Commit d095909d authored by aknecht2's avatar aknecht2
Browse files

Adjusted bowtie2 workflow generation.

parent 7c07157c
......@@ -282,7 +282,12 @@ class Workflow(object):
additional_files = {}
markers["tool"] = run["align"]
gen_prefix = "genome_%s_grch38p6" % (run["align"],)
input_files["ref_genome"] = self.run_data["genomes"][run["align"]]["grch38p6_files"]["base_file"]
# Not elegant, check if bwa or bowtie2 to create inputs
if markers["tool"] == "bwa":
input_files["ref_genome"] = self.run_data["genomes"][run["align"]]["grch38p6_files"]["base_file"]
elif markers["tool"] == "bowtie2":
input_files["ref_genome_prefix"] = gen_prefix
additional_files["ref_genome"] = self.run_data["genomes"][run["align"]]["grch38p6_files"]["base_file"]
for ext in chipathlon.conf.genomes[run["align"]]["additional_files"]:
additional_files["ref_genome." + ext] = self.run_data["genomes"][run["align"]]["grch38p6_files"]["additional_files"][ext]
for pair in run["input_sets"]:
......
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