diff --git a/workflow/configs/aws.config b/workflow/configs/aws.config index 86a5b3187b7418a2bdc16c1c6cedb4473a204177..5e28c1edf8f29b7ab2d7554a8cc387e08699fb51 100644 --- a/workflow/configs/aws.config +++ b/workflow/configs/aws.config @@ -12,27 +12,27 @@ process { cpus = 1 memory = '1 GB' - withLabel: checkDesignFile { + withName: checkDesignFile { cpus = 2 memory = '1 GB' } - withLabel: count211 { + withName: count211 { cpus = 2 memory = '30 GB' } - withLabel: count302 { + withName: count302 { cpus = 2 memory = '30 GB' } - withLabel: count310 { + withName: count310 { cpus = 2 memory = '30 GB' } - withLabel: versions { + withName: versions { cpus = 3 memory = '1 GB' } - withLabel: multiqc { + withName: multiqc { cpus = 1 memory = '1 GB' } diff --git a/workflow/configs/cluster.config b/workflow/configs/cluster.config index 4685e9b67c56ec662534a04bfc340b16fcd66873..457622ec0b0c25d8a4a901a9204587bff9ef6254 100644 --- a/workflow/configs/cluster.config +++ b/workflow/configs/cluster.config @@ -9,25 +9,25 @@ process { withLabel: checkDesignFile { executor = 'local' } - withLabel: count211 { + withName: count211 { queue = '128GB,256GB,256GBv1,384GB' } - withLabel: count220 { + withName: count220 { queue = '128GB,256GB,256GBv1,384GB' } - withLabel: count302 { + withName: count302 { queue = '128GB,256GB,256GBv1,384GB' } - withLabel: count310 { + withName: count310 { queue = '128GB,256GB,256GBv1,384GB' } - withLabel: count400 { + withName: count400 { queue = '128GB,256GB,256GBv1,384GB' } - withLabel: versions { + withName: versions { executor = 'local' } - withLabel: multiqc { + withName: multiqc { executor = 'local' } } diff --git a/workflow/main.nf b/workflow/main.nf index 34649e653f7b9c83dc554bad7a41e54a0adc8232..b186542a33ceab613434d0b6067d5b3b25d3fbdc 100755 --- a/workflow/main.nf +++ b/workflow/main.nf @@ -22,7 +22,6 @@ params.name = "run" params.fastq = "test_data/mu.v3s1r500/*.fastq.gz" params.designFile = "test_data/mu.v3s1r500/design.csv" params.genome = 'mm10-2020-A' -params.genomeLocation = '/project/apps_database/cellranger/refdata-gex-' params.expectCells = 10000 params.forceCells = 0 params.kitVersion = '3GEXv3' @@ -39,7 +38,11 @@ if (params.kitVersion == "3GEXv3" && params.version == '2.1.1') { // Define variables if astrocyte (or from config) if (params.astrocyte) { print("Running under astrocyte") - params.genomeLocation = '/project/apps_database/cellranger/refdata-cellranger-' + if (params.version == "4.0.0") { + params.genomeLocation = '/project/apps_database/cellranger/refdata-gex-' + } else { + params.genomeLocation = '/project/apps_database/cellranger/refdata-cellranger-' + } if (params.kitVersion == "3GEXv1") { params.chemistryParam ='SC3Pv1' } else if (params.kitVersion == "3GEXv2") { diff --git a/workflow/nextflow.config b/workflow/nextflow.config index c402bf3f2ca76befef3ba984286493637520e3ad..1ab9a50bd365b61631b3df6441a59dd34480855b 100644 --- a/workflow/nextflow.config +++ b/workflow/nextflow.config @@ -1,6 +1,7 @@ profiles { standard { includeConfig 'configs/biohpc.config' + includeConfig 'configs/cluster.config' } biohpc { includeConfig 'configs/biohpc.config'