{"action":"closed","issue":{"url":"https://api.github.com/repos/ewels/MultiQC/issues/365","repository_url":"https://api.github.com/repos/ewels/MultiQC","labels_url":"https://api.github.com/repos/ewels/MultiQC/issues/365/labels{/name}","comments_url":"https://api.github.com/repos/ewels/MultiQC/issues/365/comments","events_url":"https://api.github.com/repos/ewels/MultiQC/issues/365/events","html_url":"https://github.com/ewels/MultiQC/issues/365","id":196752276,"number":365,"title":"prepend_dirs (-d, -dd) not honored by several modules","user":{"login":"epruesse","id":2774474,"avatar_url":"https://avatars.githubusercontent.com/u/2774474?v=3","gravatar_id":"","url":"https://api.github.com/users/epruesse","html_url":"https://github.com/epruesse","followers_url":"https://api.github.com/users/epruesse/followers","following_url":"https://api.github.com/users/epruesse/following{/other_user}","gists_url":"https://api.github.com/users/epruesse/gists{/gist_id}","starred_url":"https://api.github.com/users/epruesse/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/epruesse/subscriptions","organizations_url":"https://api.github.com/users/epruesse/orgs","repos_url":"https://api.github.com/users/epruesse/repos","events_url":"https://api.github.com/users/epruesse/events{/privacy}","received_events_url":"https://api.github.com/users/epruesse/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2016-12-20T19:02:43Z","updated_at":"2016-12-21T09:18:03Z","closed_at":"2016-12-21T09:18:03Z","body":"The `-d` and `-dd` flags are not honored by several modules. The corresponding configuration variable `config.prepend_dirs` is only used in `BaseModule.clean_s_name()`, which is not applied to the sample names by these modules:\r\n\r\n - bamtools\r\n - bismark\r\n - fastq_screen\r\n - gatk \r\n - methylQA\r\n - preseq\r\n - rseqc\r\n - quast\r\n - samtools\r\n - snpeff\r\n - star\r\n\r\nThe prepend_dirs feature is very useful for generating reports to illustrate the effects of using differing tools or parameters. In those cases, the sample name will often be identical but the path will vary.\r\n\r\nThe name of the `clean_s_name` function is somewhat misleading, possibly warranting a rename to make it more obvious to module writers that `clean_s_name` must be applied to the sample names at some point. "}}
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