{"action":"created","issue":{"url":"https://api.github.com/repos/broadinstitute/gatk/issues/4474","repository_url":"https://api.github.com/repos/broadinstitute/gatk","labels_url":"https://api.github.com/repos/broadinstitute/gatk/issues/4474/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/gatk/issues/4474/comments","events_url":"https://api.github.com/repos/broadinstitute/gatk/issues/4474/events","html_url":"https://github.com/broadinstitute/gatk/pull/4474","id":301399700,"number":4474,"title":"Add DocOnlyArgumentCollection for better downstream toolkit extensibility","user":{"login":"magicDGS","id":7352559,"avatar_url":"https://avatars0.githubusercontent.com/u/7352559?v=4","gravatar_id":"","url":"https://api.github.com/users/magicDGS","html_url":"https://github.com/magicDGS","followers_url":"https://api.github.com/users/magicDGS/followers","following_url":"https://api.github.com/users/magicDGS/following{/other_user}","gists_url":"https://api.github.com/users/magicDGS/gists{/gist_id}","starred_url":"https://api.github.com/users/magicDGS/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/magicDGS/subscriptions","organizations_url":"https://api.github.com/users/magicDGS/orgs","repos_url":"https://api.github.com/users/magicDGS/repos","events_url":"https://api.github.com/users/magicDGS/events{/privacy}","received_events_url":"https://api.github.com/users/magicDGS/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2018-03-01T13:13:35Z","updated_at":"2018-03-09T13:59:26Z","closed_at":null,"author_association":"CONTRIBUTOR","pull_request":{"url":"https://api.github.com/repos/broadinstitute/gatk/pulls/4474","html_url":"https://github.com/broadinstitute/gatk/pull/4474","diff_url":"https://github.com/broadinstitute/gatk/pull/4474.diff","patch_url":"https://github.com/broadinstitute/gatk/pull/4474.patch"},"body":"Can you review this one @droazen - this is the last part of the temporary solution for #3998 (mentioned on ##4468). I think that in this case, because the interface is just a marker, it is easier to just modify `GATKDocOnlyArgumentCollection` for doc-only top level arguments and does not modify the API. Thanks!"},"comment":{"url":"https://api.github.com/repos/broadinstitute/gatk/issues/comments/371819413","html_url":"https://github.com/broadinstitute/gatk/pull/4474#issuecomment-371819413","issue_url":"https://api.github.com/repos/broadinstitute/gatk/issues/4474","id":371819413,"user":{"login":"cmnbroad","id":10062863,"avatar_url":"https://avatars2.githubusercontent.com/u/10062863?v=4","gravatar_id":"","url":"https://api.github.com/users/cmnbroad","html_url":"https://github.com/cmnbroad","followers_url":"https://api.github.com/users/cmnbroad/followers","following_url":"https://api.github.com/users/cmnbroad/following{/other_user}","gists_url":"https://api.github.com/users/cmnbroad/gists{/gist_id}","starred_url":"https://api.github.com/users/cmnbroad/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cmnbroad/subscriptions","organizations_url":"https://api.github.com/users/cmnbroad/orgs","repos_url":"https://api.github.com/users/cmnbroad/repos","events_url":"https://api.github.com/users/cmnbroad/events{/privacy}","received_events_url":"https://api.github.com/users/cmnbroad/received_events","type":"User","site_admin":false},"created_at":"2018-03-09T13:59:26Z","updated_at":"2018-03-09T13:59:26Z","author_association":"COLLABORATOR","body":"Args like the config file that are truly optional (have no default value at all) do not show up in the command line or headers unless they're populated with some value. It should be pretty easy for ReadTools (which I think already has a common base class for its tools), to ensure a config file is never accepted by just precluding it via custom command line validation, or arg preprocessing.\r\n\r\nBTW, all tools built with GATK already have numerous common args that may or may not apply in a given tool context. For example, all of the ReadWalkers have a `--lenientVCFProcessing` arg. So I'm not even sure we need to make this hidden. My 2 cents. Others may feel differently."}}
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