Bug fixes and small aesthetic amendments - Round 2

[drpatelh]

Many thanks to contributing to nf-core/chipseq!

Please fill in the appropriate checklist below (delete whatever is not relevant). These are the most common things requested on pull requests (PRs).

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 necessary, also make a PR on the nf-core/chipseq branch on the nf-core/test-datasets repo
• Ensure the test suite passes (nextflow run . -profile test,docker).
• Make sure your code lints (nf-core lint .).
• Documentation in docs is updated
• CHANGELOG.md is updated
• README.md is updated

Learn more about contributing: https://github.com/nf-core/chipseq/tree/master/.github/CONTRIBUTING.md

Trying to unify processes and logic with atacseq pipeline. Fixed bugs reported here and with atacseq pipeline too. See CHANGELOG.md.

[drpatelh]

Ok. Im going to merge this. Maybe do a proper review when merging to master.