Added post-mapping filter statistics generation

[jfy133]

This PR duplicates the samtools flagstat step for after mapping quality filtering. This allows a user to see the effect of mapping quality filtering.

It also includes some clean-up of code comments

Note: I've manually tested this myself. The only thing that is slightly off is that the General Stats table doesn't report the name of which samtools flagstat step it is from (but it displayes pre- and post- map quality filtering in the correct order). However the menu on the left does have the correct names.

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/eager 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/eager/tree/master/.github/CONTRIBUTING.md

[apeltzer]

Looking great - thanks @jfy133