Commit 7ef93628 authored by Penom Nom's avatar Penom Nom
Browse files

Fix bug in call of cigarlineGraph.

parent 6f9f02a5
......@@ -106,7 +106,7 @@ class AlignmentStats (Analysis):
return stderr.split()[0]
def process(self):
alignmentstats = ShellFunction(self.get_exec_path("samtools") + " view $1 | " \
alignmentstats = ShellFunction(self.get_exec_path("samtools") + " view $1 | python " \
+ self.get_exec_path("cigarline_by_pos.py") + " -i - -o $2 $3 " + self.options + " 2> $4", cmd_format='{EXE} {IN} {OUT}')
if self.csv_files_r2:
alignmentstats = MultiMap(alignmentstats, inputs=self.bam_files, outputs=[self.csv_files_r1, self.csv_files_r2, self.stderrs])
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment