DSL2 readprep

[jfy133]

This adds the read pre-processing sub-workflow including

• [x] poly-G trimming
• [x] poly-X trimming
• [ ] adapter removal and merging

PR checklist

• [ ] This comment contains a description of changes (with reason).
• [ ] If you've fixed a bug or added code that should be tested, add tests!
  • [ ] If you've added a new tool - add to the software_versions process and a regex to scrape_software_versions.py
  • [ ] If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • [ ] If necessary, also make a PR on the nf-core/eager branch on the nf-core/test-datasets repository.
• [ ] Make sure your code lints (nf-core lint .).
• [ ] Ensure the test suite passes (nextflow run . -profile test,docker).
• [ ] Usage Documentation in docs/usage.md is updated.
• [ ] Output Documentation in docs/output.md is updated.
• [ ] CHANGELOG.md is updated.
• [ ] README.md is updated (including new tool citations and authors/contributors).

[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 .

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

We highly recommend setting up markdownlint 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!

[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 yamllint
  • Install yamllint following this instructions or alternative install it in your conda environment
• Fix the markdown errors
  • Run the test locally: yamllint $(find . -type f -name "*.yml" -o -name "*.yaml") -c ./.yamllint.yml
  • 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!

[jfy133]

Going to start this one from scratch and one PR per tool :+1: