Have mutect respect snakemake threads (#459)

snakemake · Mar 9, 2022 · cb2539d · cb2539d
1 parent 330359d
commit cb2539d
Showing 1 changed file with 1 addition and 0 deletions.
diff --git a/bio/gatk/mutect/wrapper.py b/bio/gatk/mutect/wrapper.py
@@ -24,6 +24,7 @@
 with tempfile.TemporaryDirectory() as tmpdir:
     shell(
         "gatk --java-options '{java_opts}' Mutect2"  # Tool and its subprocess
+        " --native-pair-hmm-threads {snakemake.threads}"
         " --input {snakemake.input.map}"  # Path to input mapping file
         " --reference {snakemake.input.fasta}"  # Path to reference fasta file
         " {extra}"  # Extra parameters