From 4e91fc2e041a81324e8d33ba2ac776cc8df6d689 Mon Sep 17 00:00:00 2001 From: Maarten Kooyman Date: Fri, 3 Apr 2020 14:24:54 +0200 Subject: [PATCH] parse amount of threads to beagle If no amount of threads is given to beagle, all available cores will be used. This might leads to problems on shared compute resource systems(e.g. slurm) --- process.smake | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/process.smake b/process.smake index 6a31bd9..69f8e9d 100644 --- a/process.smake +++ b/process.smake @@ -19,7 +19,7 @@ rule phase_with_ref: ref_sample = get_ref_sample() threads: 64 shell: - "beaglew impute=false gt={input} ref={params.ref_sample}/{wildcards.file}.vcf.gz out={params.prefix}" + "beaglew impute=false gt={input} ref={params.ref_sample}/{wildcards.file}.vcf.gz out={params.prefix} nthreads={threads}" # # Phase WITHOUT Reference Geonme @@ -34,7 +34,7 @@ rule phase_without_ref: prefix="{dir}_PH/{file}" threads: 64 shell: - "beaglew impute=false gt={input} out={params.prefix}" + "beaglew impute=false gt={input} out={params.prefix} nthreads={threads}" #