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Commit f1075bf9 authored by Holly Ruess's avatar Holly Ruess
Browse files

fixed main for output dir

parent e9181445
1 merge request!3Resolve "update check design file"
Pipeline #5243 passed with stages
in 6 hours, 18 minutes, and 5 seconds
......@@ -15,6 +15,7 @@ params.bwaIndex = params.genome ? params.genomes[ params.genome ].bwa ?: false :
params.genomeSize = params.genome ? params.genomes[ params.genome ].genomesize ?: false : false
params.chromSizes = params.genome ? params.genomes[ params.genome ].chromsizes ?: false : false
params.tssFile = params.genome ? params.genomes[ params.genome ].tssfile ?: false : false
params.astrocyte = false
params.outDir= "${baseDir}/output"
// Check inputs
......@@ -40,6 +41,7 @@ tn5 = params.tn5
designFile = params.designFile
genomeSize = params.genomeSize
chromSizes = params.chromSizes
outDir = params.outDir
//tssFile = params.tssFile
process checkDesignFile {
......@@ -54,15 +56,31 @@ process checkDesignFile {
file("design.tsv") into designFilePaths
script:
if (pairedEnd) {
"""
python3 ${baseDir}/scripts/check_design.py -d ${designFile} -f ${readsList} -p -a
"""
if (params.astrocyte == true) {
if (pairedEnd) {
"""
module load python/3.6.1-2-anaconda
python3 ${baseDir}/scripts/check_design.py -d ${designFile} -f ${readsList} -p -a
"""
}
else {
"""
module load python/3.6.1-2-anaconda
python3 ${baseDir}/scripts/check_design.py -d ${designFile} -f ${readsList} -a
"""
}
}
else {
"""
python3 ${baseDir}/scripts/check_design.py -d ${designFile} -f ${readsList} -a
"""
if (pairedEnd) {
"""
python3 ${baseDir}/scripts/check_design.py -d ${designFile} -f ${readsList} -p -a
"""
}
else {
"""
python3 ${baseDir}/scripts/check_design.py -d ${designFile} -f ${readsList} -a
"""
}
}
}
......
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