{"action":"closed","number":11,"pull_request":{"url":"https://api.github.com/repos/dnanexus/dx_ritchie/pulls/11","id":200552391,"node_id":"MDExOlB1bGxSZXF1ZXN0MjAwNTUyMzkx","html_url":"https://github.com/dnanexus/dx_ritchie/pull/11","diff_url":"https://github.com/dnanexus/dx_ritchie/pull/11.diff","patch_url":"https://github.com/dnanexus/dx_ritchie/pull/11.patch","issue_url":"https://api.github.com/repos/dnanexus/dx_ritchie/issues/11","number":11,"state":"closed","locked":false,"title":"Sci 1025 vcf query","user":{"login":"nainathangaraj","id":6821182,"node_id":"MDQ6VXNlcjY4MjExODI=","avatar_url":"https://avatars1.githubusercontent.com/u/6821182?v=4","gravatar_id":"","url":"https://api.github.com/users/nainathangaraj","html_url":"https://github.com/nainathangaraj","followers_url":"https://api.github.com/users/nainathangaraj/followers","following_url":"https://api.github.com/users/nainathangaraj/following{/other_user}","gists_url":"https://api.github.com/users/nainathangaraj/gists{/gist_id}","starred_url":"https://api.github.com/users/nainathangaraj/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nainathangaraj/subscriptions","organizations_url":"https://api.github.com/users/nainathangaraj/orgs","repos_url":"https://api.github.com/users/nainathangaraj/repos","events_url":"https://api.github.com/users/nainathangaraj/events{/privacy}","received_events_url":"https://api.github.com/users/nainathangaraj/received_events","type":"User","site_admin":false},"body":"#dxapp.json\r\n- [x] Upgrade to 14.04\r\n- [x] Add help and extension to input spec.\r\n- [x] In `details` field specify: `whatsNew`and `citation` (leave blank for citation.\r\n- [x] In `details` consider specifying `upstreamAuthor` and `upstreamVersion` fields when applicable.\r\n- [x] Use `regionalOptions` \r\n- [x] Set applicable timeout (Be relax) and restart policy in [`runSpec`](https://wiki.dnanexus.com/API-Specification-v1.0.0/IO-and-Run-Specifications).\r\n- [x] Add subjob restartability when applicable.\r\n- [x] `version` field, set proper [semantic versioning](https://semver.org/).\r\n- [x] Setting `\"openSource\": true`. \r\n- [x] Run [dxapp linter](https://github.com/dnanexus/RoughER/blob/master/scripts/dxapp_lint.py) [[permalink](https://github.com/dnanexus/RoughER/blob/ecb3ea3f97870c020f93bf4723afc9f40a310e33/scripts/dxapp_lint.py)] on `dxapp.json`.\r\n- [x] Use AssetDepend instead of execDepend\r\n- [x] Add default instance type that works for a general use case.\r\n- [x] add new input if applicable\r\n\r\n#src/code.sh src/code.py\r\n- [ ] GATK tarball should be removed from the resource project (or make a new resource project), and the applet should require GATK tarball as a required input. This way, the users are enforced to provide their own tarball. This would avoid trouble from non-academic entities without GATK license to use your tarball.\r\n\r\n# Readme.md\r\n- [x] Improve Readme file to contain applet function, use case, input/output description, underline execution if it’s a wrapper.\r\n- [x] Read documentation for sanity check. (Unpublished app URL will be: https://platform.dnanexus.com/app/app-xxxx)\r\n\r\n# Test\r\n- [x] Basic testing using given input in Box or expected input\r\n- [x] Make a Pull Request to `master` in https://github.com/RitchieLab/dnanexus\r\n\r\n# Production\r\n- [ ] Co-test with Ritchie group\r\n- [ ] Help Ritchie group to publish (Give dx command)\r\n- [ ] Verify the versions that appear on the platform are the intended versions\r\n- [ ] Set up demo workflow in public project.\r\n","created_at":"2018-07-10T23:44:50Z","updated_at":"2018-07-16T21:00:38Z","closed_at":"2018-07-16T21:00:38Z","merged_at":"2018-07-16T21:00:38Z","merge_commit_sha":"e79ec85ebf2da601b11f2fb413e429c13f10c214","assignee":{"login":"nainathangaraj","id":6821182,"node_id":"MDQ6VXNlcjY4MjExODI=","avatar_url":"https://avatars1.githubusercontent.com/u/6821182?v=4","gravatar_id":"","url":"https://api.github.com/users/nainathangaraj","html_url":"https://github.com/nainathangaraj","followers_url":"https://api.github.com/users/nainathangaraj/followers","following_url":"https://api.github.com/users/nainathangaraj/following{/other_user}","gists_url":"https://api.github.com/users/nainathangaraj/gists{/gist_id}","starred_url":"https://api.github.com/users/nainathangaraj/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nainathangaraj/subscriptions","organizations_url":"https://api.github.com/users/nainathangaraj/orgs","repos_url":"https://api.github.com/users/nainathangaraj/repos","events_url":"https://api.github.com/users/nainathangaraj/events{/privacy}","received_events_url":"https://api.github.com/users/nainathangaraj/received_events","type":"User","site_admin":false},"assignees":[{"login":"nainathangaraj","id":6821182,"node_id":"MDQ6VXNlcjY4MjExODI=","avatar_url":"https://avatars1.githubusercontent.com/u/6821182?v=4","gravatar_id":"","url":"https://api.github.com/users/nainathangaraj","html_url":"https://github.com/nainathangaraj","followers_url":"https://api.github.com/users/nainathangaraj/followers","following_url":"https://api.github.com/users/nainathangaraj/following{/other_user}","gists_url":"https://api.github.com/users/nainathangaraj/gists{/gist_id}","starred_url":"https://api.github.com/users/nainathangaraj/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nainathangaraj/subscriptions","organizations_url":"https://api.github.com/users/nainathangaraj/orgs","repos_url":"https://api.github.com/users/nainathangaraj/repos","events_url":"https://api.github.com/users/nainathangaraj/events{/privacy}","received_events_url":"https://api.github.com/users/nainathangaraj/received_events","type":"User","site_admin":false}],"requested_reviewers":[{"login":"Arkarachai","id":1155815,"node_id":"MDQ6VXNlcjExNTU4MTU=","avatar_url":"https://avatars0.githubusercontent.com/u/1155815?v=4","gravatar_id":"","url":"https://api.github.com/users/Arkarachai","html_url":"https://github.com/Arkarachai","followers_url":"https://api.github.com/users/Arkarachai/followers","following_url":"https://api.github.com/users/Arkarachai/following{/other_user}","gists_url":"https://api.github.com/users/Arkarachai/gists{/gist_id}","starred_url":"https://api.github.com/users/Arkarachai/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Arkarachai/subscriptions","organizations_url":"https://api.github.com/users/Arkarachai/orgs","repos_url":"https://api.github.com/users/Arkarachai/repos","events_url":"https://api.github.com/users/Arkarachai/events{/privacy}","received_events_url":"https://api.github.com/users/Arkarachai/received_events","type":"User","site_admin":false}],"requested_teams":[],"labels":[],"milestone":null,"commits_url":"https://api.github.com/repos/dnanexus/dx_ritchie/pulls/11/commits","review_comments_url":"https://api.github.com/repos/dnanexus/dx_ritchie/pulls/11/comments","review_comment_url":"https://api.github.com/repos/dnanexus/dx_ritchie/pulls/comments{/number}","comments_url":"https://api.github.com/repos/dnanexus/dx_ritchie/issues/11/comments","statuses_url":"https://api.github.com/repos/dnanexus/dx_ritchie/statuses/f6f006f4783ed45aef42ffa2ca8190551c194bb7","head":{"label":"dnanexus:SCI-1025_vcf_query","ref":"SCI-1025_vcf_query","sha":"f6f006f4783ed45aef42ffa2ca8190551c194bb7","user":{"login":"dnanexus","id":1161297,"node_id":"MDEyOk9yZ2FuaXphdGlvbjExNjEyOTc=","avatar_url":"https://avatars0.githubusercontent.com/u/1161297?v=4","gravatar_id":"","url":"https://api.github.com/users/dnanexus","html_url":"https://github.com/dnanexus","followers_url":"https://api.github.com/users/dnanexus/followers","following_url":"https://api.github.com/users/dnanexus/following{/other_user}","gists_url":"https://api.github.com/users/dnanexus/gists{/gist_id}","starred_url":"https://api.github.com/users/dnanexus/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dnanexus/subscriptions","organizations_url":"https://api.github.com/users/dnanexus/orgs","repos_url":"https://api.github.com/users/dnanexus/repos","events_url":"https://api.github.com/users/dnanexus/events{/privacy}","received_events_url":"https://api.github.com/users/dnanexus/received_events","type":"Organization","site_admin":false},"repo":{"id":138663632,"node_id":"MDEwOlJlcG9zaXRvcnkxMzg2NjM2MzI=","name":"dx_ritchie","full_name":"dnanexus/dx_ritchie","owner":{"login":"dnanexus","id":1161297,"node_id":"MDEyOk9yZ2FuaXphdGlvbjExNjEyOTc=","avatar_url":"https://avatars0.githubusercontent.com/u/1161297?v=4","gravatar_id":"","url":"https://api.github.com/users/dnanexus","html_url":"https://github.com/dnanexus","followers_url":"https://api.github.com/users/dnanexus/followers","following_url":"https://api.github.com/users/dnanexus/following{/other_user}","gists_url":"https://api.github.com/users/dnanexus/gists{/gist_id}","starred_url":"https://api.github.com/users/dnanexus/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dnanexus/subscriptions","organizations_url":"https://api.github.com/users/dnanexus/orgs","repos_url":"https://api.github.com/users/dnanexus/repos","events_url":"https://api.github.com/users/dnanexus/events{/privacy}","received_events_url":"https://api.github.com/users/dnanexus/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/dnanexus/dx_ritchie","description":null,"fork":true,"url":"https://api.github.com/repos/dnanexus/dx_ritchie","forks_url":"https://api.github.com/repos/dnanexus/dx_ritchie/forks","keys_url":"https://api.github.com/repos/dnanexus/dx_ritchie/keys{/key_id}","collaborators_url":"https://api.github.com/repos/dnanexus/dx_ritchie/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/dnanexus/dx_ritchie/teams","hooks_url":"https://api.github.com/repos/dnanexus/dx_ritchie/hooks","issue_events_url":"https://api.github.com/repos/dnanexus/dx_ritchie/issues/events{/number}","events_url":"https://api.github.com/repos/dnanexus/dx_ritchie/events","assignees_url":"https://api.github.com/repos/dnanexus/dx_ritchie/assignees{/user}","branches_url":"https://api.github.com/repos/dnanexus/dx_ritchie/branches{/branch}","tags_url":"https://api.github.com/repos/dnanexus/dx_ritchie/tags","blobs_url":"https://api.github.com/repos/dnanexus/dx_ritchie/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/dnanexus/dx_ritchie/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/dnanexus/dx_ritchie/git/refs{/sha}","trees_url":"https://api.github.com/repos/dnanexus/dx_ritchie/git/trees{/sha}","statuses_url":"https://api.github.com/repos/dnanexus/dx_ritchie/statuses/{sha}","languages_url":"https://api.github.com/repos/dnanexus/dx_ritchie/languages","stargazers_url":"https://api.github.com/repos/dnanexus/dx_ritchie/stargazers","contributors_url":"https://api.github.com/repos/dnanexus/dx_ritchie/contributors","subscribers_url":"https://api.github.com/repos/dnanexus/dx_ritchie/subscribers","subscription_url":"https://api.github.com/repos/dnanexus/dx_ritchie/subscription","commits_url":"https://api.github.com/repos/dnanexus/dx_ritchie/commits{/sha}","git_commits_url":"https://api.github.com/repos/dnanexus/dx_ritchie/git/commits{/sha}","comments_url":"https://api.github.com/repos/dnanexus/dx_ritchie/comments{/number}","issue_comment_url":"https://api.github.com/repos/dnanexus/dx_ritchie/issues/comments{/number}","contents_url":"https://api.github.com/repos/dnanexus/dx_ritchie/contents/{+path}","compare_url":"https://api.github.com/repos/dnanexus/dx_ritchie/compare/{base}...{head}","merges_url":"https://api.github.com/repos/dnanexus/dx_ritchie/merges","archive_url":"https://api.github.com/repos/dnanexus/dx_ritchie/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/dnanexus/dx_ritchie/downloads","issues_url":"https://api.github.com/repos/dnanexus/dx_ritchie/issues{/number}","pulls_url":"https://api.github.com/repos/dnanexus/dx_ritchie/pulls{/number}","milestones_url":"https://api.github.com/repos/dnanexus/dx_ritchie/milestones{/number}","notifications_url":"https://api.github.com/repos/dnanexus/dx_ritchie/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/dnanexus/dx_ritchie/labels{/name}","releases_url":"https://api.github.com/repos/dnanexus/dx_ritchie/releases{/id}","deployments_url":"https://api.github.com/repos/dnanexus/dx_ritchie/deployments","created_at":"2018-06-26T00:22:09Z","updated_at":"2018-07-16T20:39:19Z","pushed_at":"2018-07-16T21:00:38Z","git_url":"git://github.com/dnanexus/dx_ritchie.git","ssh_url":"git@github.com:dnanexus/dx_ritchie.git","clone_url":"https://github.com/dnanexus/dx_ritchie.git","svn_url":"https://github.com/dnanexus/dx_ritchie","homepage":null,"size":109843,"stargazers_count":0,"watchers_count":0,"language":"C++","has_issues":false,"has_projects":true,"has_downloads":true,"has_wiki":true,"has_pages":false,"forks_count":0,"mirror_url":null,"archived":false,"open_issues_count":10,"license":null,"forks":0,"open_issues":10,"watchers":0,"default_branch":"master"}},"base":{"label":"dnanexus:master","ref":"master","sha":"a12d42525939179e974c48ee32c25a9025b76ae2","user":{"login":"dnanexus","id":1161297,"node_id":"MDEyOk9yZ2FuaXphdGlvbjExNjEyOTc=","avatar_url":"https://avatars0.githubusercontent.com/u/1161297?v=4","gravatar_id":"","url":"https://api.github.com/users/dnanexus","html_url":"https://github.com/dnanexus","followers_url":"https://api.github.com/users/dnanexus/followers","following_url":"https://api.github.com/users/dnanexus/following{/other_user}","gists_url":"https://api.github.com/users/dnanexus/gists{/gist_id}","starred_url":"https://api.github.com/users/dnanexus/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dnanexus/subscriptions","organizations_url":"https://api.github.com/users/dnanexus/orgs","repos_url":"https://api.github.com/users/dnanexus/repos","events_url":"https://api.github.com/users/dnanexus/events{/privacy}","received_events_url":"https://api.github.com/users/dnanexus/received_events","type":"Organization","site_admin":false},"repo":{"id":138663632,"node_id":"MDEwOlJlcG9zaXRvcnkxMzg2NjM2MzI=","name":"dx_ritchie","full_name":"dnanexus/dx_ritchie","owner":{"login":"dnanexus","id":1161297,"node_id":"MDEyOk9yZ2FuaXphdGlvbjExNjEyOTc=","avatar_url":"https://avatars0.githubusercontent.com/u/1161297?v=4","gravatar_id":"","url":"https://api.github.com/users/dnanexus","html_url":"https://github.com/dnanexus","followers_url":"https://api.github.com/users/dnanexus/followers","following_url":"https://api.github.com/users/dnanexus/following{/other_user}","gists_url":"https://api.github.com/users/dnanexus/gists{/gist_id}","starred_url":"https://api.github.com/users/dnanexus/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dnanexus/subscriptions","organizations_url":"https://api.github.com/users/dnanexus/orgs","repos_url":"https://api.github.com/users/dnanexus/repos","events_url":"https://api.github.com/users/dnanexus/events{/privacy}","received_events_url":"https://api.github.com/users/dnanexus/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/dnanexus/dx_ritchie","description":null,"fork":true,"url":"https://api.github.com/repos/dnanexus/dx_ritchie","forks_url":"https://api.github.com/repos/dnanexus/dx_ritchie/forks","keys_url":"https://api.github.com/repos/dnanexus/dx_ritchie/keys{/key_id}","collaborators_url":"https://api.github.com/repos/dnanexus/dx_ritchie/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/dnanexus/dx_ritchie/teams","hooks_url":"https://api.github.com/repos/dnanexus/dx_ritchie/hooks","issue_events_url":"https://api.github.com/repos/dnanexus/dx_ritchie/issues/events{/number}","events_url":"https://api.github.com/repos/dnanexus/dx_ritchie/events","assignees_url":"https://api.github.com/repos/dnanexus/dx_ritchie/assignees{/user}","branches_url":"https://api.github.com/repos/dnanexus/dx_ritchie/branches{/branch}","tags_url":"https://api.github.com/repos/dnanexus/dx_ritchie/tags","blobs_url":"https://api.github.com/repos/dnanexus/dx_ritchie/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/dnanexus/dx_ritchie/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/dnanexus/dx_ritchie/git/refs{/sha}","trees_url":"https://api.github.com/repos/dnanexus/dx_ritchie/git/trees{/sha}","statuses_url":"https://api.github.com/repos/dnanexus/dx_ritchie/statuses/{sha}","languages_url":"https://api.github.com/repos/dnanexus/dx_ritchie/languages","stargazers_url":"https://api.github.com/repos/dnanexus/dx_ritchie/stargazers","contributors_url":"https://api.github.com/repos/dnanexus/dx_ritchie/contributors","subscribers_url":"https://api.github.com/repos/dnanexus/dx_ritchie/subscribers","subscription_url":"https://api.github.com/repos/dnanexus/dx_ritchie/subscription","commits_url":"https://api.github.com/repos/dnanexus/dx_ritchie/commits{/sha}","git_commits_url":"https://api.github.com/repos/dnanexus/dx_ritchie/git/commits{/sha}","comments_url":"https://api.github.com/repos/dnanexus/dx_ritchie/comments{/number}","issue_comment_url":"https://api.github.com/repos/dnanexus/dx_ritchie/issues/comments{/number}","contents_url":"https://api.github.com/repos/dnanexus/dx_ritchie/contents/{+path}","compare_url":"https://api.github.com/repos/dnanexus/dx_ritchie/compare/{base}...{head}","merges_url":"https://api.github.com/repos/dnanexus/dx_ritchie/merges","archive_url":"https://api.github.com/repos/dnanexus/dx_ritchie/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/dnanexus/dx_ritchie/downloads","issues_url":"https://api.github.com/repos/dnanexus/dx_ritchie/issues{/number}","pulls_url":"https://api.github.com/repos/dnanexus/dx_ritchie/pulls{/number}","milestones_url":"https://api.github.com/repos/dnanexus/dx_ritchie/milestones{/number}","notifications_url":"https://api.github.com/repos/dnanexus/dx_ritchie/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/dnanexus/dx_ritchie/labels{/name}","releases_url":"https://api.github.com/repos/dnanexus/dx_ritchie/releases{/id}","deployments_url":"https://api.github.com/repos/dnanexus/dx_ritchie/deployments","created_at":"2018-06-26T00:22:09Z","updated_at":"2018-07-16T20:39:19Z","pushed_at":"2018-07-16T21:00:38Z","git_url":"git://github.com/dnanexus/dx_ritchie.git","ssh_url":"git@github.com:dnanexus/dx_ritchie.git","clone_url":"https://github.com/dnanexus/dx_ritchie.git","svn_url":"https://github.com/dnanexus/dx_ritchie","homepage":null,"size":109843,"stargazers_count":0,"watchers_count":0,"language":"C++","has_issues":false,"has_projects":true,"has_downloads":true,"has_wiki":true,"has_pages":false,"forks_count":0,"mirror_url":null,"archived":false,"open_issues_count":10,"license":null,"forks":0,"open_issues":10,"watchers":0,"default_branch":"master"}},"_links":{"self":{"href":"https://api.github.com/repos/dnanexus/dx_ritchie/pulls/11"},"html":{"href":"https://github.com/dnanexus/dx_ritchie/pull/11"},"issue":{"href":"https://api.github.com/repos/dnanexus/dx_ritchie/issues/11"},"comments":{"href":"https://api.github.com/repos/dnanexus/dx_ritchie/issues/11/comments"},"review_comments":{"href":"https://api.github.com/repos/dnanexus/dx_ritchie/pulls/11/comments"},"review_comment":{"href":"https://api.github.com/repos/dnanexus/dx_ritchie/pulls/comments{/number}"},"commits":{"href":"https://api.github.com/repos/dnanexus/dx_ritchie/pulls/11/commits"},"statuses":{"href":"https://api.github.com/repos/dnanexus/dx_ritchie/statuses/f6f006f4783ed45aef42ffa2ca8190551c194bb7"}},"author_association":"COLLABORATOR","merged":true,"mergeable":null,"rebaseable":null,"mergeable_state":"unknown","merged_by":{"login":"nainathangaraj","id":6821182,"node_id":"MDQ6VXNlcjY4MjExODI=","avatar_url":"https://avatars1.githubusercontent.com/u/6821182?v=4","gravatar_id":"","url":"https://api.github.com/users/nainathangaraj","html_url":"https://github.com/nainathangaraj","followers_url":"https://api.github.com/users/nainathangaraj/followers","following_url":"https://api.github.com/users/nainathangaraj/following{/other_user}","gists_url":"https://api.github.com/users/nainathangaraj/gists{/gist_id}","starred_url":"https://api.github.com/users/nainathangaraj/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nainathangaraj/subscriptions","organizations_url":"https://api.github.com/users/nainathangaraj/orgs","repos_url":"https://api.github.com/users/nainathangaraj/repos","events_url":"https://api.github.com/users/nainathangaraj/events{/privacy}","received_events_url":"https://api.github.com/users/nainathangaraj/received_events","type":"User","site_admin":false},"comments":2,"review_comments":11,"maintainer_can_modify":false,"commits":8,"additions":243,"deletions":103,"changed_files":6}}
{"actor":{"display_login":"nainathangaraj"}}