Bug fixes in v1.4 release

[drpatelh]

Many thanks to contributing to nf-core/rnaseq!

To ensure that your build passes, please make sure your pull request is to the dev branch rather than to master. Thank you!

Please fill in the appropriate checklist below (delete whatever is not relevant). These are the most common things requested on pull requests (PRs).

PR checklist

• PR is to dev rather than master
• 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/rnaseq branch on the nf-core/test-datasets repo
• Ensure the test suite passes (nextflow run . -profile test,docker).
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• Documentation in docs is updated
• CHANGELOG.md is updated
• README.md is updated

Learn more about contributing: https://github.com/nf-core/rnaseq/tree/master/.github/CONTRIBUTING.md

• Bump versions to 1.5dev
• Fixed parameter warnings #316 and 318
• Fixed #307 - Confusing Info Printout about GFF and GTF
• Adjusted some but not all spacing. Will need to review this all again before the next release.

[drpatelh]

Some of the version changes you sent werent consistent @apeltzer . Ive bumped everything to 1.4.1 now. Can you just double-check everything please?

[drpatelh]

Some tests are failing? 😕

[drpatelh]

Ah, its because we bumped versions and tests cant find the appropriate container...

[drpatelh]

Why are we still using 0.32.0 though for tests? You bumped that no @apeltzer ?

[drpatelh]

Ah, GitHub actions files need to be updated too. Will need to add this into bump-versions:

rnaseq/.github/workflows/ci.yml

Line 10 in 55eee0c

nxf_ver: ['0.32.0', '']

[apeltzer]

We bumped it everywhere but in the GitHub Actions tests ... (which are not auto-bumped atm).

[apeltzer]

Open an issue for that nf-core/tools#429

[drpatelh]

Ok. Tests are still failing because GitHub cant find the docker container for 1.4.1 whats the easiest way to fix this?

[drpatelh]

Looking much better. Do your thing with the patch release when youre happy 👍