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@jfy133 jfy133 commented Mar 10, 2022

PR checklist

Fixes #838

And adding a test for it...

also possibly fix an issue with PMDtools and reference masking, but I don't understand what is going on there so need input from @TCLamnidis

  • 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](https://github.com/nf-core/eager/tree/master/.github/CONTRIBUTING.md)
    • 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).

@jfy133 jfy133 changed the base branch from master to dev March 10, 2022 08:12
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This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @jfy133,

It looks like this pull-request is has been made against the nf-core/eager master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the nf-core/eager dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

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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
  • Fix the markdown errors
    • Automatically: markdownlint . --config .github/markdownlint.yml --fix
    • Manually resolve anything left from markdownlint . --config .github/markdownlint.yml

Once you push these changes the test should pass, and you can hide this comment 👍

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!

@jfy133 jfy133 requested a review from TCLamnidis March 10, 2022 08:22
@jfy133 jfy133 added the question Further information is requested label Mar 10, 2022
@apeltzer apeltzer merged commit 2b7d5bf into dev Mar 17, 2022
@apeltzer apeltzer deleted the bedfilefix branch March 17, 2022 09:46
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BED file for use with --snpcapture_bed not recognized

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