{"action":"created","issue":{"url":"https://api.github.com/repos/hammerlab/biokepi/issues/139","repository_url":"https://api.github.com/repos/hammerlab/biokepi","labels_url":"https://api.github.com/repos/hammerlab/biokepi/issues/139/labels{/name}","comments_url":"https://api.github.com/repos/hammerlab/biokepi/issues/139/comments","events_url":"https://api.github.com/repos/hammerlab/biokepi/issues/139/events","html_url":"https://github.com/hammerlab/biokepi/issues/139","id":134640302,"number":139,"title":"Add Kallisto to Pipeline DSL","user":{"login":"ihodes","id":167803,"avatar_url":"https://avatars.githubusercontent.com/u/167803?v=3","gravatar_id":"","url":"https://api.github.com/users/ihodes","html_url":"https://github.com/ihodes","followers_url":"https://api.github.com/users/ihodes/followers","following_url":"https://api.github.com/users/ihodes/following{/other_user}","gists_url":"https://api.github.com/users/ihodes/gists{/gist_id}","starred_url":"https://api.github.com/users/ihodes/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ihodes/subscriptions","organizations_url":"https://api.github.com/users/ihodes/orgs","repos_url":"https://api.github.com/users/ihodes/repos","events_url":"https://api.github.com/users/ihodes/events{/privacy}","received_events_url":"https://api.github.com/users/ihodes/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/hammerlab/biokepi/labels/target%20library","name":"target library","color":"5319e7"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":3,"created_at":"2016-02-18T17:17:41Z","updated_at":"2016-04-01T15:48:01Z","closed_at":null,"body":"https://pachterlab.github.io/kallisto/about.html"},"comment":{"url":"https://api.github.com/repos/hammerlab/biokepi/issues/comments/204443677","html_url":"https://github.com/hammerlab/biokepi/issues/139#issuecomment-204443677","issue_url":"https://api.github.com/repos/hammerlab/biokepi/issues/139","id":204443677,"user":{"login":"arahuja","id":455755,"avatar_url":"https://avatars.githubusercontent.com/u/455755?v=3","gravatar_id":"","url":"https://api.github.com/users/arahuja","html_url":"https://github.com/arahuja","followers_url":"https://api.github.com/users/arahuja/followers","following_url":"https://api.github.com/users/arahuja/following{/other_user}","gists_url":"https://api.github.com/users/arahuja/gists{/gist_id}","starred_url":"https://api.github.com/users/arahuja/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/arahuja/subscriptions","organizations_url":"https://api.github.com/users/arahuja/orgs","repos_url":"https://api.github.com/users/arahuja/repos","events_url":"https://api.github.com/users/arahuja/events{/privacy}","received_events_url":"https://api.github.com/users/arahuja/received_events","type":"User","site_admin":false},"created_at":"2016-04-01T15:48:01Z","updated_at":"2016-04-01T15:48:01Z","body":"Started poking at this last night and some ideas on what you were thinking @smondet @ihodes would be appreciated.\r\n\r\nThe main issue is that Kallisto (and I'm sure others e.g. Topiary, hla typing) doesn't result in a 'common' output like fastq or bam, but just a text/csv file. Should this result in a new type and new compilation function every time? I saw that seq2hla just had it's own output type added. Should pipeline start to split out and become more specialized?"}}