fix: set hpc resource config

RIVM-bioinformatics · Mar 22, 2024 · a2e64a3 · a2e64a3
1 parent f02eb04
commit a2e64a3
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Showing 3 changed files with 14 additions and 3 deletions.
diff --git a/Snakefile b/Snakefile
@@ -16,6 +16,8 @@ OUT = config["output_dir"]
 
 localrules:
     all,
+    copy_ref,
+    copy_mask
 
 
 include: "workflow/rules/fastqc_raw_data.smk"

diff --git a/workflow/rules/qc_mapping.smk b/workflow/rules/qc_mapping.smk
@@ -116,6 +116,9 @@ rule CollectAlignmentSummaryMetrics:
         "docker://broadinstitute/picard:2.27.5"
     params:
         use_singularity=config["use_singularity"],
+    threads: config["threads"]["picard"]
+    resources:
+        mem_gb=config["mem_gb"]["picard"],
     shell:
         """
 if [ {params.use_singularity} == True ]
@@ -143,6 +146,9 @@ rule CollectGcBiasMetrics:
         "docker://broadinstitute/picard:2.27.5"
     params:
         use_singularity=config["use_singularity"],
+    threads: config["threads"]["picard"]
+    resources:
+        mem_gb=config["mem_gb"]["picard"],
     shell:
         """
 if [ {params.use_singularity} == True ]
@@ -167,6 +173,9 @@ rule CollectQualityYieldMetrics:
         "docker://broadinstitute/picard:2.27.5"
     params:
         use_singularity=config["use_singularity"],
+    threads: config["threads"]["picard"]
+    resources:
+        mem_gb=config["mem_gb"]["picard"],
     shell:
         """
 if [ {params.use_singularity} == True ]
@@ -192,6 +201,9 @@ rule CollectWgsMetrics:
         "docker://broadinstitute/picard:2.27.5"
     params:
         use_singularity=config["use_singularity"],
+    threads: config["threads"]["picard"]
+    resources:
+        mem_gb=config["mem_gb"]["picard"],
     shell:
         """
 if [ {params.use_singularity} == True ]

diff --git a/workflow/rules/variant_filtering.smk b/workflow/rules/variant_filtering.smk
@@ -156,9 +156,6 @@ else:
             mask=OUT + "/variants_raw/mask.bed",
         log:
             OUT + "/log/copy_mask.log",
-        threads: config["threads"]["other"]
-        resources:
-            mem_gb=config["mem_gb"]["other"],
         shell:
             """
     cp {input.mask} {output.mask}