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Template update for nf-core/tools version 2.14.0 #90

Merged
merged 9 commits into from
May 10, 2024
Merged

Template update for nf-core/tools version 2.14.0 #90

merged 9 commits into from
May 10, 2024

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asp8200
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@asp8200 asp8200 commented May 9, 2024 •
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Currently, getting

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

@mirpedrol : As you can see, I did add both fasta and fasta_fai to validationSchemaIgnoreParams so why do I get that warning about fasta being uninitialised?

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/bamtofastq 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).

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github-actions bot commented May 9, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 7b7e031

+| ✅ 189 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   5 tests had warnings |!
-| ❌   2 tests failed       |-

❌ Test failures:

  • files_unchanged - .github/workflows/linting.yml does not match the template
  • actions_schema_validation - Workflow validation failed for download_pipeline.yml: {'name': 'Run the downloaded pipeline (stub run not supported)', 'id': 'run_pipeline', 'if': '${{ job.steps.stub_run_pipeline.status == failure() }}', 'env': {'NXF_SINGULARITY_CACHEDIR': './', 'NXF_SINGULARITY_HOME_MOUNT': True}} is not valid under any of the given schemas

Failed validating 'oneOf' in schema[0]['properties']['steps']['items']['allOf'][0]:
{'oneOf': [{'properties': {'uses': {'type': 'string'}},
'required': ['uses'],
'type': 'object'},
{'properties': {'run': {'type': 'string'}},
'required': ['run'],
'type': 'object'}]}

On instance['steps'][9]:
{'env': {'NXF_SINGULARITY_CACHEDIR': './',
'NXF_SINGULARITY_HOME_MOUNT': True},
'id': 'run_pipeline',
'if': '${{ job.steps.stub_run_pipeline.status == failure() }}',
'name': 'Run the downloaded pipeline (stub run not supported)'}

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • 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 in .nf-core.yml is not set to the latest version. Should be 2.14.1 but was 2.14.0

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-05-10 09:52:04

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Version 2.14.1 of the nf-core/tools pipeline template has just been released. This pull-request is now outdated and has been closed in favour of #91

Please use #91 to merge in the new changes from the nf-core template as soon as possible.

@nf-core-bot nf-core-bot closed this May 9, 2024
@asp8200 asp8200 reopened this May 10, 2024
@maxulysse maxulysse marked this pull request as ready for review May 10, 2024 07:08
@asp8200
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asp8200 commented May 10, 2024

@maxulysse : Anything else I should do as part of "back to dev"?

@maxulysse
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so this one replaces #89?

@mirpedrol
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@mirpedrol : As you can see, I did add both fasta and fasta_fai to validationSchemaIgnoreParams so why do I get that warning about fasta being uninitialised?

I am unsure what is causing this, it could be a bug on nf-schema, we see the same behaviour with monochromeLogs. I will need more time to look into this. But it shouldn't affect the correct running of your pipeline.

@asp8200 asp8200 requested review from maxulysse and mirpedrol May 10, 2024 08:57
maxulysse
maxulysse reviewed May 10, 2024
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.nf-core.yml
lint:
files_unchanged:
- .github/CONTRIBUTING.md
- .github/CONTRIBUTING.md
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why this file?

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@asp8200 asp8200 May 10, 2024 •
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You mean .github/CONTRIBUTING.md? It is like that on the dev-branch. I think this PR just adds a newline or something like that at the end of .nf-core.yml.

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The template update modified only the new line. Adding this file will skip the linting test. You should do this only if you edited CONTRIBUTING.md and don't want to lint it.

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I guess somebody put .github/CONTRIBUTING.md in .nf-core.yml because it was failing the linting test.

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ok let's deal with that in the other PR then

maxulysse
maxulysse reviewed May 10, 2024
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@maxulysse maxulysse merged commit e729868 into nf-core:dev May 10, 2024
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@maxulysse maxulysse maxulysse approved these changes

@mirpedrol mirpedrol Awaiting requested review from mirpedrol

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@asp8200 @nf-core-bot @maxulysse @mirpedrol