{"action":"opened","issue":{"url":"https://api.github.com/repos/PapenfussLab/gridss/issues/147","repository_url":"https://api.github.com/repos/PapenfussLab/gridss","labels_url":"https://api.github.com/repos/PapenfussLab/gridss/issues/147/labels{/name}","comments_url":"https://api.github.com/repos/PapenfussLab/gridss/issues/147/comments","events_url":"https://api.github.com/repos/PapenfussLab/gridss/issues/147/events","html_url":"https://github.com/PapenfussLab/gridss/issues/147","id":333526187,"node_id":"MDU6SXNzdWUzMzM1MjYxODc=","number":147,"title":"Better somatic arguments?","user":{"login":"student-t","id":7627987,"node_id":"MDQ6VXNlcjc2Mjc5ODc=","avatar_url":"https://avatars2.githubusercontent.com/u/7627987?v=4","gravatar_id":"","url":"https://api.github.com/users/student-t","html_url":"https://github.com/student-t","followers_url":"https://api.github.com/users/student-t/followers","following_url":"https://api.github.com/users/student-t/following{/other_user}","gists_url":"https://api.github.com/users/student-t/gists{/gist_id}","starred_url":"https://api.github.com/users/student-t/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/student-t/subscriptions","organizations_url":"https://api.github.com/users/student-t/orgs","repos_url":"https://api.github.com/users/student-t/repos","events_url":"https://api.github.com/users/student-t/events{/privacy}","received_events_url":"https://api.github.com/users/student-t/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-06-19T05:41:56Z","updated_at":"2018-06-19T05:41:56Z","closed_at":null,"author_association":"NONE","body":"I'm using the script on https://github.com/PapenfussLab/gridss/blob/master/example/somatic.sh for making a somatic call.\r\n\r\nWhat concern me is the inputs:\r\n\r\n\tINPUT=\"$NORMAL\" \\\r\n\tINPUT=\"$TUMOUR\" \\\r\n\r\nThey are both \"INPUT\", what if we mix up the orders - the normal sample is given to the second option? The program apparently assumes that the first file is the normal sample, and the second file is tumor. This is not very explicitly stated and might cause confusion.\r\n\r\nCan you please add something like \"NORMAL=$NORMAL\" and \"TUMOR=\"$TUMOR\"?\r\n"}}
{"actor":{"display_login":"student-t"}}