{"action":"created","issue":{"url":"https://api.github.com/repos/broadinstitute/cromwell/issues/891","repository_url":"https://api.github.com/repos/broadinstitute/cromwell","labels_url":"https://api.github.com/repos/broadinstitute/cromwell/issues/891/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/cromwell/issues/891/comments","events_url":"https://api.github.com/repos/broadinstitute/cromwell/issues/891/events","html_url":"https://github.com/broadinstitute/cromwell/issues/891","id":156808646,"number":891,"title":"JES: Files in output expressions not found","user":{"login":"cjllanwarne","id":13006282,"avatar_url":"https://avatars.githubusercontent.com/u/13006282?v=3","gravatar_id":"","url":"https://api.github.com/users/cjllanwarne","html_url":"https://github.com/cjllanwarne","followers_url":"https://api.github.com/users/cjllanwarne/followers","following_url":"https://api.github.com/users/cjllanwarne/following{/other_user}","gists_url":"https://api.github.com/users/cjllanwarne/gists{/gist_id}","starred_url":"https://api.github.com/users/cjllanwarne/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cjllanwarne/subscriptions","organizations_url":"https://api.github.com/users/cjllanwarne/orgs","repos_url":"https://api.github.com/users/cjllanwarne/repos","events_url":"https://api.github.com/users/cjllanwarne/events{/privacy}","received_events_url":"https://api.github.com/users/cjllanwarne/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/broadinstitute/cromwell/labels/in%20progress","name":"in 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following workflow fails:\n\nThis workflow fails:\n```\ntask MakeMeAFile {\n    command <<<\n      echo FILECONTENT > output.txt\n      >>>\n\n    runtime {\n      docker: \"ubuntu:latest\"\n      memory: \"1 GB\"\n      preemptible: 3\n    }\n\n    output {\n        String out = read_string(\"output.txt\")\n    }\n}\n\ntask ReadMeAFile {\n    File infile\n\n    command <<<\n        cat ${infile}\n    >>>\n\n    runtime {\n      docker: \"ubuntu:latest\"\n      memory: \"1 GB\"\n      preemptible: 3\n    }\n\n    output {\n        File out = read_string(stdout())\n    }\n}\n\nworkflow FileMakeAndRead {\n    call MakeMeAFile\n    call ReadMeAFile { input: infile = MakeMeAFile.out }\n}\n```\n\nBecause:\n```\n\"failures\": [\n  \"Could not find suitable filesystem to parse output.txt\"\n]\n```"},"comment":{"url":"https://api.github.com/repos/broadinstitute/cromwell/issues/comments/224936166","html_url":"https://github.com/broadinstitute/cromwell/issues/891#issuecomment-224936166","issue_url":"https://api.github.com/repos/broadinstitute/cromwell/issues/891","id":224936166,"user":{"login":"scottfrazer","id":58551,"avatar_url":"https://avatars.githubusercontent.com/u/58551?v=3","gravatar_id":"","url":"https://api.github.com/users/scottfrazer","html_url":"https://github.com/scottfrazer","followers_url":"https://api.github.com/users/scottfrazer/followers","following_url":"https://api.github.com/users/scottfrazer/following{/other_user}","gists_url":"https://api.github.com/users/scottfrazer/gists{/gist_id}","starred_url":"https://api.github.com/users/scottfrazer/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/scottfrazer/subscriptions","organizations_url":"https://api.github.com/users/scottfrazer/orgs","repos_url":"https://api.github.com/users/scottfrazer/repos","events_url":"https://api.github.com/users/scottfrazer/events{/privacy}","received_events_url":"https://api.github.com/users/scottfrazer/received_events","type":"User","site_admin":false},"created_at":"2016-06-09T15:42:25Z","updated_at":"2016-06-09T15:42:25Z","body":"So I'm getting much different behavior than the ticket describes... basically this WDL file is hanging indefinitely.  The first task finishes on both JES and local backends.  The second behaves in very strange ways.  It loops infinitely on JES and has a localization error on local.  I suspect it might be because of the problem with the WDL file itself (see previous comment)"}}
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