Prepare for release 1.0.0 "Naked Chicken"

[apeltzer]

This will ultimately be the first release of nf-core/openmspeptidequant, "Naked Chicken".

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/openmspeptidequant 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/openmspeptidequant/tree/master/.github/CONTRIBUTING.md

[ewels]

Naked Chicken - really?? 😆

[ewels]

Few minor things:

• main.nf is missing ASCII art for the help text
• nextflow.config has the standard profile twice
• Most of the configs in base.config could be grouped into a couple of withLabel statements
• Would be nice to harmonise the profiles a bit with the base template (add uppmax, add zurich to the template)
• Nextflow throws a warning:

  • WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition -- check channel `id_files_merged_psm_perc_filtered`
    

• Strange minor markdown rendering bug in docs:
  
• num_threads is documented (and here) and in nextflow.config but not used in main.nf
• Docs don't describe several profiles

Generally looking really good though!

Phil

[apeltzer]

Naked Chicken - really?? 😆

Yes, @Leon-Bichmann had the idea, not my choice :-D

[apeltzer]

All points mentioned by @ewels addressed now:

• ASCII Art added
• got rid of the first() statement which was unnecessary
• Added documentation fixes for markdown rendering issues
• Added Docs for Profiles present atm (others will come via Sync)
• Submitted separate PR to tools for having more profiles there (e.g. UZH, also introduced sorting there in the PR)
• Removed redundant resource statements in the base.config, these are now defaults
  • Only resource requests bigger or smaller get their own labels now
• Got rid of num_threadswhich isn't used at all in the pipeline anymore

[Leon-Bichmann]

Currently I dont produce any qc analysis and no output visualizations.
I will probably add some in a later release.

[apeltzer]

Complete rename solved :-)

[sven1103]

The openms version in the environment spec must be openms=2.4.0

[apeltzer]

Had to adapt the test-datasets first, now this works.

[apeltzer]

I guess the chicken has landed :-)

[Leon-Bichmann]

anything missing still for the chicken to leave the nest?

[apeltzer]

A review by @ewels for example ;-)

[apeltzer]

I think this is fine, will merge to dev atm