{"action":"created","comment":{"url":"https://api.github.com/repos/czbiohub/reflow-workflows/pulls/comments/188354249","pull_request_review_id":120315675,"id":188354249,"diff_hunk":"@@ -0,0 +1,62 @@\n+val dirs = make(\"$/dirs\")\n+\n+\n+\n+//\t# these are all the TM sequencing folders\n+//\tS3_FOLDERS = ['170907_A00111_0051_BH2HWLDMXX',\n+//\t              '170907_A00111_0052_AH2HTCDMXX',\n+//\t              '170910_A00111_0053_BH2HGKDMXX',\n+//\t              '170910_A00111_0054_AH2HGWDMXX',\n+//\t              '170914_A00111_0057_BH3FY7DMXX',\n+//\t              '170914_A00111_0058_AH3FYKDMXX',\n+//\t              '170918_A00111_0059_BH3G22DMXX',\n+//\t              '170918_A00111_0060_AH3FYVDMXX',\n+//\t              '170921_A00111_0062_BH3FYHDMXX',\n+//\t              '170921_A00111_0063_AH3G23DMXX',\n+//\t              '170925_A00111_0066_AH3TKNDMXX',\n+//\t              '170925_A00111_0067_BH3M5YDMXX',\n+//\t              '170928_A00111_0068_AH3YKKDMXX',\n+//\t              '170928_A00111_0069_BH52YMDMXX']\n+\n+// param (\n+//\t// sample is the name of the 1000genomes phase 3 sample\n+//\tsample string\n+//\n+//\t// out is the target of the output merged BAM file\n+//\tout string\n+//)\n+\n+\n+val dirs = make(\"$/dirs\")\n+\n+val sourmash = \"czbiohub/sourmash\"\n+\n+// Trims low-abundance reads using trim-low-abund.py from khmer\n+func Trim(r1, r2 file) file = ","path":"sourmash.rf","position":null,"original_position":35,"commit_id":"c005d16eabad6d06899433f1ce3ba4314e2b8f8e","original_commit_id":"4d17bb40e9722076250134ff76cf7a8c684bc3e2","user":{"login":"olgabot","id":806256,"avatar_url":"https://avatars2.githubusercontent.com/u/806256?v=4","gravatar_id":"","url":"https://api.github.com/users/olgabot","html_url":"https://github.com/olgabot","followers_url":"https://api.github.com/users/olgabot/followers","following_url":"https://api.github.com/users/olgabot/following{/other_user}","gists_url":"https://api.github.com/users/olgabot/gists{/gist_id}","starred_url":"https://api.github.com/users/olgabot/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/olgabot/subscriptions","organizations_url":"https://api.github.com/users/olgabot/orgs","repos_url":"https://api.github.com/users/olgabot/repos","events_url":"https://api.github.com/users/olgabot/events{/privacy}","received_events_url":"https://api.github.com/users/olgabot/received_events","type":"User","site_admin":false},"body":"nope, it didn't work :) I got mixed up on where to say `file` so I put it everywhere. The current version works!","created_at":"2018-05-15T16:32:34Z","updated_at":"2018-05-15T16:32:34Z","html_url":"https://github.com/czbiohub/reflow-workflows/pull/2#discussion_r188354249","pull_request_url":"https://api.github.com/repos/czbiohub/reflow-workflows/pulls/2","author_association":"MEMBER","_links":{"self":{"href":"https://api.github.com/repos/czbiohub/reflow-workflows/pulls/comments/188354249"},"html":{"href":"https://github.com/czbiohub/reflow-workflows/pull/2#discussion_r188354249"},"pull_request":{"href":"https://api.github.com/repos/czbiohub/reflow-workflows/pulls/2"}},"in_reply_to_id":188343327},"pull_request":{"url":"https://api.github.com/repos/czbiohub/reflow-workflows/pulls/2","id":188008223,"html_url":"https://github.com/czbiohub/reflow-workflows/pull/2","diff_url":"https://github.com/czbiohub/reflow-workflows/pull/2.diff","patch_url":"https://github.com/czbiohub/reflow-workflows/pull/2.patch","issue_url":"https://api.github.com/repos/czbiohub/reflow-workflows/issues/2","number":2,"state":"open","locked":false,"title":"[WIP] Start writing sourmash","user":{"login":"olgabot","id":806256,"avatar_url":"https://avatars2.githubusercontent.com/u/806256?v=4","gravatar_id":"","url":"https://api.github.com/users/olgabot","html_url":"https://github.com/olgabot","followers_url":"https://api.github.com/users/olgabot/followers","following_url":"https://api.github.com/users/olgabot/following{/other_user}","gists_url":"https://api.github.com/users/olgabot/gists{/gist_id}","starred_url":"https://api.github.com/users/olgabot/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/olgabot/subscriptions","organizations_url":"https://api.github.com/users/olgabot/orgs","repos_url":"https://api.github.com/users/olgabot/repos","events_url":"https://api.github.com/users/olgabot/events{/privacy}","received_events_url":"https://api.github.com/users/olgabot/received_events","type":"User","site_admin":false},"body":"Currently getting a syntax error that I can't track down:\r\n\r\n```\r\n  reflow run sourmash.rf \r\n/Users/olgabot/code/reflow-workflows/sourmash.rf:61:2: syntax error: unexpected 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