];
then tar -xvf ${tar} -I pigz;
else tar -xvf ${tar};
then tar -xvf $tar -I pigz;
else tar -xvf $tar;
fi;
"""
}
process mkfastq {
tag "${bcl.baseName}"
queue '128GB,256GB,256GBv1,384GB'
......@@ -76,8 +77,8 @@ process mkfastq {
input:
val bcl from bclPaths
file designPaths
each bcl from bclPaths.collect()
file design from designPaths
output:
......@@ -92,11 +93,10 @@ process mkfastq {
hostname
ulimit -a
sh $baseDir/scripts/versions_mkfastq.sh
cellranger mkfastq --id="${bcl.baseName}" --run=$bcl --csv=$designPaths -r \$SLURM_CPUS_ON_NODE -p \$SLURM_CPUS_ON_NODE -w \$SLURM_CPUS_ON_NODE
cellranger mkfastq --id="${bcl.baseName}" --run=$bcl --csv=$design -r \$SLURM_CPUS_ON_NODE -p \$SLURM_CPUS_ON_NODE -w \$SLURM_CPUS_ON_NODE
"""
}
process fastqc {
tag "$bclName"
queue 'super'
......
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