{"action":"created","issue":{"url":"https://api.github.com/repos/datacarpentry/genomics-workshop/issues/41","repository_url":"https://api.github.com/repos/datacarpentry/genomics-workshop","labels_url":"https://api.github.com/repos/datacarpentry/genomics-workshop/issues/41/labels{/name}","comments_url":"https://api.github.com/repos/datacarpentry/genomics-workshop/issues/41/comments","events_url":"https://api.github.com/repos/datacarpentry/genomics-workshop/issues/41/events","html_url":"https://github.com/datacarpentry/genomics-workshop/issues/41","id":314265909,"node_id":"MDU6SXNzdWUzMTQyNjU5MDk=","number":41,"title":"lesson reorganization","user":{"login":"bluegenes","id":7740734,"node_id":"MDQ6VXNlcjc3NDA3MzQ=","avatar_url":"https://avatars1.githubusercontent.com/u/7740734?v=4","gravatar_id":"","url":"https://api.github.com/users/bluegenes","html_url":"https://github.com/bluegenes","followers_url":"https://api.github.com/users/bluegenes/followers","following_url":"https://api.github.com/users/bluegenes/following{/other_user}","gists_url":"https://api.github.com/users/bluegenes/gists{/gist_id}","starred_url":"https://api.github.com/users/bluegenes/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bluegenes/subscriptions","organizations_url":"https://api.github.com/users/bluegenes/orgs","repos_url":"https://api.github.com/users/bluegenes/repos","events_url":"https://api.github.com/users/bluegenes/events{/privacy}","received_events_url":"https://api.github.com/users/bluegenes/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2018-04-13T22:17:09Z","updated_at":"2018-07-03T14:19:39Z","closed_at":null,"author_association":"NONE","body":"We propose some lesson reorganization to facilitate the Genomics workshops. \r\n\r\n**Motivating issue**: `scp` is used to download `fastqc.html` files in the quality trimming lesson in the `Wrangling Genomics` section, but windows users are unable to use `scp`. This has derailed several recently-taught workshops. \r\n\r\n*Proposed changes:*\r\n---\r\n\r\n**Setup:**\r\n\r\n- Modify Windows setup: use [gitbash] rather than PUTTY. \r\n  - benefits: enables windows users to use `scp` and use a bash-style terminal to navigate their own computers.\r\n\r\n**Cloud Genomics:**\r\n\r\n- Split into two parts:\r\n\r\n  - Part 1: Introduction to Remote Computing\r\n     - Lessons:  1 (Why of cloud computing), 2 (Logging onto Cloud) & `whoami` (from 3): \r\n     - Teach after **Organization Genomics** but before **Shell Genomics**\r\n   \r\n  - Part 2: Remote Computing Strategies (?)\r\n     - Lessons: 3 (Fine tuning your cloud setup), 5 (Which Cloud for my data)\r\n     - Teach at ~end of workshop\r\n     - reasoning: these lessons are confusing at the beginning, when users just need to get going on a remote command line, but are great for helping users go beyond the workshop and start working with their own data/setups\r\n     - If we do this, should we modify Data Roundtripping (lesson 4)? It is partially taught within wrangling genomics (see below)\r\n   \r\n**Wrangling Genomics:**\r\n\r\n*Quality control lesson (lesson 1)*: \r\n\r\n- Streamline by removing loops from this lesson (too many concepts here):\r\n   - In ‘Understanding FastQC’ just unzip one thing and look at the text file \r\n   - After ‘Running FastQC’ section, skip to ‘Understanding FastQC Output'\r\n- Keep `scp` command to download the HTML from FastQC (works in gitbash on Windows)\r\n   - This is half of Data Roundtripping (from cloud section)\r\n   - Can use this as an opportunity to discuss the structure of `scp`-style commands (e.g. `cp`, `mv`, `ln -s`): `scp [origin/file] [destination]`, since they'll have learned these commands in Shell Genomics.\r\n- Revise or eliminate the \"Documenting our Work\" section\r\n  - Too much in this lesson & we didn't think this was the best way to document work. Automation lesson may be a better spot to discuss documenting work (see below)\r\n  - If we take this out, we should show `cat` to concatenate files together elsewhere (Shell Genomics uses `cat` to join files to stdout, but does not actually `cat` files together).\r\n\r\n*Trimming and Filtering (lesson 2):*  \r\n- Add intro to `for` loops  (eliminated from QC - can move some of that section here)\r\n- We already use a `for` loop for trimming files with `Trimmomatic` = we are discussing them anyway. While loops aren't strictly necessary for understanding FastQC output in the QC lesson, we definitely need them for the trimming.\r\n\r\n*Variant Calling Workflow (lesson 3)*  \r\n- No changes, just a note that this lesson also uses `scp`\r\n\r\n*Automating a Variant Calling Workflow (lesson 4):*\r\n\r\n- Better spot for \"Documenting Our Work\" discussion? (eliminated from QC)\r\n- Could do the 2nd half of `Data Roundtripping`:\r\n   - `scp` script to home computer\r\n   - use nano to add some additional comments to improve documentation \r\n   - `scp` script back to remote server\r\n\r\n\r\n\r\nProposed reorganization reflects discussion w/ @tracykteal, @standage, @ljcohen, @karenword @jessicamizzi"},"comment":{"url":"https://api.github.com/repos/datacarpentry/genomics-workshop/issues/comments/402173963","html_url":"https://github.com/datacarpentry/genomics-workshop/issues/41#issuecomment-402173963","issue_url":"https://api.github.com/repos/datacarpentry/genomics-workshop/issues/41","id":402173963,"node_id":"MDEyOklzc3VlQ29tbWVudDQwMjE3Mzk2Mw==","user":{"login":"JasonJWilliamsNY","id":7266775,"node_id":"MDQ6VXNlcjcyNjY3NzU=","avatar_url":"https://avatars2.githubusercontent.com/u/7266775?v=4","gravatar_id":"","url":"https://api.github.com/users/JasonJWilliamsNY","html_url":"https://github.com/JasonJWilliamsNY","followers_url":"https://api.github.com/users/JasonJWilliamsNY/followers","following_url":"https://api.github.com/users/JasonJWilliamsNY/following{/other_user}","gists_url":"https://api.github.com/users/JasonJWilliamsNY/gists{/gist_id}","starred_url":"https://api.github.com/users/JasonJWilliamsNY/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/JasonJWilliamsNY/subscriptions","organizations_url":"https://api.github.com/users/JasonJWilliamsNY/orgs","repos_url":"https://api.github.com/users/JasonJWilliamsNY/repos","events_url":"https://api.github.com/users/JasonJWilliamsNY/events{/privacy}","received_events_url":"https://api.github.com/users/JasonJWilliamsNY/received_events","type":"User","site_admin":false},"created_at":"2018-07-03T14:19:39Z","updated_at":"2018-07-03T14:19:39Z","author_association":"CONTRIBUTOR","body":"Putty is very lightweight and a small file size. Never had problems teaching with it, and when necessary pscp.exe. "}}
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