diff --git a/workflow/conf/dnanexus.config b/workflow/conf/dnanexus.config new file mode 100755 index 0000000000000000000000000000000000000000..0dbcbaaec877b7c5f7398ae605d30b274b119ac2 --- /dev/null +++ b/workflow/conf/dnanexus.config @@ -0,0 +1,91 @@ +params { + refSource = "prod" +} + +process { + withName:trackStart { + executor = 'local' + } + withName:getBag { + executor = 'local' + } + withName:getData { + machineType = 'mem1_ssd1_v2_x16' + } + withName:parseMetadata { + executor = 'local' + } + withName:trimData { + machineType = 'mem1_ssd1_v2_x16' + } + withName:getRefInfer { + machineType = 'mem1_ssd1_v2_x16' + } + withName:downsampleData { + executor = 'local' + } + withName:alignSampleData { + machineType = 'mem3_ssd1_v2_x16' + } + withName:inferMetadata { + machineType = 'mem1_ssd1_v2_x16' + } + withName:checkMetadata { + executor = 'local' + } + withName:getRef { + machineType = 'mem1_ssd1_v2_x16' + } + withName:alignData { + queue = '256GB,256GBv1' + } + withName:dedupData { + machineType = 'mem1_ssd1_v2_x16' + } + withName:countData { + machineType = 'mem1_ssd1_v2_x16' + } + withName:makeBigWig { + machineType = 'mem1_ssd1_v2_x16' + } + withName:fastqc { + machineType = 'mem1_ssd1_v2_x16' + } + withName:dataQC { + machineType = 'mem1_ssd1_v2_x16' + } + withName:aggrQC { + executor = 'local' + } + withName:uploadInputBag { + executor = 'local' + } + withName:uploadExecutionRun { + executor = 'local' + } + withName:uploadQC { + executor = 'local' + } + withName:uploadProcessedFile { + executor = 'local' + } + withName:uploadOutputBag { + executor = 'local' + } + withName:finalizeExecutionRun { + executor = 'local' + } + withName:failPreExecutionRun { + executor = 'local' + } + withName:failExecutionRun { + executor = 'local' + } + withName:uploadQC_fail { + executor = 'local' + } +} + +docker { + enabled = true +} diff --git a/workflow/nextflow.config b/workflow/nextflow.config index 44f2df5255691ee4eaf11ecf9cee1af2fa27f743..927e6055431a8c18dfedd0ef3817ceef61873a62 100644 --- a/workflow/nextflow.config +++ b/workflow/nextflow.config @@ -16,6 +16,9 @@ profiles { includeConfig 'conf/aws.config' includeConfig 'conf/spot.config' } + dnanexus { + includeConfig 'conf/dnanexus.config' + } } process {