{"action":"opened","issue":{"url":"https://api.github.com/repos/BD2KGenomics/toil/issues/615","labels_url":"https://api.github.com/repos/BD2KGenomics/toil/issues/615/labels{/name}","comments_url":"https://api.github.com/repos/BD2KGenomics/toil/issues/615/comments","events_url":"https://api.github.com/repos/BD2KGenomics/toil/issues/615/events","html_url":"https://github.com/BD2KGenomics/toil/issues/615","id":120602838,"number":615,"title":"CWL secondaryFiles need to be copied into working directories","user":{"login":"kellrott","id":113868,"avatar_url":"https://avatars.githubusercontent.com/u/113868?v=3","gravatar_id":"","url":"https://api.github.com/users/kellrott","html_url":"https://github.com/kellrott","followers_url":"https://api.github.com/users/kellrott/followers","following_url":"https://api.github.com/users/kellrott/following{/other_user}","gists_url":"https://api.github.com/users/kellrott/gists{/gist_id}","starred_url":"https://api.github.com/users/kellrott/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/kellrott/subscriptions","organizations_url":"https://api.github.com/users/kellrott/orgs","repos_url":"https://api.github.com/users/kellrott/repos","events_url":"https://api.github.com/users/kellrott/events{/privacy}","received_events_url":"https://api.github.com/users/kellrott/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-12-06T02:27:50Z","updated_at":"2015-12-06T02:27:50Z","closed_at":null,"body":"Secondary files defined in CWL files (as part of the inputBinding) need to be copied into place.\r\nFor example in the case of a tool that defines a BAM file, and its index .bai file:\r\n\r\n```\r\n  - id: \"#input\"\r\n    type: File\r\n    inputBinding:\r\n      position: 1\r\n      secondaryFiles:\r\n        - .bai\r\n```\r\n\r\nWill give the error:\r\n\r\n```\r\nWARNING:toil.leader:Reporting file: Q/9/jobfpSkdv\r\nWARNING:toil.leader:Q/9/jobfpSkdv:\t---TOIL WORKER OUTPUT LOG---\r\nWARNING:toil.leader:Q/9/jobfpSkdv:\tINFO:rdflib:RDFLib Version: 4.2.1\r\nWARNING:toil.leader:Q/9/jobfpSkdv:\tTraceback (most recent call last):\r\nWARNING:toil.leader:Q/9/jobfpSkdv:\t  File \"/Users/ellrott/workspaces/mc3_cwl/venv/lib/python2.7/site-packages/toil-3.2.0a2-py2.7.egg/toil/worker.py\", line 282, in main\r\nWARNING:toil.leader:Q/9/jobfpSkdv:\t    fileStore=fileStore)\r\nWARNING:toil.leader:Q/9/jobfpSkdv:\t  File \"/Users/ellrott/workspaces/mc3_cwl/venv/lib/python2.7/site-packages/toil-3.2.0a2-py2.7.egg/toil/job.py\", line 1281, in _execute\r\nWARNING:toil.leader:Q/9/jobfpSkdv:\t    returnValues = self.run(fileStore)\r\nWARNING:toil.leader:Q/9/jobfpSkdv:\t  File \"/Users/ellrott/workspaces/mc3_cwl/venv/lib/python2.7/site-packages/toil-3.2.0a2-py2.7.egg/toil/cwl/cwltoil.py\", line 163, in run\r\nWARNING:toil.leader:Q/9/jobfpSkdv:\t    tmpdir=tmpdir)\r\nWARNING:toil.leader:Q/9/jobfpSkdv:\t  File \"/Users/ellrott/workspaces/mc3_cwl/venv/lib/python2.7/site-packages/cwltool/main.py\", line 159, in single_job_executor\r\nWARNING:toil.leader:Q/9/jobfpSkdv:\t    r.run(**kwargs)\r\nWARNING:toil.leader:Q/9/jobfpSkdv:\t  File \"/Users/ellrott/workspaces/mc3_cwl/venv/lib/python2.7/site-packages/cwltool/job.py\", line 51, in run\r\nWARNING:toil.leader:Q/9/jobfpSkdv:\t    raise WorkflowException(\"Required input file %s not found\" % self.pathmapper.mapper(f)[0])\r\nWARNING:toil.leader:Q/9/jobfpSkdv:\tWorkflowException: Required input file /Users/ellrott/workspaces/mc3_cwl/work/tmpPZLXOr/localTempDir/tvwSkaZ/inp/testexome.pair0.normal.bam.bai not found\r\nWARNING:toil.leader:Q/9/jobfpSkdv:\tExiting the worker because of a failed jobWrapper on host RJHB298\r\nWARNING:toil.leader:Q/9/jobfpSkdv:\tERROR:toil.worker:Exiting the worker because of a failed jobWrapper on host RJHB298\r\nWARNING:toil.leader:Q/9/jobfpSkdv:\tWARNING:toil.jobWrapper:Due to failure we are reducing the remaining retry count of job Q/9/jobfpSkdv to 0\r\n```"}}