{"action":"created","issue":{"url":"https://api.github.com/repos/ewels/clusterflow/issues/38","labels_url":"https://api.github.com/repos/ewels/clusterflow/issues/38/labels{/name}","comments_url":"https://api.github.com/repos/ewels/clusterflow/issues/38/comments","events_url":"https://api.github.com/repos/ewels/clusterflow/issues/38/events","html_url":"https://github.com/ewels/clusterflow/issues/38","id":57420040,"number":38,"title":"Add @merge_regex option to config","user":{"login":"ewels","id":465550,"avatar_url":"https://avatars.githubusercontent.com/u/465550?v=3","gravatar_id":"","url":"https://api.github.com/users/ewels","html_url":"https://github.com/ewels","followers_url":"https://api.github.com/users/ewels/followers","following_url":"https://api.github.com/users/ewels/following{/other_user}","gists_url":"https://api.github.com/users/ewels/gists{/gist_id}","starred_url":"https://api.github.com/users/ewels/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ewels/subscriptions","organizations_url":"https://api.github.com/users/ewels/orgs","repos_url":"https://api.github.com/users/ewels/repos","events_url":"https://api.github.com/users/ewels/events{/privacy}","received_events_url":"https://api.github.com/users/ewels/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/ewels/clusterflow/labels/enhancement","name":"enhancement","color":"84b6eb"},{"url":"https://api.github.com/repos/ewels/clusterflow/labels/testing","name":"testing","color":"fbca04"}],"state":"open","locked":false,"assignee":{"login":"ewels","id":465550,"avatar_url":"https://avatars.githubusercontent.com/u/465550?v=3","gravatar_id":"","url":"https://api.github.com/users/ewels","html_url":"https://github.com/ewels","followers_url":"https://api.github.com/users/ewels/followers","following_url":"https://api.github.com/users/ewels/following{/other_user}","gists_url":"https://api.github.com/users/ewels/gists{/gist_id}","starred_url":"https://api.github.com/users/ewels/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ewels/subscriptions","organizations_url":"https://api.github.com/users/ewels/orgs","repos_url":"https://api.github.com/users/ewels/repos","events_url":"https://api.github.com/users/ewels/events{/privacy}","received_events_url":"https://api.github.com/users/ewels/received_events","type":"User","site_admin":false},"milestone":null,"comments":5,"created_at":"2015-02-12T05:42:47Z","updated_at":"2015-03-18T12:20:33Z","closed_at":null,"body":"Would be cool if Cluster Flow could automatically recognise fastq files that should be merged before processing.\r\n\r\n- [x] Add `@merge_regex` to config so that people can define their own filename matches\r\n- [x] Write new module to merge fastq files (gzipped and normal)\r\n- [x] Update core to look for matches\r\n  - [x] Group files accurately, taking into account `--split_files`\r\n  - [x] Prepend merging module onto pipeline"},"comment":{"url":"https://api.github.com/repos/ewels/clusterflow/issues/comments/82945759","html_url":"https://github.com/ewels/clusterflow/issues/38#issuecomment-82945759","issue_url":"https://api.github.com/repos/ewels/clusterflow/issues/38","id":82945759,"user":{"login":"ewels","id":465550,"avatar_url":"https://avatars.githubusercontent.com/u/465550?v=3","gravatar_id":"","url":"https://api.github.com/users/ewels","html_url":"https://github.com/ewels","followers_url":"https://api.github.com/users/ewels/followers","following_url":"https://api.github.com/users/ewels/following{/other_user}","gists_url":"https://api.github.com/users/ewels/gists{/gist_id}","starred_url":"https://api.github.com/users/ewels/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ewels/subscriptions","organizations_url":"https://api.github.com/users/ewels/orgs","repos_url":"https://api.github.com/users/ewels/repos","events_url":"https://api.github.com/users/ewels/events{/privacy}","received_events_url":"https://api.github.com/users/ewels/received_events","type":"User","site_admin":false},"created_at":"2015-03-18T12:20:33Z","updated_at":"2015-03-18T12:20:33Z","body":"Need to improve gzip concatenation due to slide from @s-andrews:\r\n\r\n> `cat seq1.fq.gz seq2.fq.gz > all1.fq.gz`\r\n> Some decompressors (gzip for example) will read all of the data from all1.fq.gz, but others (the java GZipInputStream class for example) will not and will silently finish at the the end of the first concatenated file."}}