smrnaseq icon indicating copy to clipboard operation
smrnaseq copied to clipboard
verified publisher icon nf-core

Issue 354

Open lpantano opened this issue 1 year ago • 2 comments

Addressing the issue with Blat containers, should we update them ?

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/smrnaseq branch on the nf-core/test-datasets repository.
  • [ ] Make sure your code lints (nf-core lint).
  • [ ] Ensure the test suite passes (nf-test test main.nf.test -profile test,docker).
  • [ ] 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).

lpantano avatar Jun 28 '24 21:06 lpantano

This PR is against the master branch :x:

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @lpantano,

It looks like this pull-request is has been made against the nf-core/smrnaseq master branch. The master branch on nf-core repositories should always contain code from the latest release. Because of this, PRs to master are only allowed if they come from the nf-core/smrnaseq dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page. Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

github-actions[bot] avatar Jun 28 '24 21:06 github-actions[bot]

nf-core lint overall result: Failed :x:

Posted for pipeline commit c00d321

+| ✅ 208 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   4 tests had warnings |!
-| ❌   5 tests failed       |-

:x: Test failures:

  • files_unchanged - .github/PULL_REQUEST_TEMPLATE.md does not match the template
  • files_unchanged - .github/workflows/linting_comment.yml does not match the template
  • files_unchanged - .github/workflows/linting.yml does not match the template
  • base_config - conf/base.config contains withName:CUSTOM_DUMPSOFTWAREVERSIONS, but the corresponding process is not present in any of the Nextflow scripts.
  • modules_config - conf/modules.config contains withName:CUSTOM_DUMPSOFTWAREVERSIONS, but the corresponding process is not present in any of the Nextflow scripts.

:heavy_exclamation_mark: Test warnings:

  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • nfcore_yml - nf-core version not set in .nf-core.yml

:grey_question: Tests ignored:

  • nextflow_config - Config default ignored: params.fastp_known_mirna_adapters

:white_check_mark: Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-06-28 21:20:17

github-actions[bot] avatar Jun 28 '24 21:06 github-actions[bot]

x-ref #368 - we shoudl even consider either adding BLAT to nf-core/modules and importing from there or updating the container & using seqera containers now that this is available. That should improve the situation I hope :)

Nicolas/Anabella can work on this 👍🏻

apeltzer avatar Aug 08 '24 21:08 apeltzer

thanks, then we close this, right?

lpantano avatar Aug 09 '24 17:08 lpantano

We can I think 👍

apeltzer avatar Aug 10 '24 11:08 apeltzer