{"action":"created","issue":{"url":"https://api.github.com/repos/tseemann/nullarbor/issues/23","labels_url":"https://api.github.com/repos/tseemann/nullarbor/issues/23/labels{/name}","comments_url":"https://api.github.com/repos/tseemann/nullarbor/issues/23/comments","events_url":"https://api.github.com/repos/tseemann/nullarbor/issues/23/events","html_url":"https://github.com/tseemann/nullarbor/issues/23","id":97572213,"number":23,"title":"--force option sometimes re-performs mapping and SNP calls","user":{"login":"kwongj","id":7855976,"avatar_url":"https://avatars.githubusercontent.com/u/7855976?v=3","gravatar_id":"","url":"https://api.github.com/users/kwongj","html_url":"https://github.com/kwongj","followers_url":"https://api.github.com/users/kwongj/followers","following_url":"https://api.github.com/users/kwongj/following{/other_user}","gists_url":"https://api.github.com/users/kwongj/gists{/gist_id}","starred_url":"https://api.github.com/users/kwongj/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/kwongj/subscriptions","organizations_url":"https://api.github.com/users/kwongj/orgs","repos_url":"https://api.github.com/users/kwongj/repos","events_url":"https://api.github.com/users/kwongj/events{/privacy}","received_events_url":"https://api.github.com/users/kwongj/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-07-27T22:40:52Z","updated_at":"2015-10-03T03:00:59Z","closed_at":null,"body":"I want to run nullarbor on a subset of my samples that have already been run through nullarbor.\r\nFor organisation purposes, and for ease of viewing of just that subset for external parties, I want to regenerate the nullarbor webpage report, otherwise I would have just run snippy-core.\r\n\r\nI created a new project folder, with symlinks to the sample folders in the main nullarbor directory. I created a new samples.tab file with the list of isolates in the subset for analysis and generated a new makefile from this.\r\n\r\nHowever, when running nullarbor from this new project folder with --force, nullarbor repeats the mapping and SNP calling process. Why is this? The reference is unchanged."},"comment":{"url":"https://api.github.com/repos/tseemann/nullarbor/issues/comments/145196003","html_url":"https://github.com/tseemann/nullarbor/issues/23#issuecomment-145196003","issue_url":"https://api.github.com/repos/tseemann/nullarbor/issues/23","id":145196003,"user":{"login":"tseemann","id":453972,"avatar_url":"https://avatars.githubusercontent.com/u/453972?v=3","gravatar_id":"","url":"https://api.github.com/users/tseemann","html_url":"https://github.com/tseemann","followers_url":"https://api.github.com/users/tseemann/followers","following_url":"https://api.github.com/users/tseemann/following{/other_user}","gists_url":"https://api.github.com/users/tseemann/gists{/gist_id}","starred_url":"https://api.github.com/users/tseemann/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tseemann/subscriptions","organizations_url":"https://api.github.com/users/tseemann/orgs","repos_url":"https://api.github.com/users/tseemann/repos","events_url":"https://api.github.com/users/tseemann/events{/privacy}","received_events_url":"https://api.github.com/users/tseemann/received_events","type":"User","site_admin":false},"created_at":"2015-10-03T03:00:59Z","updated_at":"2015-10-03T03:00:59Z","body":"I think the symlinks are the problem, but .  They have a new date on them, and `make` things it has to re-do everything.  \r\n\r\nCan you just `mv report report.old` and re-run within the same folders?  \r\n\r\nI intend to change the folder layout of Nullarbor to make multiple reports easier to manage.\r\n\r\n"}}