{"action":"created","issue":{"url":"https://api.github.com/repos/broadinstitute/cromwell/issues/4140","repository_url":"https://api.github.com/repos/broadinstitute/cromwell","labels_url":"https://api.github.com/repos/broadinstitute/cromwell/issues/4140/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/cromwell/issues/4140/comments","events_url":"https://api.github.com/repos/broadinstitute/cromwell/issues/4140/events","html_url":"https://github.com/broadinstitute/cromwell/issues/4140","id":363248731,"node_id":"MDU6SXNzdWUzNjMyNDg3MzE=","number":4140,"title":"File evaluation in PAPI v2","user":{"login":"ruchim","id":14941133,"node_id":"MDQ6VXNlcjE0OTQxMTMz","avatar_url":"https://avatars3.githubusercontent.com/u/14941133?v=4","gravatar_id":"","url":"https://api.github.com/users/ruchim","html_url":"https://github.com/ruchim","followers_url":"https://api.github.com/users/ruchim/followers","following_url":"https://api.github.com/users/ruchim/following{/other_user}","gists_url":"https://api.github.com/users/ruchim/gists{/gist_id}","starred_url":"https://api.github.com/users/ruchim/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ruchim/subscriptions","organizations_url":"https://api.github.com/users/ruchim/orgs","repos_url":"https://api.github.com/users/ruchim/repos","events_url":"https://api.github.com/users/ruchim/events{/privacy}","received_events_url":"https://api.github.com/users/ruchim/received_events","type":"User","site_admin":false},"labels":[{"id":1011625646,"node_id":"MDU6TGFiZWwxMDExNjI1NjQ2","url":"https://api.github.com/repos/broadinstitute/cromwell/labels/PAPI%20v2%20Blocker","name":"PAPI v2 Blocker","color":"aa3b12","default":false}],"state":"open","locked":false,"assignee":{"login":"mcovarr","id":10790523,"node_id":"MDQ6VXNlcjEwNzkwNTIz","avatar_url":"https://avatars1.githubusercontent.com/u/10790523?v=4","gravatar_id":"","url":"https://api.github.com/users/mcovarr","html_url":"https://github.com/mcovarr","followers_url":"https://api.github.com/users/mcovarr/followers","following_url":"https://api.github.com/users/mcovarr/following{/other_user}","gists_url":"https://api.github.com/users/mcovarr/gists{/gist_id}","starred_url":"https://api.github.com/users/mcovarr/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mcovarr/subscriptions","organizations_url":"https://api.github.com/users/mcovarr/orgs","repos_url":"https://api.github.com/users/mcovarr/repos","events_url":"https://api.github.com/users/mcovarr/events{/privacy}","received_events_url":"https://api.github.com/users/mcovarr/received_events","type":"User","site_admin":false},"assignees":[{"login":"mcovarr","id":10790523,"node_id":"MDQ6VXNlcjEwNzkwNTIz","avatar_url":"https://avatars1.githubusercontent.com/u/10790523?v=4","gravatar_id":"","url":"https://api.github.com/users/mcovarr","html_url":"https://github.com/mcovarr","followers_url":"https://api.github.com/users/mcovarr/followers","following_url":"https://api.github.com/users/mcovarr/following{/other_user}","gists_url":"https://api.github.com/users/mcovarr/gists{/gist_id}","starred_url":"https://api.github.com/users/mcovarr/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mcovarr/subscriptions","organizations_url":"https://api.github.com/users/mcovarr/orgs","repos_url":"https://api.github.com/users/mcovarr/repos","events_url":"https://api.github.com/users/mcovarr/events{/privacy}","received_events_url":"https://api.github.com/users/mcovarr/received_events","type":"User","site_admin":false}],"milestone":{"url":"https://api.github.com/repos/broadinstitute/cromwell/milestones/40","html_url":"https://github.com/broadinstitute/cromwell/milestone/40","labels_url":"https://api.github.com/repos/broadinstitute/cromwell/milestones/40/labels","id":3692639,"node_id":"MDk6TWlsZXN0b25lMzY5MjYzOQ==","number":40,"title":"Q4 - Transition all FireCloud/Saturn users to using Cromwell’s Pipelines API v2 backend","description":"[P0] No FireCloud/Saturn users are utilizing the PAPI v1 backend.\r\n[P1] Ensure all FireCloud/Saturn users can run the non-NIO version of the GATK variant discovery pipeline using DOS GUIDs.\r\n","creator":{"login":"ruchim","id":14941133,"node_id":"MDQ6VXNlcjE0OTQxMTMz","avatar_url":"https://avatars3.githubusercontent.com/u/14941133?v=4","gravatar_id":"","url":"https://api.github.com/users/ruchim","html_url":"https://github.com/ruchim","followers_url":"https://api.github.com/users/ruchim/followers","following_url":"https://api.github.com/users/ruchim/following{/other_user}","gists_url":"https://api.github.com/users/ruchim/gists{/gist_id}","starred_url":"https://api.github.com/users/ruchim/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ruchim/subscriptions","organizations_url":"https://api.github.com/users/ruchim/orgs","repos_url":"https://api.github.com/users/ruchim/repos","events_url":"https://api.github.com/users/ruchim/events{/privacy}","received_events_url":"https://api.github.com/users/ruchim/received_events","type":"User","site_admin":false},"open_issues":5,"closed_issues":0,"state":"open","created_at":"2018-09-27T07:05:57Z","updated_at":"2018-09-27T07:20:09Z","due_on":"2018-12-14T08:00:00Z","closed_at":null},"comments":2,"created_at":"2018-09-24T17:38:45Z","updated_at":"2018-10-12T21:13:04Z","closed_at":null,"author_association":"CONTRIBUTOR","body":"Based on a conversation with the Epigenomics group that is using Cromwell 34 on PAPI v2 --\r\nit seems that a task can fail, not delocalize an expected output and the workflow will continue to start a downstream task but fail at running the command (as an expected input is missing). It's been confirmed that Cromwell was running in a Fail fast mode.\r\n\r\nThere seem to be two main requirements here:\r\n1. Cromwell should be evaluating if all expected outputs for a task exist before marking the task as a success.\r\n2. Cromwell should fail a job if it failed localize a specific input file. \r\n3. Cromwell should fail a job if it failed to delocalize any expected output file.\r\n\r\nAC: Ensure that the PAPI v2 backend fulfills requirements #1-3.\r\n"},"comment":{"url":"https://api.github.com/repos/broadinstitute/cromwell/issues/comments/429463944","html_url":"https://github.com/broadinstitute/cromwell/issues/4140#issuecomment-429463944","issue_url":"https://api.github.com/repos/broadinstitute/cromwell/issues/4140","id":429463944,"node_id":"MDEyOklzc3VlQ29tbWVudDQyOTQ2Mzk0NA==","user":{"login":"mcovarr","id":10790523,"node_id":"MDQ6VXNlcjEwNzkwNTIz","avatar_url":"https://avatars1.githubusercontent.com/u/10790523?v=4","gravatar_id":"","url":"https://api.github.com/users/mcovarr","html_url":"https://github.com/mcovarr","followers_url":"https://api.github.com/users/mcovarr/followers","following_url":"https://api.github.com/users/mcovarr/following{/other_user}","gists_url":"https://api.github.com/users/mcovarr/gists{/gist_id}","starred_url":"https://api.github.com/users/mcovarr/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mcovarr/subscriptions","organizations_url":"https://api.github.com/users/mcovarr/orgs","repos_url":"https://api.github.com/users/mcovarr/repos","events_url":"https://api.github.com/users/mcovarr/events{/privacy}","received_events_url":"https://api.github.com/users/mcovarr/received_events","type":"User","site_admin":false},"created_at":"2018-10-12T21:13:04Z","updated_at":"2018-10-12T21:13:04Z","author_association":"CONTRIBUTOR","body":"There was a [34 hotfix](https://github.com/broadinstitute/cromwell/pull/4149) for this a while back. This should also be fixed in Cromwells 35 and greater."}}
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