Update manta modules (nf-core#3615)

* Update manta somatic * Update manta tumoronly
JPejovicApis · Oct 10, 2023 · 2d04695 · 2d04695
1 parent 97c6087
commit 2d04695
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diff --git a/modules/nf-core/manta/somatic/main.nf b/modules/nf-core/manta/somatic/main.nf
@@ -37,8 +37,9 @@ process MANTA_SOMATIC {
         --tumorBam $input_tumor \
         --normalBam $input_normal \
         --reference $fasta \
+        --runDir manta \
         $options_manta \
-        --runDir manta
+        $args
 
     python manta/runWorkflow.py -m local -j $task.cpus
 

diff --git a/modules/nf-core/manta/tumoronly/main.nf b/modules/nf-core/manta/tumoronly/main.nf
@@ -33,8 +33,9 @@ process MANTA_TUMORONLY {
     configManta.py \
         --tumorBam $input \
         --reference $fasta \
+        --runDir manta \
         $options_manta \
-        --runDir manta
+        $args
 
     python manta/runWorkflow.py -m local -j $task.cpus