From 80c10136f54a50369f25907633d9b97b598a14b8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?P=C3=A1draic=20Corcoran?= Date: Mon, 19 Feb 2024 15:12:30 +0100 Subject: [PATCH] Update pbrun.smk --- workflow/rules/pbrun.smk | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/workflow/rules/pbrun.smk b/workflow/rules/pbrun.smk index 9976da4..abf1751 100644 --- a/workflow/rules/pbrun.smk +++ b/workflow/rules/pbrun.smk @@ -148,7 +148,7 @@ rule pbrun_mutectcaller_t: extra=config.get("pbrun_mutectcaller_t", {}).get("extra", ""), num_gpus=lambda wildcards: get_num_gpus("pbrun_mutectcaller_t", wildcards), tmp=config.get("pbrun_mutectcaller_t", {}).get( - "tmp_dir", "/parabricks/pbrun_mutectcaller_t/{wildcards.sample}_{wildcards.type}" + "tmp_dir", "parabricks/pbrun_mutectcaller_t/{wildcards.sample}_{wildcards.type}" ), log: "parabricks/pbrun_mutectcaller_t/{sample}_T.vcf.log", @@ -244,7 +244,7 @@ rule pbrun_rna_fq2bam: extra=config.get("pbrun_rna_fq2bam", {}).get("extra", ""), in_fq=get_in_fq, num_gpus=lambda wildcards: get_num_gpus("pbrun_rna_fq2bam", wildcards), - tmp=config.get("pbrun_rna_fq2bam", {}).get("tmp_dir", "/parabricks/pbrun_rna_fq2bam/{wildcards.sample}_{wildcards.type}"), + tmp=config.get("pbrun_rna_fq2bam", {}).get("tmp_dir", "parabricks/pbrun_rna_fq2bam/{wildcards.sample}_{wildcards.type}"), log: "parabricks/pbrun_rna_fq2bam/{sample}_{type}.bam.log", benchmark: