Update convert reads.

workflow/scripts/convert_reads.py

@@ -84,9 +84,9 @@ def convert_mapped(bam, tag_filename, chrm):
         r"""awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}'"""]
 
     if chrm:
-        steps.extend["grep -v 'chrM'"]
+        steps.extend(["grep -v 'chrM'"])
 
-    steps.extend["gzip -nc"]
+    steps.extend(["gzip -nc"])
 
     out, err = utils.run_pipe(steps, outfile=tag_filename)
 
@@ -107,13 +107,13 @@ def convert_mapped_pe(bam, bam_basename, tag_filename, chrm):
 
     steps = ["bamToBed -bedpe -mate1 -i %s" % (nmsrt_bam_filename)]
 
-    steps.extend["gzip -nc"]
+    steps.extend(["gzip -nc"])
 
     out, err = utils.run_pipe(steps, outfile=bedpe_filename)
     os.remove(nmsrt_bam_filename)
 
     if chrm:
-        steps.extend["grep -v 'chrM'"]
+        steps.extend(["grep -v 'chrM'"])
 
     # Convert read pairs to reads into standard tagAlign file
     tag_steps = ["zcat -f %s" % (bedpe_filename)]