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: