Change sample names for convert reads.

workflow/scripts/convert_reads.py

@@ -109,7 +109,7 @@ def main():
 
     # Convert PE or SE to tagAlign
     bam_basename = os.path.basename(
-        utils.strip_extensions(bam, ['.bam']))
+        utils.strip_extensions(bam, ['.bam', '.dedup']))
 
     tag_filename = bam_basename + '.tagAlign.gz'
     convert_mapped(bam, tag_filename)

workflow/tests/test_convert_reads.py

@@ -9,11 +9,11 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
 
 @pytest.mark.singleend
 def test_convert_reads_singleend():
-    assert os.path.exists(os.path.join(test_output_path, 'ENCFF646LXU.filt.nodup.tagAlign.gz'))
-    assert os.path.exists(os.path.join(test_output_path, 'ENCFF646LXU.filt.nodup.bedse.gz'))
+    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'))
 
 
 @pytest.mark.pairedend
 def test_map_qc_pairedend():
-    assert os.path.exists(os.path.join(test_output_path, 'ENCFF293YFE_val_2ENCFF330MCZ_val_1.filt.nodup.tagAlign.gz'))
-    assert os.path.exists(os.path.join(test_output_path, 'ENCFF293YFE_val_2ENCFF330MCZ_val_1.filt.nodup.bedpe.gz'))
+    assert os.path.exists(os.path.join(test_output_path, 'ENCLB568IYX.tagAlign.gz'))
+    assert os.path.exists(os.path.join(test_output_path, 'ENCLB568IYX.bedpe.gz'))