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Commit a1edc582 authored by Gervaise Henry's avatar Gervaise Henry 🤠
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Set options reguardless of astrocyte

parent 99218b98
2 merge requests!63Develop,!60Resolve "Add 3':5' param"
Pipeline #6524 canceled with stages
...@@ -13,6 +13,7 @@ params.name = "run" ...@@ -13,6 +13,7 @@ params.name = "run"
params.fastq = "${baseDir}/../test_data/*.fastq.gz" params.fastq = "${baseDir}/../test_data/*.fastq.gz"
params.designFile = "${baseDir}/../test_data/design.csv" params.designFile = "${baseDir}/../test_data/design.csv"
params.genome = 'GRCh38-3.0.0' params.genome = 'GRCh38-3.0.0'
params.genomeLocation = '/project/apps_database/cellranger/refdata-cellranger-'
params.expectCells = 10000 params.expectCells = 10000
params.forceCells = 0 params.forceCells = 0
params.kitVersion = '3GEXv3' params.kitVersion = '3GEXv3'
...@@ -27,27 +28,18 @@ if (params.kitVersion == "3GEXv3" && params.version == '2.1.1') { ...@@ -27,27 +28,18 @@ if (params.kitVersion == "3GEXv3" && params.version == '2.1.1') {
System.exit(32) System.exit(32)
} }
// Assign variables if astrocyte if (params.kitVersion == "3GEXv1") {
if (params.astrocyte) { params.chemistryParam ='SC3Pv1'
print("Running under astrocyte") } else if (params.kitVersion == "3GEXv2") {
params.genomeLocation = '/project/apps_database/cellranger/refdata-cellranger-' params.chemistryParam ='SC3Pv2'
if (params.kitVersion == "3GEXv1") { } else if (params.kitVersion == "3GEXv3") {
params.chemistryParam ='SC3Pv1' params.chemistryParam ='SC3Pv3'
} else if (params.kitVersion == "3GEXv2") { } else if (params.kitVersion == "5GEX") {
params.chemistryParam ='SC3Pv2' params.chemistryParam ='fiveprime'
} else if (params.kitVersion == "3GEXv3") {
params.chemistryParam ='SC3Pv3'
} else if (params.kitVersion == "5GEX") {
params.chemistryParam ='fiveprime'
} else {
params.chemistryParam = 'auto'
}
} else { } else {
params.genomes = [] params.chemistryParam = 'auto'
params.genomeLocation = params.genome ? params.genomes[ params.genome ].loc ?: false : false
params.chemistry = []
params.chemistryParam = params.kitVersion ? params.chemistry[ params.kitVersion ].param ?: false : false
} }
params.genomeLocationFull = params.genomeLocation+params.genome params.genomeLocationFull = params.genomeLocation+params.genome
// Define regular variables // Define regular variables
......
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