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 v2.10 #1025

Merged
merged 4 commits into from
Oct 6, 2023
Merged

Important! Template update for nf-core/tools v2.10 #1025

merged 4 commits into from
Oct 6, 2023

Conversation

nf-core-bot
Copy link
Member

Version 2.10 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-2.10 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 v2.10 release page.

jfy133
jfy133 approved these changes Sep 30, 2023
View reviewed changes
README.md Outdated Show resolved Hide resolved
@github-actions
Copy link

github-actions bot commented Sep 30, 2023 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 4bf3681

+| ✅ 159 tests passed       |+
!| ❗  20 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
  • pipeline_todos - TODO string in README.md: Include a figure that guides the user through the major workflow steps. Many nf-core
  • pipeline_todos - TODO string in README.md: Fill in short bullet-pointed list of the default steps in the pipeline
  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • pipeline_todos - TODO string in test.config: Specify the paths to your test data on nf-core/test-datasets
  • pipeline_todos - TODO string in test.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in test_humanbam.config: Specify the paths to your test data on nf-core/test-datasets
  • pipeline_todos - TODO string in test_humanbam.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • pipeline_todos - TODO string in WorkflowEager.groovy: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
  • schema_description - No description provided in schema for parameter: skip_qualimap
  • schema_description - No description provided in schema for parameter: skip_damage_calculation

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-09-30 06:44:42

scarlhoff
scarlhoff approved these changes Oct 6, 2023
View reviewed changes
Copy link
Contributor

@scarlhoff scarlhoff left a comment

Choose a reason for hiding this comment

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

Seems good

@scarlhoff scarlhoff merged commit bc9c7b5 into dev Oct 6, 2023
18 checks passed
@scarlhoff scarlhoff deleted the nf-core-template-merge-2.10 branch October 6, 2023 08:50
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@scarlhoff scarlhoff scarlhoff approved these changes

@jfy133 jfy133 jfy133 approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
3 participants
@nf-core-bot @jfy133 @scarlhoff