Update pbrun.smk

hydra-genetics · Feb 19, 2024 · cb4658b · cb4658b
1 parent 658acd7
commit cb4658b
Showing 1 changed file with 3 additions and 6 deletions.
diff --git a/workflow/rules/pbrun.smk b/workflow/rules/pbrun.smk
@@ -15,8 +15,7 @@ rule pbrun_deepvariant:
         cuda=get_cuda_devices,
         extra=config.get("pbrun_deepvariant", {}).get("extra", ""),
         num_gpus=lambda wildcards: get_num_gpus("pbrun_deepvariant", wildcards),
-        tmp=config.get("pbrun_deepvariant", {}).get(
-            "tmp_dir", "parabricks/pbrun_deepvariant/{wildcards.sample}_{wildcards.type}"),
+        tmp=config.get("pbrun_deepvariant", {}).get("tmp_dir", "parabricks/pbrun_deepvariant/{wildcards.sample}_{wildcards.type}"),
     log:
         "parabricks/pbrun_deepvariant/{sample}_{type}.vcf.log",
     benchmark:
@@ -58,8 +57,7 @@ rule pbrun_fq2bam:
         extra=config.get("pbrun_fq2bam", {}).get("extra", ""),
         in_fq=get_in_fq,
         num_gpus=lambda wildcards: get_num_gpus("pbrun_fq2bam", wildcards),
-        tmp=config.get("pbrun_fq2bam", {}).get(
-            "tmp_dir", "parabricks/pbrun_fq2bam/{wildcards.sample}_{wildcards.type}"),
+        tmp=config.get("pbrun_fq2bam", {}).get("tmp_dir", "parabricks/pbrun_fq2bam/{wildcards.sample}_{wildcards.type}"),
     log:
         "parabricks/pbrun_fq2bam/{sample}_{type}.bam.log",
     benchmark:
@@ -246,8 +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: