{"action":"closed","issue":{"url":"https://api.github.com/repos/ga4gh/dockstore/issues/396","repository_url":"https://api.github.com/repos/ga4gh/dockstore","labels_url":"https://api.github.com/repos/ga4gh/dockstore/issues/396/labels{/name}","comments_url":"https://api.github.com/repos/ga4gh/dockstore/issues/396/comments","events_url":"https://api.github.com/repos/ga4gh/dockstore/issues/396/events","html_url":"https://github.com/ga4gh/dockstore/issues/396","id":175767723,"number":396,"title":"Expose extra cwltool parameters for debugging","user":{"login":"denis-yuen","id":1730679,"avatar_url":"https://avatars.githubusercontent.com/u/1730679?v=3","gravatar_id":"","url":"https://api.github.com/users/denis-yuen","html_url":"https://github.com/denis-yuen","followers_url":"https://api.github.com/users/denis-yuen/followers","following_url":"https://api.github.com/users/denis-yuen/following{/other_user}","gists_url":"https://api.github.com/users/denis-yuen/gists{/gist_id}","starred_url":"https://api.github.com/users/denis-yuen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/denis-yuen/subscriptions","organizations_url":"https://api.github.com/users/denis-yuen/orgs","repos_url":"https://api.github.com/users/denis-yuen/repos","events_url":"https://api.github.com/users/denis-yuen/events{/privacy}","received_events_url":"https://api.github.com/users/denis-yuen/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":{"login":"agduncan94","id":6331159,"avatar_url":"https://avatars.githubusercontent.com/u/6331159?v=3","gravatar_id":"","url":"https://api.github.com/users/agduncan94","html_url":"https://github.com/agduncan94","followers_url":"https://api.github.com/users/agduncan94/followers","following_url":"https://api.github.com/users/agduncan94/following{/other_user}","gists_url":"https://api.github.com/users/agduncan94/gists{/gist_id}","starred_url":"https://api.github.com/users/agduncan94/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/agduncan94/subscriptions","organizations_url":"https://api.github.com/users/agduncan94/orgs","repos_url":"https://api.github.com/users/agduncan94/repos","events_url":"https://api.github.com/users/agduncan94/events{/privacy}","received_events_url":"https://api.github.com/users/agduncan94/received_events","type":"User","site_admin":false},"assignees":[{"login":"agduncan94","id":6331159,"avatar_url":"https://avatars.githubusercontent.com/u/6331159?v=3","gravatar_id":"","url":"https://api.github.com/users/agduncan94","html_url":"https://github.com/agduncan94","followers_url":"https://api.github.com/users/agduncan94/followers","following_url":"https://api.github.com/users/agduncan94/following{/other_user}","gists_url":"https://api.github.com/users/agduncan94/gists{/gist_id}","starred_url":"https://api.github.com/users/agduncan94/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/agduncan94/subscriptions","organizations_url":"https://api.github.com/users/agduncan94/orgs","repos_url":"https://api.github.com/users/agduncan94/repos","events_url":"https://api.github.com/users/agduncan94/events{/privacy}","received_events_url":"https://api.github.com/users/agduncan94/received_events","type":"User","site_admin":false}],"milestone":null,"comments":1,"created_at":"2016-09-08T14:24:46Z","updated_at":"2016-09-08T16:14:56Z","closed_at":"2016-09-08T16:14:56Z","body":"## Feature Request \r\n\r\nWhen debugging tools (and workflows), it would be useful to expose additional parameters from cwltool. In particular, `--leave-tmpdir` and `--leave-container`.  `--debug` might also be useful (might already be exposed by `dockstore --debug`)\r\n\r\n### Desired behaviour\r\n\r\nA new flag in the configuration file (defaults to blank) that allows one to set additional parameters to cwltool launch. \r\n\r\n```\r\nubuntu@dkfz-psuedo-mega-testing:~/dkfz_dockered_workflows$ cat ~/.dockstore/config \r\ntoken: <blah>\r\nserver-url: https://staging.dockstore.org:8443\r\nuse-cache = true\r\ncwltool-extra-parameters = -- debug --leave-container\r\n```"}}
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