diff --git a/workflows/conf/docker.conf b/workflows/conf/docker.conf index 5a33863..8d72a9a 100644 --- a/workflows/conf/docker.conf +++ b/workflows/conf/docker.conf @@ -2,6 +2,26 @@ process { docker.runOptions = '-u $(id -u):$(id -g)' + // Parabricks configurations + // Specify the GPU devices visible to each process + withName:'pbrun_fq2bam' { + container = "nvcr.io/nvidia/clara/clara-parabricks:4.3.0-1" + containerOptions = '--gpus \'"device=0,1,2,3"\' --rm' + } + withName:'pbrun_applybqsr' { + container = "nvcr.io/nvidia/clara/clara-parabricks:4.3.0-1" + containerOptions = '--gpus \'"device=0"\' --rm' + } + withName:'pbrun_haplotypecaller' { + container = "nvcr.io/nvidia/clara/clara-parabricks:4.3.0-1" + containerOptions = '--gpus \'"device=0,1,2,3"\' --rm' + } + withName:'pbrun_deepvariant' { + container = "nvcr.io/nvidia/clara/clara-parabricks:4.3.0-1" + containerOptions = '--gpus \'"device=0,1,2,3"\' --rm' + } + + withName:'bwa' { container = "pubudusaneth/bwa_samtools_amd64:v0.7.17.v1.18" // Source: https://github.com/NAICNO/NAIC-Dockerfiles/blob/main/bwa-samtools/Dockerfile @@ -9,10 +29,6 @@ process { withName:'gatk_.*' { container = "docker.io/broadinstitute/gatk:4.3.0.0" } - withName:'pbrun_.*' { - container = "nvcr.io/nvidia/clara/clara-parabricks:4.3.0-1" - containerOptions = '--gpus all --rm' - } withName:"deepvariant" { container = "google/deepvariant:1.5.0" } diff --git a/workflows/conf/resource.conf b/workflows/conf/resource.conf index 54e15aa..3c3e499 100644 --- a/workflows/conf/resource.conf +++ b/workflows/conf/resource.conf @@ -30,14 +30,28 @@ process { cpus='12' } + // Parabricks configurations + // Specify resources for each process + + withName:'pbrun_fq2bam' { + memory='120 GB' + cpus='42' + gpu='4' + } // pbrun_applybqsr is recommended to run on 1 GPU withName:'pbrun_applybqsr' { + memory='120 GB' + cpus='42' gpu='1' } withName:'pbrun_deepvariant' { + memory='120 GB' + cpus='42' gpu='4' } withName:'pbrun_haplotypecaller' { + memory='120 GB' + cpus='42' gpu='4' }