diff --git a/workflow/main.nf b/workflow/main.nf index 92c55698720d11abfb3f1ea78fb9166dae151e52..e6fa4781e61061d43ecfec174f4619bb9ec5fdd5 100755 --- a/workflow/main.nf +++ b/workflow/main.nf @@ -13,6 +13,7 @@ params.name = "run" params.fastq = "${baseDir}/../test_data/*.fastq.gz" params.designFile = "${baseDir}/../test_data/design.csv" params.genome = 'GRCh38-3.0.0' +params.genomeLocation = '/project/apps_database/cellranger/refdata-cellranger-' params.expectCells = 10000 params.forceCells = 0 params.kitVersion = '3GEXv3' @@ -27,27 +28,18 @@ if (params.kitVersion == "3GEXv3" && params.version == '2.1.1') { System.exit(32) } -// Assign variables if astrocyte -if (params.astrocyte) { - print("Running under astrocyte") - params.genomeLocation = '/project/apps_database/cellranger/refdata-cellranger-' - if (params.kitVersion == "3GEXv1") { - params.chemistryParam ='SC3Pv1' - } else if (params.kitVersion == "3GEXv2") { - params.chemistryParam ='SC3Pv2' - } else if (params.kitVersion == "3GEXv3") { - params.chemistryParam ='SC3Pv3' - } else if (params.kitVersion == "5GEX") { - params.chemistryParam ='fiveprime' - } else { - params.chemistryParam = 'auto' - } +if (params.kitVersion == "3GEXv1") { + params.chemistryParam ='SC3Pv1' +} else if (params.kitVersion == "3GEXv2") { + params.chemistryParam ='SC3Pv2' +} else if (params.kitVersion == "3GEXv3") { + params.chemistryParam ='SC3Pv3' +} else if (params.kitVersion == "5GEX") { + params.chemistryParam ='fiveprime' } else { - params.genomes = [] - 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.chemistryParam = 'auto' } + params.genomeLocationFull = params.genomeLocation+params.genome // Define regular variables