Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Important! Template update for nf-core/tools v2.13.1 #345

Merged
merged 12 commits into from
Mar 13, 2024
Merged

Important! Template update for nf-core/tools v2.13.1 #345

merged 12 commits into from
Mar 13, 2024

Conversation

nf-core-bot
Copy link
Member

Version 2.13.1 of nf-core/tools has just been released with updates to the nf-core template. This automated pull-request attempts to apply the relevant updates to this pipeline.

Please make sure to merge this pull-request as soon as possible, resolving any merge conflicts in the nf-core-template-merge-2.13.1 branch (or your own fork, if you prefer). Once complete, make a new minor release of your pipeline.

For instructions on how to merge this PR, please see https://nf-co.re/docs/contributing/sync/.

For more information about this release of nf-core/tools, please see the v2.13.1 release page.

@nf-core-bot nf-core-bot mentioned this pull request Feb 29, 2024
Closed
jasmezz
jasmezz reviewed Mar 12, 2024
View reviewed changes
main.nf Outdated Show resolved Hide resolved
main.nf Outdated Show resolved Hide resolved
subworkflows/local/utils_nfcore_funcscan_pipeline/main.nf Outdated Show resolved Hide resolved
subworkflows/local/utils_nfcore_funcscan_pipeline/main.nf Outdated Show resolved Hide resolved
subworkflows/local/utils_nfcore_funcscan_pipeline/main.nf Outdated Show resolved Hide resolved
subworkflows/local/utils_nfcore_funcscan_pipeline/main.nf Outdated Show resolved Hide resolved
workflows/funcscan.nf Outdated Show resolved Hide resolved
@github-actions GitHub Actions
Copy link

github-actions bot commented Mar 12, 2024 •
edited
Loading

nf-core lint overall result: Passed ✅

Posted for pipeline commit 2d2f902

+| ✅ 223 tests passed       |+

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-03-13 10:19:01

@jasmezz
Copy link
Collaborator

jasmezz commented Mar 12, 2024

Closes #342

mashehu
mashehu approved these changes Mar 13, 2024
View reviewed changes
main.nf Outdated Show resolved Hide resolved
main.nf Outdated Show resolved Hide resolved
nextflow.config Outdated Show resolved Hide resolved
jasmezz and others added 2 commits March 13, 2024 08:15
@jasmezz @mashehu
Apply suggestions from code review
22e654b 
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
@jasmezz
Apply suggestion from code review
1150fd1
@jasmezz jasmezz mentioned this pull request Mar 13, 2024
Closed
10 tasks
jfy133
jfy133 reviewed Mar 13, 2024
View reviewed changes
Copy link
Member

@jfy133 jfy133 left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I think this looks OK. There is this error though:

WARN: Access to undefined parameter `fasta` -- Initialise it to a default value eg. `params.fasta = some_value`

when running, so we need to add params.fasta back in and just leave to ignore, or try and remove where it is used

workflows/funcscan.nf Outdated Show resolved Hide resolved
@jasmezz jasmezz added this to the 1.2 - Brazilian Escondidinho milestone Mar 13, 2024
jasmezz
jasmezz reviewed Mar 13, 2024
View reviewed changes
workflows/funcscan.nf Outdated Show resolved Hide resolved
@jasmezz jasmezz merged commit ec600ff into dev Mar 13, 2024
@jasmezz jasmezz deleted the nf-core-template-merge-2.13.1 branch March 13, 2024 10:52
@jasmezz
Copy link
Collaborator

jasmezz commented Mar 13, 2024

Thanks @mashehu for the quick review and @jfy133 for streamlining it even more! 🚀

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@jasmezz jasmezz jasmezz approved these changes

@jfy133 jfy133 jfy133 approved these changes

@mashehu mashehu mashehu approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
2.0 - Brazilian Escondidinho
Development

Successfully merging this pull request may close these issues.
4 participants
@nf-core-bot @jasmezz @mashehu @jfy133