Make initial release

[hverdonk]

@d-callan I'm ready to release when you are! The major features are implemented and tested, and new features can be PRed as needed/completed.

PR checklist

• This comment contains a description of changes (with reason).
• 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).

[hverdonk]

CI tests are failing because of an OverlappingFileLockException - probably because the same CI tests are also running on an earlier commit to dev. I can re-run the tests once the dev commit finishes and see if there's still an error

[hverdonk]

The failing tests seem to be failing now because they're tests from the main branch (or perhaps because they're testing the main branch), and main is just a skeleton with no functional code. @d-callan, what do you recommend here? All of the CI tests pass on the dev branch. I suggest forcing the CI tests on dev to include conda and singularity, then merging if we're successful.

[hverdonk]

Never mind - it seems that the OverlappingFileLockException is actually an old Nextflow bug. Upgrading the minimum supported version of Nextflow to 25.10.0 has resolved the issue. I also removed the redundant test case (runs MEME, FEL, PRIME, and BUSTED), since we're already running test_full(all of the above, plus Contrast-FEL and RELAX).

[hverdonk]

The two failing tests (nf-core template version comment and Test successful pipeline download with 'nf-core pipelines download') are nf-core specific tests that run because the test files exist in the pipeline skeleton on main. I don't expect them to pass (because we're not an official nf-core pipeline), so their failure should be disregarded.

[d-callan]

Nice detective work w the tests. I'd be inclined to removing the two tests still failing, and then merging.

[hverdonk]

Thank you! I'm glad I finally figured out the issue - it was bugging me.

I tried removing the failing tests, but main is protected. I'll just merge anyway, since I already removed the failing tests from dev.