diff --git a/src/nextflow.config b/src/nextflow.config index dfebf4d31a76c838e52220135f1a430972d1d698..df01d720d2cf26b934e32739a9cced9e7b3d209b 100644 --- a/src/nextflow.config +++ b/src/nextflow.config @@ -17,6 +17,7 @@ profiles { docker.temp = "auto" docker.enabled = true process { + memory = '16 GB' withLabel: big_mem_mono_cpus { cpus = 1 } @@ -29,6 +30,7 @@ profiles { singularity.enabled = true singularity.cacheDir = "./bin/" process { + memory = '16 GB' withLabel: big_mem_mono_cpus { cpus = 1 } @@ -46,7 +48,7 @@ profiles { executor = "sge" clusterOptions = "-cwd -V" cpus = 1 - memory = "20GB" + memory = "128GB" time = "12h" queue = "monointeldeb128" } @@ -55,7 +57,7 @@ profiles { executor = "sge" clusterOptions = "-cwd -V" cpus = 32 - memory = "30GB" + memory = "192GB" time = "24h" queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D" penv = "openmp32" @@ -75,6 +77,7 @@ profiles { executor = "sge" clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n" cpus = 1 + memory = "8GB" queue = "huge" } withLabel: big_mem_multi_cpus { @@ -83,9 +86,9 @@ profiles { stageInMode = "copy" stageOutMode = "rsync" executor = "sge" - clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\ - " + clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n" cpus = 1 + memory = "8GB" queue = "huge" } } diff --git a/src/nf_modules/picard/main.nf b/src/nf_modules/picard/main.nf index 9a6b702fa48cfbbb0d2d95ac8a0f8ae9f5e22e76..0faec2e001ce79e92c6377abfc07e2a7b6138b22 100644 --- a/src/nf_modules/picard/main.nf +++ b/src/nf_modules/picard/main.nf @@ -6,7 +6,6 @@ process mark_duplicate { label "big_mem_mono_cpus" tag "$file_id" publishDir "results/mapping/ddup/", mode: 'copy' - memory '30 GB' input: tuple val(file_id), path(bam)