diff --git a/workflow/main.nf b/workflow/main.nf index 7ed5bcafc9dc998145ce258cde014c8bb5480f39..bb2946dd50a3ec192ccf8c62bf4cec31eb067289 100755 --- a/workflow/main.nf +++ b/workflow/main.nf @@ -14,16 +14,12 @@ params.forceCells = 0 params.kitVersion = 'three' params.version = '3.0.2' -params.astrocyte = 'false' +params.astrocyte = false params.outDir = "$baseDir/output" // Assign variables if astrocyte -if (params.astrocyte == 'false') { - 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 -} else if (params.astrocyte == 'true') { +if (params.astrocyte) { + print("Running under astrocyte") params.genomeLocation = '/project/apps_database/cellranger/refdata-cellranger-' if (params.kitVersion == "one") { params.chemistryParam ='SC3Pv1' @@ -34,6 +30,12 @@ if (params.astrocyte == 'false') { } else { params.chemistryParam = 'auto' } +} 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.genomeLocationFull = params.genomeLocation+params.genome