From 20cd5076aaa0fa163ace013f262dc20e738df731 Mon Sep 17 00:00:00 2001 From: skchronicles Date: Wed, 26 Jun 2024 16:53:06 -0400 Subject: [PATCH] Run partition option cannot be run on a single GPU and is not compatible with --gvcf flag --- workflow/rules/germline.smk | 10 +++------- 1 file changed, 3 insertions(+), 7 deletions(-) diff --git a/workflow/rules/germline.smk b/workflow/rules/germline.smk index c60716c..60ad96e 100644 --- a/workflow/rules/germline.smk +++ b/workflow/rules/germline.smk @@ -94,7 +94,7 @@ rule parabricks_gatk_germline_1gpu_normal_memory_optimized: output: bam = join(workpath, "gatk_germline", "1gpu_normal_memory_optimized", "{sample}", "{name}.bam"), # Gzipped VCF cannot be created with --run-partition option - gvcf = join(workpath, "gatk_germline", "1gpu_normal_memory_optimized", "{sample}", "{name}.g.vcf"), + gvcf = join(workpath, "gatk_germline", "1gpu_normal_memory_optimized", "{sample}", "{name}.vcf"), recal = join(workpath, "gatk_germline", "1gpu_normal_memory_optimized", "{sample}", "{name}.recal"), params: # Rule specific parameters @@ -135,14 +135,12 @@ rule parabricks_gatk_germline_1gpu_normal_memory_optimized: --out-bam {output.bam} \\ --out-variants {output.gvcf} \\ --out-recal-file {output.recal} \\ - --gvcf \\ --bwa-options="-M" \\ --monitor-usage \\ --memory-limit {params.RUNNING_MEMORY_GB} \\ --tmp-dir /tmp \\ --num-cpu-threads-per-stage {threads} \\ --bwa-cpu-thread-pool {threads} \\ - --run-partition \\ --read-from-tmp-dir \\ --gpusort \\ --gpuwrite \\ @@ -379,7 +377,7 @@ rule parabricks_gatk_germline_2gpu_normal_memory_optimized: output: bam = join(workpath, "gatk_germline", "2gpu_normal_memory_optimized", "{sample}", "{name}.bam"), # Gzipped VCF cannot be created with --run-partition option - gvcf = join(workpath, "gatk_germline", "2gpu_normal_memory_optimized", "{sample}", "{name}.g.vcf"), + gvcf = join(workpath, "gatk_germline", "2gpu_normal_memory_optimized", "{sample}", "{name}.vcf"), recal = join(workpath, "gatk_germline", "2gpu_normal_memory_optimized", "{sample}", "{name}.recal"), params: # Rule specific parameters @@ -420,7 +418,6 @@ rule parabricks_gatk_germline_2gpu_normal_memory_optimized: --out-bam {output.bam} \\ --out-variants {output.gvcf} \\ --out-recal-file {output.recal} \\ - --gvcf \\ --bwa-options="-M" \\ --monitor-usage \\ --memory-limit {params.RUNNING_MEMORY_GB} \\ @@ -596,7 +593,7 @@ rule parabricks_gatk_germline_4gpu_normal_memory_optimized: output: bam = join(workpath, "gatk_germline", "4gpu_normal_memory_optimized", "{sample}", "{name}.bam"), # Gzipped VCF cannot be created with --run-partition option - gvcf = join(workpath, "gatk_germline", "4gpu_normal_memory_optimized", "{sample}", "{name}.g.vcf"), + gvcf = join(workpath, "gatk_germline", "4gpu_normal_memory_optimized", "{sample}", "{name}.vcf"), recal = join(workpath, "gatk_germline", "4gpu_normal_memory_optimized", "{sample}", "{name}.recal"), params: # Rule specific parameters @@ -637,7 +634,6 @@ rule parabricks_gatk_germline_4gpu_normal_memory_optimized: --out-bam {output.bam} \\ --out-variants {output.gvcf} \\ --out-recal-file {output.recal} \\ - --gvcf \\ --bwa-options="-M" \\ --monitor-usage \\ --memory-limit {params.RUNNING_MEMORY_GB} \\