Commit 661cb8de authored by Gervaise Henry's avatar Gervaise Henry 🤠
Browse files

Add mask as a param (non-Astrocyte)

parent 6d14bd6c
......@@ -12,6 +12,7 @@ main.nf
params.name = "run"
params.bcl = "${baseDir}/../test_data/simple1/*.tar.gz"
params.designFile = "${baseDir}/../test_data/single1/cellranger-tiny-bcl-simple-1_2_0.csv"
params.mask = ""
params.outDir = "${baseDir}/output"
// Define list of files
......@@ -26,6 +27,7 @@ name = params.name
designLocation = Channel
.fromPath(params.designFile)
.ifEmpty { exit 1, "design file not found: ${params.designFile}" }
mask = params.mask
outDir = params.outDir
// Define script files
......@@ -76,10 +78,6 @@ process checkDesignFile {
"""
}
/* nextflow workflow version calls that aren't compatible with nextflow 0.31.0
echo "${workflow.manifest.version}" > version_pipeline.txt
echo "${workflow.nextflow.version}" > version_nextflow.txt
*/
process untarBCL {
......@@ -130,7 +128,7 @@ process mkfastq {
hostname
ulimit -u 16384
ulimit -a
cellranger mkfastq --id=mkfastq_${bcl.simpleName} --run=${bcl} --csv=${design} --ignore-dual-index
cellranger mkfastq --id=mkfastq_${bcl.simpleName} --run=${bcl} --csv=${design} --ignore-dual-index ${mask}
mkdir fq
mkdir "fq/${bcl.simpleName}"
find . -name "*.fastq.gz" -exec cp {} fq/${bcl.simpleName}/ \\;
......
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