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ntm / grexome-TIMC-Secondary

exome pipeline from TIMC - secondary analyses (GVCF to analysis-ready TSVs)
GNU General Public License v3.0
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How to edit &subCohorts() in config.pm? W grexome-TIMC-secondary.pl: sub-cohort file defined in &subCohorts() but this file doesn't exist. Skipping this sub-cohort #6

Closed Chris-lang478 closed 2 years ago

Chris-lang478 commented 2 years ago

@ntm I have no subcohort file. And I modify the confog.pm as

sub subCohorts { my %subCohorts = ("" => ""); return(\%subCohorts); }

After I run the secondary.pl, the log file shows that W grexome-TIMC-secondary.pl: sub-cohort file defined in &subCohorts() but this file doesn't exist. Skipping this sub-cohort.

Is there better way to modify the config.pm? Thanks again for your attention and great work!

Best regards, Chris

ntm commented 2 years ago

just declare an empty hash, ie: my %subCohorts = ();

Chris-lang478 commented 2 years ago

Thanks for your help!!! I finally run all successfully.