Pmdtools reference masking fix , sequencetools update

[TCLamnidis]

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

[github-actions]

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[github-actions]

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

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Thanks again for your contribution!