Commit 46ff85c7 authored by Hanna  JULIENNE's avatar Hanna JULIENNE
Browse files

Update __main__.py

Remove --index-type argument
the index type is specified in the meta data file describing the study
parent 0d7f22cb
Pipeline #75171 passed with stages
in 1 minute and 37 seconds
......@@ -2,7 +2,7 @@
Read raw GWAS summary statistics, filter and format
Write clean GWAS datasets by chromosome
"""
__updated__ = '2018-26-06'
__updated__ = '2022-03-02'
import pandas as pd
import jass_preprocessing as jp
......@@ -95,7 +95,6 @@ def add_preprocessing_argument():
parser.add_argument('--additional-masked-region', required=False, help= "List of dictionary containing coordinate of region to mask. For example :[{'chr':6, 'start':50000000, 'end': 70000000}, {'chr':6, 'start':100000000, 'end': 120000000}]", default='None')
parser.add_argument('--imputation-quality-treshold', required=False, help= "minimum imputation quality in summary statistics", default='None')
parser.add_argument('--index-type', required=False, help= "type of index : rsID or chr:postion:ref_allele:alt_allele", default='rs-number')
parser.set_defaults(func=launch_preprocessing)
......
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