Coverage tracks

[suhrig]

I have added bigWig coverage tracks to the outputs using bedtools genomecov. Stranded libraries produce two tracks, <SAMPLE>.forward.bigWig and <SAMPLE>.reverse.bigWig. Unstranded libraries produce a single track <SAMPLE>.unstranded.bigWig.

The track creation needed to be divided into three processes:

1. Splitting BAMs into forward and reverse reads, because bedtools genomecov does not handle the strand of paired-end mates properly (it always uses the strand of the mate, not the strand of the first-of-pair)
2. Conversion of the split BAMs to bedGraph
3. Conversion of the bedGraphs to bigWig to reduce storage consumption

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 you've added a new tool - have you followed the pipeline conventions in the contribution docs
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[suhrig]

@nf-core-bot fix linting

[pinin4fjords]

did you mean to change this?

[suhrig]

Yes. The link was wrong. I admit to taking the quick and easy route instead of making a separate PR for this.

[suhrig]

@nf-core-bot fix linting