{"action":"closed","issue":{"url":"https://api.github.com/repos/SciLifeLab/CAW/issues/317","repository_url":"https://api.github.com/repos/SciLifeLab/CAW","labels_url":"https://api.github.com/repos/SciLifeLab/CAW/issues/317/labels{/name}","comments_url":"https://api.github.com/repos/SciLifeLab/CAW/issues/317/comments","events_url":"https://api.github.com/repos/SciLifeLab/CAW/issues/317/events","html_url":"https://github.com/SciLifeLab/CAW/issues/317","id":224158957,"number":317,"title":"Change annotation tools process","user":{"login":"MaxUlysse","id":1019628,"avatar_url":"https://avatars0.githubusercontent.com/u/1019628?v=3","gravatar_id":"","url":"https://api.github.com/users/MaxUlysse","html_url":"https://github.com/MaxUlysse","followers_url":"https://api.github.com/users/MaxUlysse/followers","following_url":"https://api.github.com/users/MaxUlysse/following{/other_user}","gists_url":"https://api.github.com/users/MaxUlysse/gists{/gist_id}","starred_url":"https://api.github.com/users/MaxUlysse/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/MaxUlysse/subscriptions","organizations_url":"https://api.github.com/users/MaxUlysse/orgs","repos_url":"https://api.github.com/users/MaxUlysse/repos","events_url":"https://api.github.com/users/MaxUlysse/events{/privacy}","received_events_url":"https://api.github.com/users/MaxUlysse/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":{"login":"MaxUlysse","id":1019628,"avatar_url":"https://avatars0.githubusercontent.com/u/1019628?v=3","gravatar_id":"","url":"https://api.github.com/users/MaxUlysse","html_url":"https://github.com/MaxUlysse","followers_url":"https://api.github.com/users/MaxUlysse/followers","following_url":"https://api.github.com/users/MaxUlysse/following{/other_user}","gists_url":"https://api.github.com/users/MaxUlysse/gists{/gist_id}","starred_url":"https://api.github.com/users/MaxUlysse/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/MaxUlysse/subscriptions","organizations_url":"https://api.github.com/users/MaxUlysse/orgs","repos_url":"https://api.github.com/users/MaxUlysse/repos","events_url":"https://api.github.com/users/MaxUlysse/events{/privacy}","received_events_url":"https://api.github.com/users/MaxUlysse/received_events","type":"User","site_admin":false},"assignees":[{"login":"MaxUlysse","id":1019628,"avatar_url":"https://avatars0.githubusercontent.com/u/1019628?v=3","gravatar_id":"","url":"https://api.github.com/users/MaxUlysse","html_url":"https://github.com/MaxUlysse","followers_url":"https://api.github.com/users/MaxUlysse/followers","following_url":"https://api.github.com/users/MaxUlysse/following{/other_user}","gists_url":"https://api.github.com/users/MaxUlysse/gists{/gist_id}","starred_url":"https://api.github.com/users/MaxUlysse/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/MaxUlysse/subscriptions","organizations_url":"https://api.github.com/users/MaxUlysse/orgs","repos_url":"https://api.github.com/users/MaxUlysse/repos","events_url":"https://api.github.com/users/MaxUlysse/events{/privacy}","received_events_url":"https://api.github.com/users/MaxUlysse/received_events","type":"User","site_admin":false}],"milestone":null,"comments":0,"created_at":"2017-04-25T14:31:46Z","updated_at":"2017-04-27T08:45:43Z","closed_at":"2017-04-27T08:45:43Z","body":"At the moment, we only run annotation tools conjointly with variant callers.\r\nIt could be good to run annotation tools in another run.\r\nBut we would need to restart variant callers.\r\nThe way I see it, we can something like:\r\n- `vcfsForAnnotation = Channel.fromPath( 'VariantCalling/{MuTect1,MuTect2,Strelka}/*' )` and then run selected tools on these vcfs.\r\n- specify a vcf or list of vcf via command line and run the selected tools on these vcfs.\r\n- specify a tool and fetch the vcfs from the `VariantCalling` directory\r\n- don't do anything\r\n\r\nWhich ideas do you like?\r\nDo you have any others?"}}
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