Give user control of output format and compression

[tkchafin]

Addresses https://github.com/sanger-tol/readmapping/issues/64

• Adds --outfmt option
• Adds --compression option
• Updates documentation

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).

[tkchafin]

Hi @SandraBabirye I have pushed some changes hopefully addressing issue https://github.com/sanger-tol/readmapping/issues/64 for the readmapping pipeline.

I thought this might be a good chance to try out doing a code review! Could you test that the pipeline works and generates the correct outputs for each combination of the new arguments:

nextflow run main.nf -profile test,docker --outfmt bam,cram --compression none 
nextflow run main.nf -profile test,docker --outfmt bam,cram --compression cram 
nextflow run main.nf -profile test,docker --outfmt bam
nextflow run main.nf -profile test,docker --outfmt cram

And take a look at my implementation please? There should be an "add review" button in green in the top right