{"action":"created","issue":{"url":"https://api.github.com/repos/ewels/clusterflow/issues/39","labels_url":"https://api.github.com/repos/ewels/clusterflow/issues/39/labels{/name}","comments_url":"https://api.github.com/repos/ewels/clusterflow/issues/39/comments","events_url":"https://api.github.com/repos/ewels/clusterflow/issues/39/events","html_url":"https://github.com/ewels/clusterflow/issues/39","id":57545054,"number":39,"title":"htseq_counts cannot accept gtf files with 'gene_id' field","user":{"login":"stu2","id":6446882,"avatar_url":"https://avatars.githubusercontent.com/u/6446882?v=3","gravatar_id":"","url":"https://api.github.com/users/stu2","html_url":"https://github.com/stu2","followers_url":"https://api.github.com/users/stu2/followers","following_url":"https://api.github.com/users/stu2/following{/other_user}","gists_url":"https://api.github.com/users/stu2/gists{/gist_id}","starred_url":"https://api.github.com/users/stu2/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/stu2/subscriptions","organizations_url":"https://api.github.com/users/stu2/orgs","repos_url":"https://api.github.com/users/stu2/repos","events_url":"https://api.github.com/users/stu2/events{/privacy}","received_events_url":"https://api.github.com/users/stu2/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-02-13T01:06:43Z","updated_at":"2015-02-13T08:13:46Z","closed_at":null,"body":"Hi Phil,\r\n\r\nI've been trying to use `htseq_counts.cfmod` with the mouse genome `.gtf` file from `mm10`. In this gtf file the gene is marked by `gene_id` not `ID`. However, `ID` is hardcoded into the command that htseq_counts produces ([line 103](https://github.com/ewels/clusterflow/blob/v0.4devel/modules/htseq_counts.cfmod#L103):  `-i 'ID'` ), so it chokes. Could this be made into an argument for flexibility?\r\n\r\nCheers \r\n\r\nedit: storing the ID tag in the clusterflow genome info for that genome/gtf set might be even better."},"comment":{"url":"https://api.github.com/repos/ewels/clusterflow/issues/comments/74218960","html_url":"https://github.com/ewels/clusterflow/issues/39#issuecomment-74218960","issue_url":"https://api.github.com/repos/ewels/clusterflow/issues/39","id":74218960,"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":"2015-02-13T08:13:46Z","updated_at":"2015-02-13T08:13:46Z","body":"Hey,\r\n\r\nYeah of course. Whilst I agree that it would be nice to store the tag with the genome info as it will always be the same for that reference GTF file, I'm a bit hesitant to start adding extra information to that file as I think it could get very complicated very quickly.\r\n\r\nParameters would be the obvious choice, defaulting to `ID` if not provided. Or better still, is there any way that the module can scan the gtf file and look for a hierarchy of tags? _eg._ try to find `gene_id` if it's not there, then look for `ID` (and so on, with a list of potential tags). Or alternatively have a regex that looks for ensembl `ENSG\\d+` gene ID and pull out the associated identifier?\r\n\r\nWhat do you think? Maybe a combination of all of these things.\r\n\r\nPhil"}}