Fix picard java opts

moiexpositoalonsolab · Feb 12, 2025 · 636565b · 636565b
1 parent 9d7c550
commit 636565b
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Showing 3 changed files with 11 additions and 11 deletions.
diff --git a/workflow/rules/calling-freebayes.smk b/workflow/rules/calling-freebayes.smk
@@ -141,14 +141,17 @@ rule merge_variants:
         done=touch("calling/genotyped-all.vcf.gz.done"),
     params:
         # See duplicates-picard.smk for the reason whe need this on MacOS.
+        java_opts=config["params"]["picard"]["MergeVcfs-java-opts"],
         extra=(
             " --USE_JDK_DEFLATER true --USE_JDK_INFLATER true" if platform.system() == "Darwin" else ""
         ),
+    resources:
+        mem_mb=config["params"]["picard"].get("MergeVcfs-mem-mb", 1024),
     log:
         "logs/calling/picard/merge-genotyped.log",
     benchmark:
         "benchmarks/calling/genotyped/picard/merge-genotyped.log"
     conda:
         "../envs/picard.yaml"
     wrapper:
-        "0.51.3/bio/picard/mergevcfs"
+        "v5.7.0/bio/picard/mergevcfs"
diff --git a/workflow/rules/filtering.smk b/workflow/rules/filtering.smk
@@ -84,7 +84,7 @@ rule merge_calls:
         # We use different naming for the VQSR intermediate files,
         # to make it a bit more understandable to the user which file is which...
         # not sure if that helps, or is more confusing in the end :-O
-        vcf=expand(
+        vcfs=expand(
             "calling/filtered/all.{vartype}.{filtertype}.vcf.gz",
             vartype=["SNP", "INDEL"],
             filtertype=(
@@ -108,14 +108,17 @@ rule merge_calls:
         done=touch("calling/filtered-all.vcf.gz.done"),
     params:
         # See duplicates-picard.smk for the reason whe need this on MacOS.
+        java_opts=config["params"]["picard"]["MergeVcfs-java-opts"],
         extra=(
             " --USE_JDK_DEFLATER true --USE_JDK_INFLATER true" if platform.system() == "Darwin" else ""
         ),
+    resources:
+        mem_mb=config["params"]["picard"].get("MergeVcfs-mem-mb", 1024),
     log:
         "logs/calling/picard-mergevcfs.log",
     benchmark:
         "benchmarks/calling/filtered/picard-mergevcfs.log"
     conda:
         "../envs/picard.yaml"
     wrapper:
-        "0.27.1/bio/picard/mergevcfs"
+        "v5.7.0/bio/picard/mergevcfs"
diff --git a/workflow/rules/qc-bam.smk b/workflow/rules/qc-bam.smk
@@ -226,19 +226,13 @@ rule picard_collectmultiplemetrics:
     log:
         "logs/qc/picard-collectmultiplemetrics/{sample}.log",
     params:
-        config["params"]["picard"]["CollectMultipleMetrics-java-opts"]
-        + " "
-        + config["params"]["picard"]["CollectMultipleMetrics-extra"]
+        java_opts = config["params"]["picard"]["CollectMultipleMetrics-java-opts"],
+        extra = config["params"]["picard"]["CollectMultipleMetrics-extra"]
         + (" --USE_JDK_DEFLATER true --USE_JDK_INFLATER true" if platform.system() == "Darwin" else ""),
     resources:
         mem_mb=config["params"]["picard"].get("CollectMultipleMetrics-mem-mb", 1024),
     conda:
         "../envs/picard.yaml"
-    # script:
-        # We use our own version of the wrapper here, which fixes issues with missing files in cases
-        # where Picard does not have enough data for a specific metric to run.
-        # "../scripts/picard-collectmultiplemetrics.py"
-        # Update: fixed in the new wrapper now, so should be good.
     wrapper:
         "v5.7.0/bio/picard/collectmultiplemetrics"