From cddfb49786312a8c5a18a92f30e9323fd50f9e21 Mon Sep 17 00:00:00 2001 From: Clemens Messerschmidt Date: Fri, 1 Feb 2019 14:55:14 +0100 Subject: [PATCH] Sanitize planned_reads. --- digestiflow_demux/snakemake_support.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/digestiflow_demux/snakemake_support.py b/digestiflow_demux/snakemake_support.py index b59bfa6..6149cad 100644 --- 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 " @@ -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)