Fix passing of bedpe reads.

workflow/main.nf

@@ -203,7 +203,7 @@ process convertReads {
 
   output:
 
-  set sampleId, file('*.tagAlign.gz'), file('*.bedpe.gz'), biosample, factor, treatment, replicate, controlId into tagReads
+  set sampleId, file('*.tagAlign.gz'), file('*.bed{pe,se}.gz'), biosample, factor, treatment, replicate, controlId into tagReads
 
   script:
 

workflow/scripts/convert_reads.py

@@ -64,10 +64,9 @@ def check_tools():
         raise Exception('Missing samtools')
 
 
-def convert_mapped(bam, bam_basename):
+def convert_mapped(bam, tag_filename):
     '''Use bedtools to convert to tagAlign.'''
 
-    tag_filename = bam_basename + '.tagAlign.gz'
     out, err = utils.run_pipe([
         "bamToBed -i %s" % (bam),
         r"""awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}'""",
@@ -110,10 +109,14 @@ def main():
     bam_basename = os.path.basename(
         utils.strip_extensions(bam, ['.bam']))
 
-    convert_mapped(bam, bam_basename)
+    tag_filename = bam_basename + 'tagAlign.gz'
+    convert_mapped(bam, tag_filename)
 
     if paired:  # paired-end data
         convert_mapped_pe(bam, bam_basename)
+    else:
+        bedse_filename =  bam_basename + ".bedse.gz"
+        shutil(tag_filename, bedse_filename)
 
 
 if __name__ == '__main__':

workflow/tests/test_convert_reads.py

@@ -9,6 +9,7 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
 
 def test_convert_reads_singleend():
     assert os.path.exists(os.path.join(test_output_path, 'ENCFF646LXU.tagAlign.gz'))
+    assert os.path.exists(os.path.join(test_output_path, 'ENCFF646LXU.bedse.gz'))
 
 
 def test_map_qc_pairedend():