specify a default for the tmp-dir when not in the config

hydra-genetics · Feb 20, 2024 · 0525bfc · 0525bfc
1 parent 80c1013
commit 0525bfc
Showing 1 changed file with 12 additions and 6 deletions.
diff --git a/workflow/rules/pbrun.smk b/workflow/rules/pbrun.smk
@@ -15,7 +15,9 @@ 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", lambda wildcards: f"parabricks/pbrun_deepvariant/{wildcards.sample}_{wildcards.type}"
+        ),
     log:
         "parabricks/pbrun_deepvariant/{sample}_{type}.vcf.log",
     benchmark:
@@ -57,7 +59,9 @@ 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", lambda wildcards: f"parabricks/pbrun_fq2bam/{wildcards.sample}_{wildcards.type}"
+        ),
     log:
         "parabricks/pbrun_fq2bam/{sample}_{type}.bam.log",
     benchmark:
@@ -102,7 +106,7 @@ rule pbrun_fq2bam_recal:
         in_fq=get_in_fq,
         num_gpus=lambda wildcards: get_num_gpus("pbrun_fq2bam_recal", wildcards),
         tmp=config.get("pbrun_fq2bam_recal", {}).get(
-            "tmp_dir", "parabricks/pbrun_fq2bam_recal/{wildcards.sample}_{wildcards.type}"
+            "tmp_dir", lambda wildcards: f"parabricks/pbrun_fq2bam_recal/{wildcards.sample}_{wildcards.type}"
         ),
     log:
         "parabricks/pbrun_fq2bam_recal/{sample}_{type}.bam.log",
@@ -148,7 +152,7 @@ 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", lambda wildcards: f"parabricks/pbrun_mutectcaller_t/{wildcards.sample}_{wildcards.type}"
         ),
     log:
         "parabricks/pbrun_mutectcaller_t/{sample}_T.vcf.log",
@@ -197,7 +201,7 @@ rule pbrun_mutectcaller_tn:
         extra=config.get("pbrun_mutectcaller_tn", {}).get("extra", ""),
         num_gpus=lambda wildcards: get_num_gpus("pbrun_mutectcaller_tn", wildcards),
         tmp=config.get("pbrun_mutectcaller_tn", {}).get(
-            "tmp_dir", "parabricks/pbrun_mutectcaller_tn/{wildcards.sample}_{wildcards.type}"
+            "tmp_dir", lambda wildcards: f"parabricks/pbrun_mutectcaller_tn/{wildcards.sample}_{wildcards.type}"
         ),
     log:
         "parabricks/pbrun_mutectcaller_tn/{sample}.vcf.log",
@@ -244,7 +248,9 @@ 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", lambda wildcards: f"parabricks/pbrun_rna_fq2bam/{wildcards.sample}_{wildcards.type}"
+        ),
     log:
         "parabricks/pbrun_rna_fq2bam/{sample}_{type}.bam.log",
     benchmark: