add fastq trimming step

[kaitlinchaung]

• use trimgalore to trim fastq files prior to any processing -added trimming params, all currently set to null

[github-actions[bot]]

Markdown linting is failing

To keep the code consistent with lots of contributors, we run automated code consistency checks. To fix this CI test, please run:

• Install markdownlint-cli
  • On Mac: brew install markdownlint-cli
  • Everything else: Install npm then install markdownlint-cli (npm install -g markdownlint-cli)
• Fix the markdown errors
  • Automatically: markdownlint . --fix
  • Manually resolve anything left from markdownlint .

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[github-actions[bot]]

YAML linting is failing

To keep the code consistent with lots of contributors, we run automated code consistency checks. To fix this CI test, please run:

• Install yaml-lint
  • Install npm then install yaml-lint (npm install -g yaml-lint)
• Fix the markdown errors
  • Run the test locally: yamllint $(find . -type f -name "*.yml" -o -name "*.yaml")
  • Fix any reported errors in your YAML files

Once you push these changes the test should pass, and you can hide this comment :+1:

We highly recommend setting up yaml-lint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!

Thanks again for your contribution!