Fix input arguments to merge_fastqs in Singularity file

cfe-lab · Oct 20, 2023 · 2d913bb · 2d913bb
1 parent ca35982
commit 2d913bb
Showing 1 changed file with 6 additions and 1 deletion.
diff --git a/Singularity b/Singularity
@@ -212,4 +212,9 @@ From: centos:7
     KIVE_MEMORY 200
 
 %apprun merge_fastqs
-    PYTHONPATH=/opt/micall python -m micall.core.merge_fastqs "$@"
+    PYTHONPATH=/opt/micall \
+    	python -m micall.core.merge_fastqs \
+                "$1" "$2" "$3" "$4" \
+                --bad_cycles_a_csv "$5" \
+                --bad_cycles_b_csv "$6" \
+                "$7" "$8"