Upgrade Manta and fix wrapper (#197)

bihealth · Sep 7, 2022 · 2d81f7c · 2d81f7c
1 parent 7158762
commit 2d81f7c
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Showing 2 changed files with 5 additions and 4 deletions.
diff --git a/snappy_wrappers/wrappers/manta/germline_wgs/environment.yaml b/snappy_wrappers/wrappers/manta/germline_wgs/environment.yaml
@@ -3,4 +3,4 @@ channels:
 - bioconda
 - r
 dependencies:
-- manta ==1.2.1
+- manta ==1.6.0
diff --git a/snappy_wrappers/wrappers/manta/germline_wgs/wrapper.py b/snappy_wrappers/wrappers/manta/germline_wgs/wrapper.py
@@ -27,9 +27,10 @@
     --runDir $workdir \
     $(echo "{snakemake.input}" | tr ' ' '\n' | grep -v 'bai$' | sed 's/^/--bam /g')
 
-python $workdir/runWorkflow.py \
-    -m local \
-    -j 16
+perl -p -i -e 's/isEmail = .*/isEmail = False/g' $workdir/runWorkflow.py
+
+python2 $workdir/runWorkflow.py \
+    --jobs 16
 
 cp -ra $workdir/results $outdir
 rm -rf $workdir