process { executor = 'slurm' queue='super' // Process specific configuration $checkDesignFile { module = ['python/3.6.1-2-anaconda'] executor = 'local' } $count211 { module = ['cellranger/2.1.1'] queue = '128GB,256GB,256GBv1,384GB' } $count301 { module = ['cellranger/3.0.1'] queue = '128GB,256GB,256GBv1,384GB' } $count302 { module = ['cellranger/3.0.2'] queue = '128GB,256GB,256GBv1,384GB' } } params { // Reference file paths on BioHPC genomes { 'GRCh38-3.0.0' { loc = '/project/apps_database/cellranger/refdata-cellranger-' } 'GRCh38-1.2.0' { loc = '/project/apps_database/cellranger/refdata-cellranger-' } 'hg19-3.0.0' { loc = '/project/apps_database/cellranger/refdata-cellranger-' } 'hg19-1.2.0' { loc = '/project/apps_database/cellranger/refdata-cellranger-' } 'mm10-3.0.0' { loc = '/project/apps_database/cellranger/refdata-cellranger-' } 'mm10-1.2.0' { loc = '/project/apps_database/cellranger/refdata-cellranger-' } 'hg19_and_mm10-3.0.0' { loc = '/project/apps_database/cellranger/refdata-cellranger-' } 'hg19_and_mm10-1.2.0' { loc = '/project/apps_database/cellranger/refdata-cellranger-' } 'ercc92-1.2.0' { loc = '/project/apps_database/cellranger/refdata-cellranger-' } } // Chemistry mapping parameter chemistry { 'auto' { param = 'auto' } 'one' { param = 'SC3Pv1' } 'two' { param = 'SC3Pv2' } 'three' { param = 'SC3Pv3' } } } trace { enabled = true file = 'pipeline_trace.txt' fields = 'task_id,native_id,process,name,status,exit,submit,start,complete,duration,realtime,%cpu,%mem,rss' } timeline { enabled = true file = 'timeline.html' } report { enabled = true file = 'report.html' }