{"action":"closed","number":34,"pull_request":{"url":"https://api.github.com/repos/qiime2/q2-dada2/pulls/34","id":101620461,"html_url":"https://github.com/qiime2/q2-dada2/pull/34","diff_url":"https://github.com/qiime2/q2-dada2/pull/34.diff","patch_url":"https://github.com/qiime2/q2-dada2/pull/34.patch","issue_url":"https://api.github.com/repos/qiime2/q2-dada2/issues/34","number":34,"state":"closed","locked":false,"title":"Paired end workflow","user":{"login":"benjjneb","id":5797204,"avatar_url":"https://avatars.githubusercontent.com/u/5797204?v=3","gravatar_id":"","url":"https://api.github.com/users/benjjneb","html_url":"https://github.com/benjjneb","followers_url":"https://api.github.com/users/benjjneb/followers","following_url":"https://api.github.com/users/benjjneb/following{/other_user}","gists_url":"https://api.github.com/users/benjjneb/gists{/gist_id}","starred_url":"https://api.github.com/users/benjjneb/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/benjjneb/subscriptions","organizations_url":"https://api.github.com/users/benjjneb/orgs","repos_url":"https://api.github.com/users/benjjneb/repos","events_url":"https://api.github.com/users/benjjneb/events{/privacy}","received_events_url":"https://api.github.com/users/benjjneb/received_events","type":"User","site_admin":false},"body":"This branch implements, on the R side, an updated multithreaded workflow (`run_dada_faster.R`) that also estimates error rates from a subset of the data. The speedup relative to the old workflow will vary based on the size of the dataset and the computational resources available, but will increase for larger datasets and more available cores. On small datasets (eg. the mothur Miseq tutorial dataset) and a laptop the speedup is about 2x. On large datasets (eg. our Hiseq lanes with 800 multiplexed samples) and a 32-core compute node, the speedup is about 100x.\r\n\r\nThis branch also implements, on the R side, a similarly performant paired-end workflow (`run_dada_faster_paired.R`).\r\n\r\nI've also tried to make the standard output somewhat more informative for this push-button application, and to improve the commented documentation of the R scripts.\r\n\r\nThe previous script (`run_dada.R`) remains unchanged (excepting comments) for testing purposes.\r\n\r\nNOTHING WORKS FROM THE QIIME2/PYTHON SIDE YET! I've only updated the R scripts, and tested them with direct Rscript invocations. Corresponding changes are now needed on the python side.\r\n\r\nThis branch addresses #9, #12, #16 and #31. It depends on #33 as it expects dada2 version 1.2","created_at":"2017-01-16T02:05:00Z","updated_at":"2017-01-30T19:41:30Z","closed_at":"2017-01-30T19:41:30Z","merged_at":null,"merge_commit_sha":"824946a4812daa042e0ceed23ce7512d8891a2a1","assignee":null,"assignees":[],"milestone":null,"commits_url":"https://api.github.com/repos/qiime2/q2-dada2/pulls/34/commits","review_comments_url":"https://api.github.com/repos/qiime2/q2-dada2/pulls/34/comments","review_comment_url":"https://api.github.com/repos/qiime2/q2-dada2/pulls/comments{/number}","comments_url":"https://api.github.com/repos/qiime2/q2-dada2/issues/34/comments","statuses_url":"https://api.github.com/repos/qiime2/q2-dada2/statuses/577a1c12034abb3f8e2cbe7dc5bee286146eedc4","head":{"label":"qiime2:paired-end-workflow","ref":"paired-end-workflow","sha":"577a1c12034abb3f8e2cbe7dc5bee286146eedc4","user":{"login":"qiime2","id":18176583,"avatar_url":"https://avatars.githubusercontent.com/u/18176583?v=3","gravatar_id":"","url":"https://api.github.com/users/qiime2","html_url":"https://github.com/qiime2","followers_url":"https://api.github.com/users/qiime2/followers","following_url":"https://api.github.com/users/qiime2/following{/other_user}","gists_url":"https://api.github.com/users/qiime2/gists{/gist_id}","starred_url":"https://api.github.com/users/qiime2/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/qiime2/subscriptions","organizations_url":"https://api.github.com/users/qiime2/orgs","repos_url":"https://api.github.com/users/qiime2/repos","events_url":"https://api.github.com/users/qiime2/events{/privacy}","received_events_url":"https://api.github.com/users/qiime2/received_events","type":"Organization","site_admin":false},"repo":{"id":65170702,"name":"q2-dada2","full_name":"qiime2/q2-dada2","owner":{"login":"qiime2","id":18176583,"avatar_url":"https://avatars.githubusercontent.com/u/18176583?v=3","gravatar_id":"","url":"https://api.github.com/users/qiime2","html_url":"https://github.com/qiime2","followers_url":"https://api.github.com/users/qiime2/followers","following_url":"https://api.github.com/users/qiime2/following{/other_user}","gists_url":"https://api.github.com/users/qiime2/gists{/gist_id}","starred_url":"https://api.github.com/users/qiime2/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/qiime2/subscriptions","organizations_url":"https://api.github.com/users/qiime2/orgs","repos_url":"https://api.github.com/users/qiime2/repos","events_url":"https://api.github.com/users/qiime2/events{/privacy}","received_events_url":"https://api.github.com/users/qiime2/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/qiime2/q2-dada2","description":"R scripts for DADA2 QIIME2 plugin","fork":false,"url":"https://api.github.com/repos/qiime2/q2-dada2","forks_url":"https://api.github.com/repos/qiime2/q2-dada2/forks","keys_url":"https://api.github.com/repos/qiime2/q2-dada2/keys{/key_id}","collaborators_url":"https://api.github.com/repos/qiime2/q2-dada2/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/qiime2/q2-dada2/teams","hooks_url":"https://api.github.com/repos/qiime2/q2-dada2/hooks","issue_events_url":"https://api.github.com/repos/qiime2/q2-dada2/issues/events{/number}","events_url":"https://api.github.com/repos/qiime2/q2-dada2/events","assignees_url":"https://api.github.com/repos/qiime2/q2-dada2/assignees{/user}","branches_url":"https://api.github.com/repos/qiime2/q2-dada2/branches{/branch}","tags_url":"https://api.github.com/repos/qiime2/q2-dada2/tags","blobs_url":"https://api.github.com/repos/qiime2/q2-dada2/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/qiime2/q2-dada2/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/qiime2/q2-dada2/git/refs{/sha}","trees_url":"https://api.github.com/repos/qiime2/q2-dada2/git/trees{/sha}","statuses_url":"https://api.github.com/repos/qiime2/q2-dada2/statuses/{sha}","languages_url":"https://api.github.com/repos/qiime2/q2-dada2/languages","stargazers_url":"https://api.github.com/repos/qiime2/q2-dada2/stargazers","contributors_url":"https://api.github.com/repos/qiime2/q2-dada2/contributors","subscribers_url":"https://api.github.com/repos/qiime2/q2-dada2/subscribers","subscription_url":"https://api.github.com/repos/qiime2/q2-dada2/subscription","commits_url":"https://api.github.com/repos/qiime2/q2-dada2/commits{/sha}","git_commits_url":"https://api.github.com/repos/qiime2/q2-dada2/git/commits{/sha}","comments_url":"https://api.github.com/repos/qiime2/q2-dada2/comments{/number}","issue_comment_url":"https://api.github.com/repos/qiime2/q2-dada2/issues/comments{/number}","contents_url":"https://api.github.com/repos/qiime2/q2-dada2/contents/{+path}","compare_url":"https://api.github.com/repos/qiime2/q2-dada2/compare/{base}...{head}","merges_url":"https://api.github.com/repos/qiime2/q2-dada2/merges","archive_url":"https://api.github.com/repos/qiime2/q2-dada2/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/qiime2/q2-dada2/downloads","issues_url":"https://api.github.com/repos/qiime2/q2-dada2/issues{/number}","pulls_url":"https://api.github.com/repos/qiime2/q2-dada2/pulls{/number}","milestones_url":"https://api.github.com/repos/qiime2/q2-dada2/milestones{/number}","notifications_url":"https://api.github.com/repos/qiime2/q2-dada2/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/qiime2/q2-dada2/labels{/name}","releases_url":"https://api.github.com/repos/qiime2/q2-dada2/releases{/id}","deployments_url":"https://api.github.com/repos/qiime2/q2-dada2/deployments","created_at":"2016-08-08T03:47:29Z","updated_at":"2016-11-02T19:01:32Z","pushed_at":"2017-01-30T19:40:14Z","git_url":"git://github.com/qiime2/q2-dada2.git","ssh_url":"git@github.com:qiime2/q2-dada2.git","clone_url":"https://github.com/qiime2/q2-dada2.git","svn_url":"https://github.com/qiime2/q2-dada2","homepage":null,"size":12056,"stargazers_count":0,"watchers_count":0,"language":"Python","has_issues":true,"has_downloads":true,"has_wiki":true,"has_pages":false,"forks_count":5,"mirror_url":null,"open_issues_count":12,"forks":5,"open_issues":12,"watchers":0,"default_branch":"master"}},"base":{"label":"qiime2:master","ref":"master","sha":"bc5d7634671dc1cd67f713a621e0d3cb53236572","user":{"login":"qiime2","id":18176583,"avatar_url":"https://avatars.githubusercontent.com/u/18176583?v=3","gravatar_id":"","url":"https://api.github.com/users/qiime2","html_url":"https://github.com/qiime2","followers_url":"https://api.github.com/users/qiime2/followers","following_url":"https://api.github.com/users/qiime2/following{/other_user}","gists_url":"https://api.github.com/users/qiime2/gists{/gist_id}","starred_url":"https://api.github.com/users/qiime2/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/qiime2/subscriptions","organizations_url":"https://api.github.com/users/qiime2/orgs","repos_url":"https://api.github.com/users/qiime2/repos","events_url":"https://api.github.com/users/qiime2/events{/privacy}","received_events_url":"https://api.github.com/users/qiime2/received_events","type":"Organization","site_admin":false},"repo":{"id":65170702,"name":"q2-dada2","full_name":"qiime2/q2-dada2","owner":{"login":"qiime2","id":18176583,"avatar_url":"https://avatars.githubusercontent.com/u/18176583?v=3","gravatar_id":"","url":"https://api.github.com/users/qiime2","html_url":"https://github.com/qiime2","followers_url":"https://api.github.com/users/qiime2/followers","following_url":"https://api.github.com/users/qiime2/following{/other_user}","gists_url":"https://api.github.com/users/qiime2/gists{/gist_id}","starred_url":"https://api.github.com/users/qiime2/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/qiime2/subscriptions","organizations_url":"https://api.github.com/users/qiime2/orgs","repos_url":"https://api.github.com/users/qiime2/repos","events_url":"https://api.github.com/users/qiime2/events{/privacy}","received_events_url":"https://api.github.com/users/qiime2/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/qiime2/q2-dada2","description":"R scripts for DADA2 QIIME2 plugin","fork":false,"url":"https://api.github.com/repos/qiime2/q2-dada2","forks_url":"https://api.github.com/repos/qiime2/q2-dada2/forks","keys_url":"https://api.github.com/repos/qiime2/q2-dada2/keys{/key_id}","collaborators_url":"https://api.github.com/repos/qiime2/q2-dada2/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/qiime2/q2-dada2/teams","hooks_url":"https://api.github.com/repos/qiime2/q2-dada2/hooks","issue_events_url":"https://api.github.com/repos/qiime2/q2-dada2/issues/events{/number}","events_url":"https://api.github.com/repos/qiime2/q2-dada2/events","assignees_url":"https://api.github.com/repos/qiime2/q2-dada2/assignees{/user}","branches_url":"https://api.github.com/repos/qiime2/q2-dada2/branches{/branch}","tags_url":"https://api.github.com/repos/qiime2/q2-dada2/tags","blobs_url":"https://api.github.com/repos/qiime2/q2-dada2/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/qiime2/q2-dada2/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/qiime2/q2-dada2/git/refs{/sha}","trees_url":"https://api.github.com/repos/qiime2/q2-dada2/git/trees{/sha}","statuses_url":"https://api.github.com/repos/qiime2/q2-dada2/statuses/{sha}","languages_url":"https://api.github.com/repos/qiime2/q2-dada2/languages","stargazers_url":"https://api.github.com/repos/qiime2/q2-dada2/stargazers","contributors_url":"https://api.github.com/repos/qiime2/q2-dada2/contributors","subscribers_url":"https://api.github.com/repos/qiime2/q2-dada2/subscribers","subscription_url":"https://api.github.com/repos/qiime2/q2-dada2/subscription","commits_url":"https://api.github.com/repos/qiime2/q2-dada2/commits{/sha}","git_commits_url":"https://api.github.com/repos/qiime2/q2-dada2/git/commits{/sha}","comments_url":"https://api.github.com/repos/qiime2/q2-dada2/comments{/number}","issue_comment_url":"https://api.github.com/repos/qiime2/q2-dada2/issues/comments{/number}","contents_url":"https://api.github.com/repos/qiime2/q2-dada2/contents/{+path}","compare_url":"https://api.github.com/repos/qiime2/q2-dada2/compare/{base}...{head}","merges_url":"https://api.github.com/repos/qiime2/q2-dada2/merges","archive_url":"https://api.github.com/repos/qiime2/q2-dada2/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/qiime2/q2-dada2/downloads","issues_url":"https://api.github.com/repos/qiime2/q2-dada2/issues{/number}","pulls_url":"https://api.github.com/repos/qiime2/q2-dada2/pulls{/number}","milestones_url":"https://api.github.com/repos/qiime2/q2-dada2/milestones{/number}","notifications_url":"https://api.github.com/repos/qiime2/q2-dada2/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/qiime2/q2-dada2/labels{/name}","releases_url":"https://api.github.com/repos/qiime2/q2-dada2/releases{/id}","deployments_url":"https://api.github.com/repos/qiime2/q2-dada2/deployments","created_at":"2016-08-08T03:47:29Z","updated_at":"2016-11-02T19:01:32Z","pushed_at":"2017-01-30T19:40:14Z","git_url":"git://github.com/qiime2/q2-dada2.git","ssh_url":"git@github.com:qiime2/q2-dada2.git","clone_url":"https://github.com/qiime2/q2-dada2.git","svn_url":"https://github.com/qiime2/q2-dada2","homepage":null,"size":12056,"stargazers_count":0,"watchers_count":0,"language":"Python","has_issues":true,"has_downloads":true,"has_wiki":true,"has_pages":false,"forks_count":5,"mirror_url":null,"open_issues_count":12,"forks":5,"open_issues":12,"watchers":0,"default_branch":"master"}},"_links":{"self":{"href":"https://api.github.com/repos/qiime2/q2-dada2/pulls/34"},"html":{"href":"https://github.com/qiime2/q2-dada2/pull/34"},"issue":{"href":"https://api.github.com/repos/qiime2/q2-dada2/issues/34"},"comments":{"href":"https://api.github.com/repos/qiime2/q2-dada2/issues/34/comments"},"review_comments":{"href":"https://api.github.com/repos/qiime2/q2-dada2/pulls/34/comments"},"review_comment":{"href":"https://api.github.com/repos/qiime2/q2-dada2/pulls/comments{/number}"},"commits":{"href":"https://api.github.com/repos/qiime2/q2-dada2/pulls/34/commits"},"statuses":{"href":"https://api.github.com/repos/qiime2/q2-dada2/statuses/577a1c12034abb3f8e2cbe7dc5bee286146eedc4"}},"merged":false,"mergeable":true,"mergeable_state":"clean","merged_by":null,"comments":2,"review_comments":0,"maintainer_can_modify":false,"commits":9,"additions":454,"deletions":4,"changed_files":3}}
{"actor":{"display_login":"gregcaporaso"}}