Commit 3dc599e7 authored by Maxime Manno's avatar Maxime Manno 🍜
Browse files

Update : Commit from production file

parent 88fa2e34
......@@ -101,8 +101,8 @@ class GeneDiversity (NG6Workflow):
def define_parameters(self, function="process"):
self.add_multiple_parameter_list("merge", "The list of samples to merge")
self.add_parameter("name", "Merge group name", required=True, add_to="merge")
self.add_parameter_list("sample_name", "The name of the sample", required=True, add_to="merge")
self.add_parameter("name", "Merge group name", required=False, add_to="merge")
self.add_parameter_list("sample_name", "The name of the sample", required=False, add_to="merge")
self.add_input_file("database", "The reference set contains protein representative sequences of the gene target" +
"and should be compiled to have a good coverage of diversity of the gene family", required=True, group="Gene section")
......@@ -149,7 +149,7 @@ class GeneDiversity (NG6Workflow):
trim_R2 = self.add_component("Trimmer", [self.get_all_reads('read2'), 1, self.trim_read_2], component_prefix="R2")
# Make some statistics on raw file
fastqc = self.add_component("FastQC", [trim_R1.output_files + trim_R2.output_files, False, True])
#fastqc = self.add_component("FastQC", [trim_R1.output_files + trim_R2.output_files, False, True])
# Merge overlapping pair
join_pairs = self.add_component("Flash", [trim_R1.output_files, trim_R2.output_files, self.mismatch_ratio, self.min_overlap, self.max_overlap])
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