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Pmdtools reference masking fix , sequencetools update #853

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Merged
jfy133 merged 11 commits into from
Mar 17, 2022
Merged

Pmdtools reference masking fix , sequencetools update #853

jfy133 merged 11 commits into from
Mar 17, 2022

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@TCLamnidis
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@TCLamnidis TCLamnidis commented Mar 17, 2022

Changes

  • Added masking of reference fasta prior to running pmdtools, when requested.
    • Updated explanation of pmdtools_reference_mask parameter in schema.
  • Bumped sequencetools 1.4.0.5 -> 1.5.2

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!
  • Make sure your code lints (nf-core lint .).
  • Ensure the test suite passes (nextflow run . -profile test,docker).
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.

Closes #844
Closes #829

@TCLamnidis TCLamnidis requested a review from jfy133 March 17, 2022 15:33
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github-actions bot commented Mar 17, 2022

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 merged commit 4528211 into dev Mar 17, 2022
@jfy133 jfy133 deleted the pmdtools_mask branch March 17, 2022 16:16
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github-actions bot commented Mar 17, 2022

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
  • 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 👍

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 jfy133 linked an issue Mar 18, 2022 that may be closed by this pull request
Update sequenceTools #829
Closed
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Update sequenceTools

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@TCLamnidis @jfy133