{"action":"created","comment":{"url":"https://api.github.com/repos/fulcrumgenomics/dagr/pulls/comments/98573222","pull_request_review_id":19219002,"id":98573222,"diff_hunk":"@@ -108,24 +111,32 @@ private class VarDictJava(tumorBam: PathToBam,\n   }\n }\n \n-/**\n-  * Tumor-only single-sample variant calling with VarDictJava: https://github.com/AstraZeneca-NGS/VarDictJava\n-  *\n-  * The output Tumor name will be inferred from the the first read group in the input BAM if not provided.\n-  */\n-class VarDictJavaEndToEnd(tumorBam: PathToBam,\n-                          bed: FilePath,\n-                          ref: PathToFasta,\n-                          out: PathToVcf,\n-                          tumorName: Option[String] = None,\n-                          minimumAf: Double = 0.01,\n-                          includeNonPf: Boolean = false,\n-                          minimumQuality: Option[Int] = None,\n-                          maximumMismatches: Option[Int] = None,\n-                          minimumAltReads: Option[Int] = None,\n-                          pileupMode: Boolean = false,\n-                          minThreads: Int = 1,\n-                          maxThreads: Int = 32) extends Pipeline {\n+/** Pipeline to call variants from a tumor-only sample using VarDictJava. */\n+@clp(\n+  description =\n+    \"\"\"\n+      |Calls somatic variants in a tumor-only sample using VarDictJava.\n+      |\n+      |Tumor-only single-sample variant calling with VarDictJava: https://github.com/AstraZeneca-NGS/VarDictJava\n+      |\n+      |The output Tumor name will be inferred from the the first read group in the input BAM if not provided.\n+    \"\"\"\",\n+  group = classOf[Pipelines]\n+)\n+class VarDictJavaEndToEnd\n+(@arg(flag=\"i\", doc=\"The input tumor BAM file.\") tumorBam: PathToBam,\n+ @arg(flag=\"l\", doc=\"The intervals oer which to call variants.\") intervals: PathToIntervals,","path":"tasks/src/main/scala/dagr/tasks/vc/VarDictJava.scala","position":55,"original_position":55,"commit_id":"91ce8dd2edc78f6661b0f912b67d8b7655dd9d9b","original_commit_id":"91ce8dd2edc78f6661b0f912b67d8b7655dd9d9b","user":{"login":"tfenne","id":1609210,"avatar_url":"https://avatars.githubusercontent.com/u/1609210?v=3","gravatar_id":"","url":"https://api.github.com/users/tfenne","html_url":"https://github.com/tfenne","followers_url":"https://api.github.com/users/tfenne/followers","following_url":"https://api.github.com/users/tfenne/following{/other_user}","gists_url":"https://api.github.com/users/tfenne/gists{/gist_id}","starred_url":"https://api.github.com/users/tfenne/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tfenne/subscriptions","organizations_url":"https://api.github.com/users/tfenne/orgs","repos_url":"https://api.github.com/users/tfenne/repos","events_url":"https://api.github.com/users/tfenne/events{/privacy}","received_events_url":"https://api.github.com/users/tfenne/received_events","type":"User","site_admin":false},"body":"oer -> over","created_at":"2017-01-31T00:10:58Z","updated_at":"2017-01-31T00:13:00Z","html_url":"https://github.com/fulcrumgenomics/dagr/pull/253#discussion_r98573222","pull_request_url":"https://api.github.com/repos/fulcrumgenomics/dagr/pulls/253","_links":{"self":{"href":"https://api.github.com/repos/fulcrumgenomics/dagr/pulls/comments/98573222"},"html":{"href":"https://github.com/fulcrumgenomics/dagr/pull/253#discussion_r98573222"},"pull_request":{"href":"https://api.github.com/repos/fulcrumgenomics/dagr/pulls/253"}}},"pull_request":{"url":"https://api.github.com/repos/fulcrumgenomics/dagr/pulls/253","id":103844963,"html_url":"https://github.com/fulcrumgenomics/dagr/pull/253","diff_url":"https://github.com/fulcrumgenomics/dagr/pull/253.diff","patch_url":"https://github.com/fulcrumgenomics/dagr/pull/253.patch","issue_url":"https://api.github.com/repos/fulcrumgenomics/dagr/issues/253","number":253,"state":"open","locked":false,"title":"Expose VarDictJava on the command 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