Creating A Single Pipeline for Metagenomic Taxonomic Classification

[macelik]

Project Lead: Muhammet Celik, Gokcen Sahin

Mentor: Mallory Freeberg

Welcome to OLS-2! This issue will be used to track your project and progress during the program. Please use this checklist over the next few weeks as you start Open Life Science program 🎉.

---

Week 1 (31 August - 4 September 2020): Meet your mentor!

• Create an account on GitHub
• Check if you have access to the HackMD notes set up for your meetings with your mentor
• Prepare to meet your mentor(s) by completing a short homework provided in the HackMD notes
• Complete your own copy of the open leadership self-assessment and share it to your mentor
  If you're a group, each teammate should complete this assessment individually. This is here to help you set your own personal goals during the program. No need to share your results, but be ready to share your thoughts with your mentor.
• Make sure you know when and how you'll be meeting with your mentor.

Before Week 2 (7 - 11 September 2020): Cohort Call (Welcome to Open Life Science!)

• Create an issue on the OLS-2 GitHub repository for your OLS work and share the link to your mentor.

• Draft a brief vision statement using your goals

  This lesson from the Open Leadership Training Series (OLTS) might be helpful

• Leave a comment on this issue with your draft vision statement & be ready to share this on the call

• Check the Syllabus for notes and connection info for all the cohort calls.

Before Week 3 (14 - 18 September 2020): Meet your mentor!

• Look up two other projects and comment on their issues with feedback on their vision statement
• Complete this compare and contrast assignment about current and desired community interactions and value exchanges
• Complete your Open Canvas (instructions, canvas)
• Share a link to your Open Canvas in your GitHub issue
  My Canvas
• Start your Roadmap
• Comment on your issue with your draft Roadmap
• Suggest a cohort name at the bottom of the shared notes and vote on your favorite with a +1

Before Week 4 (21 - 25 September 2020): Cohort Call (Tooling and roadmapping for Open projects)

• Look up two other projects and comment on their issues with feedback on their open canvas.

Week 5 and later

• Create a GitHub repository for your project
• Add the link to your repository in your issue
• Use your canvas to start writing a README.md file, or landing page, for your project
• Link to your README in a comment on this issue
• Add an open license to your repository as a file called LICENSE.md
• Add a Code of Conduct to your repository as a file called CODE_OF_CONDUCT.md
• Invite new contributors to into your work!

This issue is here to help you keep track of work as you start Open Life Science program. Please refer to the OLS-2 Syllabus for more detailed weekly notes and assignments past week 4.

[malvikasharan]

@macelik can you please update this issue with the new team member. Please share links to your assignments here, specifically your vision statement, open canvas and Github repository for your project if already available.

Also, can you please check out a few projects in the issues and check what others are working on and if you can share some ideas with them on their work or invite discussions.

[macelik]

@malvikasharan Hello Malvika, Yes I have talked to her and we are going to have a meeting tomorrow. I think I have shared my canvas and assignments on HackMD but yeah I will share them on here too as well as I ll get to the other projects too. I appreciate the concers and thank you. :)

[macelik]

@malvikasharan I have shared my canvas up in the issue and sharing it in here too. :) Would be nice to hear comments from you :)

Canvas

[hzahroh]

@macelik it's a cool project. Good to know that you will make it available on Github and Galaxy ✨ 👍

[macelik]

Compare & Contrast Assignment

link

[macelik]

Meta-Pipeline repo on GitHub

[macelik]

Vision: to create a pipeline to compile the state of the art tools (such as Kraken2, Centrifuge and CLARK) and create a single pipeline that will produce a visualized output file for each tool so the user can compare.