{"action":"created","issue":{"url":"https://api.github.com/repos/CGATOxford/cgat/issues/131","labels_url":"https://api.github.com/repos/CGATOxford/cgat/issues/131/labels{/name}","comments_url":"https://api.github.com/repos/CGATOxford/cgat/issues/131/comments","events_url":"https://api.github.com/repos/CGATOxford/cgat/issues/131/events","html_url":"https://github.com/CGATOxford/cgat/issues/131","id":57030629,"number":131,"title":"mergeBAMfiles in pipeline_mapping","user":{"login":"csandorfr","id":8971619,"avatar_url":"https://avatars.githubusercontent.com/u/8971619?v=3","gravatar_id":"","url":"https://api.github.com/users/csandorfr","html_url":"https://github.com/csandorfr","followers_url":"https://api.github.com/users/csandorfr/followers","following_url":"https://api.github.com/users/csandorfr/following{/other_user}","gists_url":"https://api.github.com/users/csandorfr/gists{/gist_id}","starred_url":"https://api.github.com/users/csandorfr/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/csandorfr/subscriptions","organizations_url":"https://api.github.com/users/csandorfr/orgs","repos_url":"https://api.github.com/users/csandorfr/repos","events_url":"https://api.github.com/users/csandorfr/events{/privacy}","received_events_url":"https://api.github.com/users/csandorfr/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-02-09T13:32:13Z","updated_at":"2015-02-09T13:36:03Z","closed_at":null,"body":"I was wondering why the function mergeBAMfiles was removed in pipeline_mapping\r\n\r\npython /net/isi-scratch/cynthia/CGAT-DEPS/cgat/CGATPipelines/pipeline_mapping.py -v5 --local make mergeBAMFiles\r\n\r\n Target task 'mergeBAMFiles' is not a pipelined task in Ruffus. Have you mis-spelt the function name?"},"comment":{"url":"https://api.github.com/repos/CGATOxford/cgat/issues/comments/73508961","html_url":"https://github.com/CGATOxford/cgat/issues/131#issuecomment-73508961","issue_url":"https://api.github.com/repos/CGATOxford/cgat/issues/131","id":73508961,"user":{"login":"AndreasHeger","id":4426336,"avatar_url":"https://avatars.githubusercontent.com/u/4426336?v=3","gravatar_id":"","url":"https://api.github.com/users/AndreasHeger","html_url":"https://github.com/AndreasHeger","followers_url":"https://api.github.com/users/AndreasHeger/followers","following_url":"https://api.github.com/users/AndreasHeger/following{/other_user}","gists_url":"https://api.github.com/users/AndreasHeger/gists{/gist_id}","starred_url":"https://api.github.com/users/AndreasHeger/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/AndreasHeger/subscriptions","organizations_url":"https://api.github.com/users/AndreasHeger/orgs","repos_url":"https://api.github.com/users/AndreasHeger/repos","events_url":"https://api.github.com/users/AndreasHeger/events{/privacy}","received_events_url":"https://api.github.com/users/AndreasHeger/received_events","type":"User","site_admin":false},"created_at":"2015-02-09T13:36:03Z","updated_at":"2015-02-09T13:36:03Z","body":"mergeBAMfiles is only visible if the regular expresssion\ntelling which files should be merged are set:\n\n```\nif \"merge_pattern_input\" in PARAMS and PARAMS[\"merge_pattern_input\"]:\n```\n\nCould this be the reason?\n\nBest wishes,\nAndreas\n\n\nOn 02/09/15 13:32, csandorfr wrote:\n> I was wondering why the function mergeBAMfiles was removed in\n> pipeline_mapping\n>\n> python\n> /net/isi-scratch/cynthia/CGAT-DEPS/cgat/CGATPipelines/pipeline_mapping.py -v5\n> --local make mergeBAMFiles\n>\n> Target task 'mergeBAMFiles' is not a pipelined task in Ruffus. Have you\n> mis-spelt the function name?\n>\n> —\n> Reply to this email directly or view it on GitHub\n> <https://github.com/CGATOxford/cgat/issues/131>.\n>\n\n"}}