fix: bwa_mem2 wrapper only used right read (#316)

bihealth · Jan 2, 2023 · 53c88aa · 53c88aa
1 parent 7c35ec3
commit 53c88aa
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/snappy_pipeline/workflows/variant_calling/__init__.py b/snappy_pipeline/workflows/variant_calling/__init__.py
@@ -790,7 +790,7 @@ def get_resource_usage(self, action: str) -> ResourceUsage:
         self._validate_action(action)
         return ResourceUsage(
             threads=1,
-            time="00:10:00",
+            time="01:00:00",
             memory="4G",
         )
 

diff --git a/snappy_wrappers/wrappers/bwa_mem2/wrapper.py b/snappy_wrappers/wrappers/bwa_mem2/wrapper.py
@@ -67,7 +67,7 @@
         (zcat force {input_right})
     else
         seqtk mergepe \
-            <(zcat {input_right} | tee >(wc -l > $TMPDIR/count_left)) \
+            <(zcat {input_left} | tee >(wc -l > $TMPDIR/count_left)) \
             <(zcat {input_right} | tee >(wc -l > $TMPDIR/count_right))
     fi
 }}