Commit b7f26684 authored by Gervaise Henry's avatar Gervaise Henry 🤠
Browse files

Add quotes around paths in case of spaces

parent da0674c2
Pipeline #3648 passed with stages
in 3 minutes and 19 seconds
# v1.1.0
# v1.1.1
### User Facing
* Fix design file not visible in Astrocyte
* Fix handling of multiple flowcells in 1 submission
### Background
* Move multiqc config to conf folder
* Add CI test for multiple flowcells
* Add changelog
\ No newline at end of file
* Add changelog
* Quote design/tarball/$baseDir path in processes in case of spaces
### *Known Bugs*
* cellranger mkfastq will not accept spaces in path for run param even if quoted, issue raised on 10XGenomics/cellranger github issue [#31](https://github.com/10XGenomics/cellranger/issues/31)
......@@ -37,7 +37,7 @@ process checkDesignFile {
"""
hostname
ulimit -a
python3 $baseDir/scripts/check_design.py -d $designLocation
python3 "$baseDir/scripts/check_design.py" -d "$designLocation"
"""
}
......@@ -62,8 +62,8 @@ 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 "$tar";
fi;
"""
}
......@@ -91,7 +91,7 @@ process mkfastq {
"""
hostname
ulimit -a
cellranger mkfastq --id="${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
"""
}
......@@ -115,7 +115,7 @@ process fastqc {
hostname
ulimit -a
find *.fastq.gz -exec mv {} $bclName.{} \\;
bash $baseDir/scripts/fastqc.sh
bash "$baseDir/scripts/fastqc.sh"
"""
}
......@@ -138,9 +138,9 @@ 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 $baseDir/scripts/generate_versions.py -f version_*.txt -o versions
bash "$baseDir/scripts/versions_mkfastq.sh"
bash "$baseDir/scripts/versions_fastqc.sh"
python3 "$baseDir/scripts/generate_versions.py" -f version_*.txt -o versions
"""
}
......@@ -165,6 +165,6 @@ process multiqc {
"""
hostname
ulimit -a
multiqc . -c $baseDir/conf/multiqc_config.yaml
multiqc . -c "$baseDir/conf/multiqc_config.yaml"
"""
}
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