Resolve "Include Phantompeakqualtools step"

Closes #5 (closed) Adds in phantompeakcalls step to produce plots.

workflow/tests/test_convert_reads.py

@@ -8,8 +8,8 @@ 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'))
+    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'))
 
 
 def test_map_qc_pairedend():