Fix bedtools coverage in DSL1

[IdoBar]

Remove the -sorted flag so bedtools won't assume that the reference genome file is sorted.

PR checklist

• [x] This comment contains a description of changes (with reason).
• [ ] If you've fixed a bug or added code that should be tested, add tests!
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  • [ ] 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]]

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Hi @IdoBar,

It looks like this pull-request is has been made against the IdoBar/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 IdoBar/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!

[TCLamnidis]

Hi Ido!

Thanks for the PR. I will look into it and try to incorporate it into a patch release with a couple more small changes in the beginning of next year.

[TCLamnidis]

Had another look into why we added that flag #824 . It seems without it, the memory footprint of bedtools coverage is extremely large. I think I will instead add an option to REMOVE the -sorted flag.

[TCLamnidis]

Changes implemented in #1052 , so closing this PR. Thank you for the contribution!