Hi, I am validating our files before submission and I notice that for validateGENIE.py script, all the positional arguments for specifying the file type are {maf,clinical,fusions,cnv,vcf,seg,bed}. May I know how are we supposed to validate Log2 Copy Number file (‘cnv' argument doesn’t work and gives an incorrect filename error) and Workflow/methods file? Thanks,

Created by Sushant Patil spatil6
Dear Sushant, Apologies for the delay in response! Please use the `--offline` tag to skip the filename checking. `python sage_processing/validateGENIE.py cnv data_linear_CNA_UCHI.txt UCHI --offline` or please rename your file to data_CNA_UCHI.txt. Best, Tom
python sage_processing/validateGENIE.py cnv data_linear_CNA_UCHI.txt UCHI Traceback (most recent call last): File "sage_processing/validateGENIE.py", line 846, in perform_main(syn, args) File "sage_processing/validateGENIE.py", line 814, in perform_main message = main(syn, args.fileType, args.file, args.center, pool, args.oncotreeLink, args.offline, args.uploadToSynapse) File "sage_processing/validateGENIE.py", line 759, in main raise ValueError("Your filename is incorrect!\n%s\nPlease change your filename before you run the validator again." % e) ValueError: Your filename is incorrect! cnv filename must be: data_CNA_UCHI.txt! Please change your filename before you run the validator again.
Dear Sushant, What is the exact command that you run? Also workflow files are not able to be validated right now. Best, Tom

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