Commit d79ccbe6 authored by Penom Nom's avatar Penom Nom
Browse files

casava project name (optional)

parent 253dcdf4
......@@ -280,6 +280,7 @@ class CasavaNG6Workflow(NG6Workflow):
def __add_sample_parameters__(self):
self.add_input_directory("casava_directory", "Path to the CASAVA directory to use", required=True, get_files_fn=get_files_from_casava, group="Sample description")
self.add_parameter("casava_lane", "The lane number to be retrieved from the casava directory", required=True, type=int, group="Sample description")
self.add_parameter('casava_project', 'The name of the project to retrieve in casava directory. The default name is the name of the project', group="Sample description")
self.add_parameter('mismatch_index', 'Set this value to true if the index sequence in the sample fastq files allows at least 1 mismatch', type ='bool', group="Sample description")
......@@ -310,8 +311,13 @@ class CasavaNG6Workflow(NG6Workflow):
assert len(barcodes_list) == len(sample_ids_list) == len(subdirs_list), "Invalid lane {0} in".format(lane_number)
# get the casava project_name from subdirs
project_name = self.project_name.replace(" ", "_")
# get the casava project_name
if self.casava_project :
project_name = self.casava_project
else :
project_name = self.project_name
project_name = project_name.replace(" ", "_")
input_files = casava_directory.get_files( lane_number, project_name)
if len(input_files) == 0 :
raise Exception("Error while parsing casava directory %s, invalid project name '%s' for lane %s"% (casava_directory, project_name, lane_number))
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