Commit 47fa3240 authored by aknecht2's avatar aknecht2
Browse files

Fixed typo in _add_align. Adjusted naming in _check_grch38.

parent 265b2178
......@@ -175,8 +175,9 @@ class Workflow(object):
base_file_ext = base_file_ext[1:]
base_file_name = gen_prefix + "." + base_file_ext
self._add_file(base_file_name, base_file, "local")
self.run_data["genomes"][run["align"]][assembly]["base_file"] = base_file_name
self.run_data["genomes"][run["align"]][assembly]["additional_files"] = []
genome_files = self.run_data["genomes"][run["align"]][assembly + "_files"] = {}
genome_files["base_file"] = base_file_name
genome_files["additional_files"] = []
if base_file_ext in chipathlon.conf.genomes[run["align"]]["base_file"]:
prefix = os.path.splitext(base_file)[0]
missing = []
......@@ -188,7 +189,7 @@ class Workflow(object):
name = "%s.%s%s" % (gen_prefix, "" if no_ext else base_file_ext + ".", ext)
path = "%s.%s" % (prefix if no_ext else base_file, ext)
self._add_file(name, path, "local")
self.run_data["genomes"][run["align"]][assembly]["additional_files"].append(name)
genome_files["additional_files"].append(name)
if len(missing) > 0:
self.err += "Genome defined with tool '%s' and assembly '%s' is missing additional_files with extensions %s.\n" % (run["align"], assembly, missing)
else:
......@@ -270,10 +271,10 @@ 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"]["base_file"]
for add_file in self.run_data["genomes"][run["align"]]["grch38p6"]["additional_files"]:
input_files["ref_genome"] = self.run_data["genomes"][run["align"]]["grch38p6_files"]["base_file"]
for add_file in self.run_data["genomes"][run["align"]]["grch38p6_files"]["additional_files"]:
ext = os.path.splitext(add_file)[1]
additional_files["ref_genom." + ext] = add_file
additional_files["ref_genome" + ext] = add_file
for pair in run["input_sets"]:
for f in pair:
prefix = "%s_%s" % (run["experiment"], f["accession"])
......
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