{"action":"closed","issue":{"url":"https://api.github.com/repos/bcbio/bcbio-nextgen/issues/2311","repository_url":"https://api.github.com/repos/bcbio/bcbio-nextgen","labels_url":"https://api.github.com/repos/bcbio/bcbio-nextgen/issues/2311/labels{/name}","comments_url":"https://api.github.com/repos/bcbio/bcbio-nextgen/issues/2311/comments","events_url":"https://api.github.com/repos/bcbio/bcbio-nextgen/issues/2311/events","html_url":"https://github.com/bcbio/bcbio-nextgen/issues/2311","id":302421717,"number":2311,"title":"Small RNA pipeline","user":{"login":"ahsen1402","id":19558317,"avatar_url":"https://avatars0.githubusercontent.com/u/19558317?v=4","gravatar_id":"","url":"https://api.github.com/users/ahsen1402","html_url":"https://github.com/ahsen1402","followers_url":"https://api.github.com/users/ahsen1402/followers","following_url":"https://api.github.com/users/ahsen1402/following{/other_user}","gists_url":"https://api.github.com/users/ahsen1402/gists{/gist_id}","starred_url":"https://api.github.com/users/ahsen1402/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ahsen1402/subscriptions","organizations_url":"https://api.github.com/users/ahsen1402/orgs","repos_url":"https://api.github.com/users/ahsen1402/repos","events_url":"https://api.github.com/users/ahsen1402/events{/privacy}","received_events_url":"https://api.github.com/users/ahsen1402/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":4,"created_at":"2018-03-05T19:03:48Z","updated_at":"2018-03-16T00:28:46Z","closed_at":"2018-03-16T00:28:46Z","author_association":"NONE","body":"Hi All,\r\n\r\nFirst thanks for this great tool. I have just discovered it. I would like to run the smallRNA pipeline but I am confused with the parameters to set. Per my library preparation i need to run the following command:\r\n\r\ncutadapt -m 15 -u 3 -a AAAAAAAAAA input.fastq > output.fastq\r\n\r\nBasically, trim the first 3 bases from 5' end and remove the polyA tail from the 3'. I think the atropos trimmer in the bcbio is fully compatable with cutadpt so that same parameters would run perfectly with it. But I am not sure how to specify these parameters in the configuration file? I think the 'trim_ends' parameter is what I am looking for but it is mentioned that it is Only implemented for variant calling pipelines. Any help is appreciated. If this is not possible is there a way to skip trimming for the smallRNA pipeline if I wish to input already trimmed reads? Thanks in advance.\r\n\r\n\r\n"}}
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