Sanitize planned_reads.

bihealth · Feb 1, 2019 · cddfb49 · cddfb49
1 parent 2768d2a
commit cddfb49
Showing 1 changed file with 3 additions and 0 deletions.
diff --git a/digestiflow_demux/snakemake_support.py b/digestiflow_demux/snakemake_support.py
@@ -3,6 +3,8 @@
 import functools
 import os
 
+from bases_mask import return_bases_mask
+
 __author__ = "Manuel Holtgrewe <manuel.holtgrewe@bihealth.de>"
 
 
@@ -121,6 +123,7 @@ def out_prefix(path):
 
     flowcell = config["flowcell"]
     demux_reads = flowcell.get("demux_reads") or flowcell["planned_reads"]
+    demux_reads = return_bases_mask(flowcell["planned_reads"], demux_reads, "picard")
     is_paired = demux_reads.count("T") > 1
     sample_map = build_sample_map(flowcell)