Commit c1d2d205 authored by Gerald Salin's avatar Gerald Salin
Browse files

Update alignmentstats.py

parent 05fc6517
......@@ -156,7 +156,7 @@ class AlignmentStats (Analysis):
xmx="-Xmx"+self.memory.lower()
if self.search_dupl:
self.tmp_bam = self.get_outputs('{basename_woext}_noDupl.bam', self.bam_files)
self.add_shell_execution(self.get_exec_path("javaPICARD")+ xmx +"-jar " + self.get_exec_path("Picard") + " MarkDuplicates INPUT=$1 METRICS_FILE=$2 OUTPUT=$3" + self.duplication_options + " 2> $4",
self.add_shell_execution(self.get_exec_path("javaPICARD")+ " "+ xmx +"-jar " + self.get_exec_path("Picard") + " MarkDuplicates INPUT=$1 METRICS_FILE=$2 OUTPUT=$3" + self.duplication_options + " 2> $4",
cmd_format='{EXE} {IN} {OUT}', map=True,
inputs=self.bam_files, outputs=[self.duplication_files, self.tmp_bam, self.dupl_stderrs])
......
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