Read coverage review

[muffato]

(reopening because I accidentally closed #175)

This is the first part of my review of #171. I was testing things locally and thought I'd just push my changes as a pull-request for you to review rather than adding comments onto your PR.

• I removed samtools/faidx which wasn't used.
• A small change in blobtk_depth because we pass a BAM file, not CRAM.
• I renamed some variables in subworkflows/local/convert_stats.nf
• In subworkflows/local/convert_stats.nf, ch_cram was getting BAM, not CRAM.
• For modules/local/change_name.nf, in order to make it ligher:
  • Force the local executor.
  • Don't declare any Conda environment or container. We can assume ln to exist on the host.
  • Then we don't really need to record the version used.
  • This pipeline doesn't have any process_* labels. But the defaults resources are already for 1 CPU
  • I added the -f option in ln for re-runs, just in case

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 lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[sanger-tolsoft]

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.2.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.