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

Update .nf-core.yml #33

Open
wants to merge 4 commits into
base: dev
Choose a base branch
from
Open

Update .nf-core.yml #33

wants to merge 4 commits into from

Conversation

daisymut
Copy link
Collaborator

.nf-core.yml prevented the automated PR for the template update

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/sammyseq branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile 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).

mirpedrol
mirpedrol reviewed Oct 11, 2024
View reviewed changes
Copy link
Member

@mirpedrol mirpedrol left a comment

Choose a reason for hiding this comment

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

You can continue skipping the report_comment linting step, but multiqc_config should be a list:

lint:
  multiqc_config:
    - report_comment

@github-actions GitHub Actions
Copy link

github-actions bot commented Oct 11, 2024 •
edited
Loading

nf-core pipelines lint overall result: Failed ❌

Posted for pipeline commit ed0c332

+| ✅ 157 tests passed       |+
!| ❗  29 tests had warnings |!
-| ❌  22 tests failed       |-

❌ Test failures:

  • files_exist - File must be removed: lib/NfcoreTemplate.groovy
  • files_exist - File must be removed: lib/Utils.groovy
  • files_exist - File must be removed: lib/WorkflowMain.groovy
  • files_exist - File must be removed: lib/WorkflowSammyseq.groovy
  • files_exist - File must be removed: lib/nfcore_external_java_deps.jar
  • nextflow_config - Plugin 'nf-validation' does not have a pinned version
  • nextflow_config - Config variable (incorrectly) found: params.max_cpus
  • nextflow_config - Config variable (incorrectly) found: params.max_memory
  • nextflow_config - Config variable (incorrectly) found: params.max_time
  • nextflow_config - Old lines for loading custom profiles found. File should contain: ```groovy
    // Load nf-core custom profiles from different Institutions
    includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
  • files_unchanged - .github/CONTRIBUTING.md does not match the template
  • files_unchanged - .github/PULL_REQUEST_TEMPLATE.md does not match the template
  • files_unchanged - .github/workflows/branch.yml 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
  • files_unchanged - assets/email_template.html does not match the template
  • files_unchanged - assets/email_template.txt does not match the template
  • files_unchanged - assets/nf-core-sammyseq_logo_light.png does not match the template
  • files_unchanged - docs/images/nf-core-sammyseq_logo_light.png does not match the template
  • files_unchanged - docs/images/nf-core-sammyseq_logo_dark.png does not match the template
  • files_unchanged - .gitignore does not match the template
  • actions_awsfulltest - .github/workflows/awsfulltest.yml is not triggered correctly

❗ Test warnings:

  • files_exist - File not found: conf/igenomes_ignored.config
  • nextflow_config - nf-validation has been detected in the pipeline. Please migrate to nf-schema: https://nextflow-io.github.io/nf-schema/latest/migration_guide/
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in README.md: If applicable, make list of people who have also contributed
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in main.nf: If in doubt look at other nf-core/modules to see how we are doing things! :)
  • pipeline_todos - TODO string in main.nf: A module file SHOULD only define input and output files as command-line parameters.
  • pipeline_todos - TODO string in main.nf: Software that can be piped together SHOULD be added to separate module files
  • pipeline_todos - TODO string in main.nf: Optional inputs are not currently supported by Nextflow. However, using an empty
  • pipeline_todos - TODO string in main.nf: List required Conda package(s).
  • pipeline_todos - TODO string in main.nf: See section in main README for further information regarding finding and adding container addresses to the section below.
  • pipeline_todos - TODO string in main.nf: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
  • pipeline_todos - TODO string in main.nf: Where applicable please provide/convert compressed files as input/output
  • pipeline_todos - TODO string in main.nf: Named file extensions MUST be emitted for ALL output channels
  • pipeline_todos - TODO string in main.nf: List additional required output channels/values here
  • pipeline_todos - TODO string in main.nf: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
  • pipeline_todos - TODO string in main.nf: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive
  • pipeline_todos - TODO string in main.nf: If the tool supports multi-threading then you MUST provide the appropriate parameter
  • pipeline_todos - TODO string in main.nf: Please replace the example samtools command below with your module's command
  • pipeline_todos - TODO string in main.nf: Please indent the command appropriately (4 spaces!!) to help with readability ;)
  • pipeline_todos - TODO string in main.nf: A stub section should mimic the execution of the original module as best as possible
  • 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 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 WorkflowSammyseq.groovy: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required
  • nfcore_yml - nf-core version not set in .nf-core.yml

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-10-11 15:34:18

@mirpedrol
Copy link
Member

Also, linting will fail because it is expecting the updates form the last template version, so don't worry for this PR, they can be ignored 🙂 let's just fix the .nf-core.yml and afterwards you can do the template update to fix the rest

@daisymut
Copy link
Collaborator Author

I didn't get what is the problem in the file preventing the creation of the template update PR, is it ok now?

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

@mirpedrol mirpedrol mirpedrol left review comments

At least 1 approving review is required to merge this pull request.

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

Successfully merging this pull request may close these issues.
2 participants
@daisymut @mirpedrol