v4.0.0 release

[fmalmeida]

• Depends on Bump version 4.0.0 #446

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
• If necessary, also make a PR on the nf-core/scrnaseq branch on the nf-core/test-datasets repository.
• 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>).
• 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).

[apeltzer]

Should be ok now for a release :-)

[DongzeHE]

OK one last thing (I promise) before the release:

Compare with the current release, the simpleaf/quant module publishes mapping results in addition to quantification results. If save_reference=true, the simpleaf/index module publishes the augmented transcriptomic files in addition to the index folder.

My questions is, do we want to keep those extra files, or we want to align with the current release?

[grst]

Hi @DongzeHE, what do you mean with "mapping results"? Something like pseudo-BAM?

I don't think the save_reference flag is the appropriate argument for that, that's meant only for the reference. There's a save_align_intermeds flag though, that sounds better for your use-case.

[grst]

@fmalmeida, bump version to 4.0 as discussed above and we are good to go? Or did I miss anything?

[fmalmeida]

Hi @grst ,
That is correct. The other reviews have been resolved:
#446

[apeltzer]

All fine for me too

[grst]

ok, perfect!
@fmalmeida feel free to proceed with the release as described here: https://nf-co.re/docs/checklists/pipeline_release