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Update .nf-core.yml #33

Merged
merged 5 commits into from
Oct 15, 2024
Merged

Update .nf-core.yml #33

merged 5 commits into from
Oct 15, 2024

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daisymut
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.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).

@daisymut daisymut requested a review from mirpedrol October 11, 2024 10:15
mirpedrol
mirpedrol reviewed Oct 11, 2024
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@mirpedrol mirpedrol left a comment

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

lint:
  multiqc_config:
    - report_comment

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github-actions bot commented Oct 11, 2024 •
edited
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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
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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
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I didn't get what is the problem in the file preventing the creation of the template update PR, is it ok now?

mirpedrol
mirpedrol approved these changes Oct 14, 2024
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looks good now, thanks for the fix 🙂

@daisymut
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@mirpedrol can you please help me in fixing or skipping the linting error and merge? I can't find which file triggers the error message

ERROR: Invalid requirement: 'nf-core==': Expected end or semicolon (after name and no valid version specifier)
nf-core==
^
Error: Process completed with exit code 1.

@daisymut daisymut self-assigned this Oct 14, 2024
@mirpedrol
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This error will be fixed with the template update 3.0.2. I would advice to merge this PR with failing test and do the template update in a different PR, to simplify things.
For the template update you can install the last version of nf-core/tools 3.0.2 and run nf-core pipelines syn
Alternatively you can also execute the GitHub Action we have with the Run workflow button and making sure to write your pipeline name in the textbox (replacing "all")

@daisymut
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@mirpedrol thank you, I probably don't have the privileges to merge this PR with a failing required check :( the Merge button is still inactive despite your approval. Can you please force it?

@mirpedrol mirpedrol merged commit bff2fe1 into dev Oct 15, 2024
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@mirpedrol
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Done, you can now do the template update, thanks for this fix!

@daisymut
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Thank you for your help!

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@mirpedrol mirpedrol mirpedrol approved these changes

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@daisymut @mirpedrol