don't split pipes if shell is specified; fix bug in zipped bam to fas…

…tq awk
databio · May 2, 2019 · 8676255 · 8676255
1 parent d2565c2
commit 8676255
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Showing 2 changed files with 4 additions and 3 deletions.
diff --git a/pypiper/manager.py b/pypiper/manager.py
@@ -878,7 +878,8 @@ def make_dict(command):
             cmd = "docker exec " + container + " " + cmd
 
         param_list = [make_dict(c) for c in split_by_pipes(cmd)] \
-            if check_shell_pipes(cmd) else [dict(args=cmd, stdout=None, shell=True)]
+            if not shell and check_shell_pipes(cmd) else [dict(args=cmd, stdout=None, shell=True)]
+
 
         proc_name = get_proc_name(cmd)
 

diff --git a/pypiper/ngstk.py b/pypiper/ngstk.py
@@ -232,8 +232,8 @@ def bam_to_fastq_awk(self, bam_file, out_fastq_pre, paired_end, zipmode=False):
         if zipmode:
             fq1 = fq1 + ".gz"
             fq2 = fq2 + ".gz"
-            fq1_target = " | " + self.ziptool + " -c > " + fq1
-            fq2_target = " | " + self.ziptool + " -c > " + fq2
+            fq1_target = " | \"" + self.ziptool + " -c  > " + fq1 + '"'
+            fq2_target = " | \"" + self.ziptool + " -c  > " + fq2 + '"'
         else:
             fq1_target = ' > "' + fq1 + '"'
             fq2_target = ' > "' + fq2 + '"'