{"action":"created","comment":{"url":"https://api.github.com/repos/hammerlab/epidisco/pulls/comments/91147947","pull_request_review_id":11655641,"id":91147947,"diff_hunk":"@@ -261,64 +258,147 @@ module Full (Bfx: Extended_edsl.Semantics) = struct\n   type rna_results =\n     { rna_bam: [ `Bam ] Bfx.repr;\n       stringtie: [ `Gtf ] Bfx.repr;\n-      seq2hla: [ `Seq2hla_result ] Bfx.repr option;\n-      optitype_rna: [ `Optitype_result ] Bfx.repr option;\n       rna_bam_flagstat: [ `Flagstat ] Bfx.repr }\n+\n   let rna_pipeline\n-      ~parameters ~reference_build ~with_seq2hla ~with_optitype_rna samples =\n-    let bam = rna_bam ~parameters ~reference_build samples in\n-    let fqs = concat_samples samples in\n+      ~parameters ~reference_build samples =\n+    let bam = to_bam_rna ~parameters ~reference_build samples in\n     (* Seq2HLA does not work on mice: *)\n-    let seq2hla, optitype_rna =\n-      (match reference_build, with_seq2hla, with_optitype_rna with\n-     | \"mm10\", _, _ -> (None, None)\n-     | _, false, false -> (None, None)\n-     | _, false, true -> (None, Some (optitype_hla fqs `RNA \"RNA\"))\n-     | _, true, false -> (Some (seq2hla_hla fqs), None)\n-     | _, true, true -> (Some (seq2hla_hla fqs), Some (optitype_hla fqs `RNA \"RNA\"))) in\n     { rna_bam = bam |> Bfx.save \"rna-bam\";\n       stringtie = bam |> Bfx.stringtie |> Bfx.save \"stringtie\";\n-      rna_bam_flagstat = bam |> Bfx.flagstat |> Bfx.save \"rna-bam-flagstat\";\n-      seq2hla; optitype_rna; }\n+      rna_bam_flagstat = bam |> Bfx.flagstat |> Bfx.save \"rna-bam-flagstat\";}\n+\n+  type fastqc_results = {\n+    normal_fastqcs: [ `Fastqc ] Bfx.repr list;\n+    tumor_fastqcs: [ `Fastqc ] Bfx.repr list;\n+    rna_fastqcs: [ `Fastqc ] Bfx.repr list option; }\n+  let fastqc_pipeline ~normal_samples ~tumor_samples ?rna_samples () =\n+    let normal_fastqcs =\n+      List.mapi\n+        ~f:(fun i fq -> qc fq |> Bfx.save (sprintf \"QC:normal-%d\" i))\n+        normal_samples\n+    in\n+    let tumor_fastqcs =\n+      List.mapi\n+        ~f:(fun i fq -> qc fq |> Bfx.save (sprintf \"QC:tumor-%d\" i))\n+        tumor_samples\n+    in\n+    let rna_fastqcs =\n+      match rna_samples with\n+      | None -> None\n+      | Some rna_samples ->\n+        Some\n+          (List.mapi\n+             ~f:(fun i fq -> qc fq |> Bfx.save (sprintf \"QC:rna-%d\" i))\n+             rna_samples)\n+    in\n+    { normal_fastqcs; tumor_fastqcs; rna_fastqcs }\n+\n+\n+  let email_pipeline\n+      ?rna_results ~parameters ~normal_bam_flagstat ~tumor_bam_flagstat ~fastqcs\n+    =\n+    let rna_bam_flagstat =\n+      rna_results >>= fun {rna_bam_flagstat; _} -> return rna_bam_flagstat in","path":"src/lib/pipeline.ml","position":119,"original_position":119,"commit_id":"1d64d0cbea5ea55c291196992fa91775fbf1a6a7","original_commit_id":"1d64d0cbea5ea55c291196992fa91775fbf1a6a7","user":{"login":"smondet","id":617111,"avatar_url":"https://avatars.githubusercontent.com/u/617111?v=3","gravatar_id":"","url":"https://api.github.com/users/smondet","html_url":"https://github.com/smondet","followers_url":"https://api.github.com/users/smondet/followers","following_url":"https://api.github.com/users/smondet/following{/other_user}","gists_url":"https://api.github.com/users/smondet/gists{/gist_id}","starred_url":"https://api.github.com/users/smondet/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/smondet/subscriptions","organizations_url":"https://api.github.com/users/smondet/orgs","repos_url":"https://api.github.com/users/smondet/repos","events_url":"https://api.github.com/users/smondet/events{/privacy}","received_events_url":"https://api.github.com/users/smondet/received_events","type":"User","site_admin":false},"body":"The `open Option` is too far up,` `Option` is not meant to be opened globally (Esp. since this case is actually an `Option.map` rather than `bind`).","created_at":"2016-12-06T19:04:19Z","updated_at":"2016-12-06T19:04:19Z","html_url":"https://github.com/hammerlab/epidisco/pull/102#discussion_r91147947","pull_request_url":"https://api.github.com/repos/hammerlab/epidisco/pulls/102","_links":{"self":{"href":"https://api.github.com/repos/hammerlab/epidisco/pulls/comments/91147947"},"html":{"href":"https://github.com/hammerlab/epidisco/pull/102#discussion_r91147947"},"pull_request":{"href":"https://api.github.com/repos/hammerlab/epidisco/pulls/102"}}},"pull_request":{"url":"https://api.github.com/repos/hammerlab/epidisco/pulls/102","id":96783224,"html_url":"https://github.com/hammerlab/epidisco/pull/102","diff_url":"https://github.com/hammerlab/epidisco/pull/102.diff","patch_url":"https://github.com/hammerlab/epidisco/pull/102.patch","issue_url":"https://api.github.com/repos/hammerlab/epidisco/issues/102","number":102,"state":"open","locked":false,"title":"Run qc on samples","user":{"login":"ihodes","id":167803,"avatar_url":"https://avatars.githubusercontent.com/u/167803?v=3","gravatar_id":"","url":"https://api.github.com/users/ihodes","html_url":"https://github.com/ihodes","followers_url":"https://api.github.com/users/ihodes/followers","following_url":"https://api.github.com/users/ihodes/following{/other_user}","gists_url":"https://api.github.com/users/ihodes/gists{/gist_id}","starred_url":"https://api.github.com/users/ihodes/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ihodes/subscriptions","organizations_url":"https://api.github.com/users/ihodes/orgs","repos_url":"https://api.github.com/users/ihodes/repos","events_url":"https://api.github.com/users/ihodes/events{/privacy}","received_events_url":"https://api.github.com/users/ihodes/received_events","type":"User","site_admin":false},"body":"fixes https://github.com/hammerlab/epidisco/issues/101","created_at":"2016-12-06T18:51:35Z","updated_at":"2016-12-06T19:06:26Z","closed_at":null,"merged_at":null,"merge_commit_sha":"0cf98c33e3218201b56fdf30521647fc80538c96","assignee":{"login":"smondet","id":617111,"avatar_url":"https://avatars.githubusercontent.com/u/617111?v=3","gravatar_id":"","url":"https://api.github.com/users/smondet","html_url":"https://github.com/smondet","followers_url":"https://api.github.com/users/smondet/followers","following_url":"https://api.github.com/users/smondet/following{/other_user}","gists_url":"https://api.github.com/users/smondet/gists{/gist_id}","starred_url":"https://api.github.com/users/smondet/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/smondet/subscriptions","organizations_url":"https://api.github.com/users/smondet/orgs","repos_url":"https://api.github.com/users/smondet/repos","events_url":"https://api.github.com/users/smondet/events{/privacy}","received_events_url":"https://api.github.com/users/smondet/received_events","type":"User","site_admin":false},"assignees":[{"login":"smondet","id":617111,"avatar_url":"https://avatars.githubusercontent.com/u/617111?v=3","gravatar_id":"","url":"https://api.github.com/users/smondet","html_url":"https://github.com/smondet","followers_url":"https://api.github.com/users/smondet/followers","following_url":"https://api.github.com/users/smondet/following{/other_user}","gists_url":"https://api.github.com/users/smondet/gists{/gist_id}","starred_url":"https://api.github.com/users/smondet/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/smondet/subscriptions","organizations_url":"https://api.github.com/users/smondet/orgs","repos_url":"https://api.github.com/users/smondet/repos","events_url":"https://api.github.com/users/smondet/events{/privacy}","received_events_url":"https://api.github.com/users/smondet/received_events","type":"User","site_admin":false}],"milestone":null,"commits_url":"https://api.github.com/repos/hammerlab/epidisco/pulls/102/commits","review_comments_url":"https://api.github.com/repos/hammerlab/epidisco/pulls/102/comments","review_comment_url":"https://api.github.com/repos/hammerlab/epidisco/pulls/comments{/number}","comments_url":"https://api.github.com/repos/hammerlab/epidisco/issues/102/comments","statuses_url":"https://api.github.com/repos/hammerlab/epidisco/statuses/1d64d0cbea5ea55c291196992fa91775fbf1a6a7","head":{"label":"hammerlab:run-qc-on-samples","ref":"run-qc-on-samples","sha":"1d64d0cbea5ea55c291196992fa91775fbf1a6a7","user":{"login":"hammerlab","id":6563873,"avatar_url":"https://avatars.githubusercontent.com/u/6563873?v=3","gravatar_id":"","url":"https://api.github.com/users/hammerlab","html_url":"https://github.com/hammerlab","followers_url":"https://api.github.com/users/hammerlab/followers","following_url":"https://api.github.com/users/hammerlab/following{/other_user}","gists_url":"https://api.github.com/users/hammerlab/gists{/gist_id}","starred_url":"https://api.github.com/users/hammerlab/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hammerlab/subscriptions","organizations_url":"https://api.github.com/users/hammerlab/orgs","repos_url":"https://api.github.com/users/hammerlab/repos","events_url":"https://api.github.com/users/hammerlab/events{/privacy}","received_events_url":"https://api.github.com/users/hammerlab/received_events","type":"Organization","site_admin":false},"repo":{"id":65234922,"name":"epidisco","full_name":"hammerlab/epidisco","owner":{"login":"hammerlab","id":6563873,"avatar_url":"https://avatars.githubusercontent.com/u/6563873?v=3","gravatar_id":"","url":"https://api.github.com/users/hammerlab","html_url":"https://github.com/hammerlab","followers_url":"https://api.github.com/users/hammerlab/followers","following_url":"https://api.github.com/users/hammerlab/following{/other_user}","gists_url":"https://api.github.com/users/hammerlab/gists{/gist_id}","starred_url":"https://api.github.com/users/hammerlab/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hammerlab/subscriptions","organizations_url":"https://api.github.com/users/hammerlab/orgs","repos_url":"https://api.github.com/users/hammerlab/repos","events_url":"https://api.github.com/users/hammerlab/events{/privacy}","received_events_url":"https://api.github.com/users/hammerlab/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/hammerlab/epidisco","description":"Personalized cancer epitope discovery and peptide vaccine prediction pipeline","fork":false,"url":"https://api.github.com/repos/hammerlab/epidisco","forks_url":"https://api.github.com/repos/hammerlab/epidisco/forks","keys_url":"https://api.github.com/repos/hammerlab/epidisco/keys{/key_id}","collaborators_url":"https://api.github.com/repos/hammerlab/epidisco/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/hammerlab/epidisco/teams","hooks_url":"https://api.github.com/repos/hammerlab/epidisco/hooks","issue_events_url":"https://api.github.com/repos/hammerlab/epidisco/issues/events{/number}","events_url":"https://api.github.com/repos/hammerlab/epidisco/events","assignees_url":"https://api.github.com/repos/hammerlab/epidisco/assignees{/user}","branches_url":"https://api.github.com/repos/hammerlab/epidisco/branches{/branch}","tags_url":"https://api.github.com/repos/hammerlab/epidisco/tags","blobs_url":"https://api.github.com/repos/hammerlab/epidisco/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/hammerlab/epidisco/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/hammerlab/epidisco/git/refs{/sha}","trees_url":"https://api.github.com/repos/hammerlab/epidisco/git/trees{/sha}","statuses_url":"https://api.github.com/repos/hammerlab/epidisco/statuses/{sha}","languages_url":"https://api.github.com/repos/hammerlab/epidisco/languages","stargazers_url":"https://api.github.com/repos/hammerlab/epidisco/stargazers","contributors_url":"https://api.github.com/repos/hammerlab/epidisco/contributors","subscribers_url":"https://api.github.com/repos/hammerlab/epidisco/subscribers","subscription_url":"https://api.github.com/repos/hammerlab/epidisco/subscription","commits_url":"https://api.github.com/repos/hammerlab/epidisco/commits{/sha}","git_commits_url":"https://api.github.com/repos/hammerlab/epidisco/git/commits{/sha}","comments_url":"https://api.github.com/repos/hammerlab/epidisco/comments{/number}","issue_comment_url":"https://api.github.com/repos/hammerlab/epidisco/issues/comments{/number}","contents_url":"https://api.github.com/repos/hammerlab/epidisco/contents/{+path}","compare_url":"https://api.github.com/repos/hammerlab/epidisco/compare/{base}...{head}","merges_url":"https://api.github.com/repos/hammerlab/epidisco/merges","archive_url":"https://api.github.com/repos/hammerlab/epidisco/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/hammerlab/epidisco/downloads","issues_url":"https://api.github.com/repos/hammerlab/epidisco/issues{/number}","pulls_url":"https://api.github.com/repos/hammerlab/epidisco/pulls{/number}","milestones_url":"https://api.github.com/repos/hammerlab/epidisco/milestones{/number}","notifications_url":"https://api.github.com/repos/hammerlab/epidisco/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/hammerlab/epidisco/labels{/name}","releases_url":"https://api.github.com/repos/hammerlab/epidisco/releases{/id}","deployments_url":"https://api.github.com/repos/hammerlab/epidisco/deployments","created_at":"2016-08-08T19:59:58Z","updated_at":"2016-11-30T19:34:08Z","pushed_at":"2016-12-06T18:54:59Z","git_url":"git://github.com/hammerlab/epidisco.git","ssh_url":"git@github.com:hammerlab/epidisco.git","clone_url":"https://github.com/hammerlab/epidisco.git","svn_url":"https://github.com/hammerlab/epidisco","homepage":"","size":96,"stargazers_count":8,"watchers_count":8,"language":"OCaml","has_issues":true,"has_downloads":true,"has_wiki":true,"has_pages":false,"forks_count":0,"mirror_url":null,"open_issues_count":36,"forks":0,"open_issues":36,"watchers":8,"default_branch":"master"}},"base":{"label":"hammerlab:master","ref":"master","sha":"1394dc4511e90fdf8be734c9c6490c70bc7a0b10","user":{"login":"hammerlab","id":6563873,"avatar_url":"https://avatars.githubusercontent.com/u/6563873?v=3","gravatar_id":"","url":"https://api.github.com/users/hammerlab","html_url":"https://github.com/hammerlab","followers_url":"https://api.github.com/users/hammerlab/followers","following_url":"https://api.github.com/users/hammerlab/following{/other_user}","gists_url":"https://api.github.com/users/hammerlab/gists{/gist_id}","starred_url":"https://api.github.com/users/hammerlab/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hammerlab/subscriptions","organizations_url":"https://api.github.com/users/hammerlab/orgs","repos_url":"https://api.github.com/users/hammerlab/repos","events_url":"https://api.github.com/users/hammerlab/events{/privacy}","received_events_url":"https://api.github.com/users/hammerlab/received_events","type":"Organization","site_admin":false},"repo":{"id":65234922,"name":"epidisco","full_name":"hammerlab/epidisco","owner":{"login":"hammerlab","id":6563873,"avatar_url":"https://avatars.githubusercontent.com/u/6563873?v=3","gravatar_id":"","url":"https://api.github.com/users/hammerlab","html_url":"https://github.com/hammerlab","followers_url":"https://api.github.com/users/hammerlab/followers","following_url":"https://api.github.com/users/hammerlab/following{/other_user}","gists_url":"https://api.github.com/users/hammerlab/gists{/gist_id}","starred_url":"https://api.github.com/users/hammerlab/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hammerlab/subscriptions","organizations_url":"https://api.github.com/users/hammerlab/orgs","repos_url":"https://api.github.com/users/hammerlab/repos","events_url":"https://api.github.com/users/hammerlab/events{/privacy}","received_events_url":"https://api.github.com/users/hammerlab/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/hammerlab/epidisco","description":"Personalized cancer epitope discovery and peptide vaccine prediction pipeline","fork":false,"url":"https://api.github.com/repos/hammerlab/epidisco","forks_url":"https://api.github.com/repos/hammerlab/epidisco/forks","keys_url":"https://api.github.com/repos/hammerlab/epidisco/keys{/key_id}","collaborators_url":"https://api.github.com/repos/hammerlab/epidisco/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/hammerlab/epidisco/teams","hooks_url":"https://api.github.com/repos/hammerlab/epidisco/hooks","issue_events_url":"https://api.github.com/repos/hammerlab/epidisco/issues/events{/number}","events_url":"https://api.github.com/repos/hammerlab/epidisco/events","assignees_url":"https://api.github.com/repos/hammerlab/epidisco/assignees{/user}","branches_url":"https://api.github.com/repos/hammerlab/epidisco/branches{/branch}","tags_url":"https://api.github.com/repos/hammerlab/epidisco/tags","blobs_url":"https://api.github.com/repos/hammerlab/epidisco/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/hammerlab/epidisco/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/hammerlab/epidisco/git/refs{/sha}","trees_url":"https://api.github.com/repos/hammerlab/epidisco/git/trees{/sha}","statuses_url":"https://api.github.com/repos/hammerlab/epidisco/statuses/{sha}","languages_url":"https://api.github.com/repos/hammerlab/epidisco/languages","stargazers_url":"https://api.github.com/repos/hammerlab/epidisco/stargazers","contributors_url":"https://api.github.com/repos/hammerlab/epidisco/contributors","subscribers_url":"https://api.github.com/repos/hammerlab/epidisco/subscribers","subscription_url":"https://api.github.com/repos/hammerlab/epidisco/subscription","commits_url":"https://api.github.com/repos/hammerlab/epidisco/commits{/sha}","git_commits_url":"https://api.github.com/repos/hammerlab/epidisco/git/commits{/sha}","comments_url":"https://api.github.com/repos/hammerlab/epidisco/comments{/number}","issue_comment_url":"https://api.github.com/repos/hammerlab/epidisco/issues/comments{/number}","contents_url":"https://api.github.com/repos/hammerlab/epidisco/contents/{+path}","compare_url":"https://api.github.com/repos/hammerlab/epidisco/compare/{base}...{head}","merges_url":"https://api.github.com/repos/hammerlab/epidisco/merges","archive_url":"https://api.github.com/repos/hammerlab/epidisco/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/hammerlab/epidisco/downloads","issues_url":"https://api.github.com/repos/hammerlab/epidisco/issues{/number}","pulls_url":"https://api.github.com/repos/hammerlab/epidisco/pulls{/number}","milestones_url":"https://api.github.com/repos/hammerlab/epidisco/milestones{/number}","notifications_url":"https://api.github.com/repos/hammerlab/epidisco/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/hammerlab/epidisco/labels{/name}","releases_url":"https://api.github.com/repos/hammerlab/epidisco/releases{/id}","deployments_url":"https://api.github.com/repos/hammerlab/epidisco/deployments","created_at":"2016-08-08T19:59:58Z","updated_at":"2016-11-30T19:34:08Z","pushed_at":"2016-12-06T18:54:59Z","git_url":"git://github.com/hammerlab/epidisco.git","ssh_url":"git@github.com:hammerlab/epidisco.git","clone_url":"https://github.com/hammerlab/epidisco.git","svn_url":"https://github.com/hammerlab/epidisco","homepage":"","size":96,"stargazers_count":8,"watchers_count":8,"language":"OCaml","has_issues":true,"has_downloads":true,"has_wiki":true,"has_pages":false,"forks_count":0,"mirror_url":null,"open_issues_count":36,"forks":0,"open_issues":36,"watchers":8,"default_branch":"master"}},"_links":{"self":{"href":"https://api.github.com/repos/hammerlab/epidisco/pulls/102"},"html":{"href":"https://github.com/hammerlab/epidisco/pull/102"},"issue":{"href":"https://api.github.com/repos/hammerlab/epidisco/issues/102"},"comments":{"href":"https://api.github.com/repos/hammerlab/epidisco/issues/102/comments"},"review_comments":{"href":"https://api.github.com/repos/hammerlab/epidisco/pulls/102/comments"},"review_comment":{"href":"https://api.github.com/repos/hammerlab/epidisco/pulls/comments{/number}"},"commits":{"href":"https://api.github.com/repos/hammerlab/epidisco/pulls/102/commits"},"statuses":{"href":"https://api.github.com/repos/hammerlab/epidisco/statuses/1d64d0cbea5ea55c291196992fa91775fbf1a6a7"}}}}
{"actor":{"display_login":"smondet"}}