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fix download_pipeline test #47

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fix download_pipeline test #47

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nikhil
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@nikhil nikhil commented Jul 8, 2024

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
  • 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 Jul 8, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 54cf55c

+| ✅ 144 tests passed       |+
#| ❔  16 tests were ignored |#
!| ❗  26 tests had warnings |!
-| ❌   6 tests failed       |-

❌ Test failures:

  • files_unchanged - .github/PULL_REQUEST_TEMPLATE.md 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
  • actions_schema_validation - Workflow validation failed for download_pipeline.yml: {'name': 'Run the downloaded pipeline', 'env': {'NXF_SINGULARITY_CACHEDIR': './'}} 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'][7]:
{'env': {'NXF_SINGULARITY_CACHEDIR': './'},
'name': 'Run the downloaded pipeline'}

  • base_config - conf/base.config contains withName:CUSTOM_DUMPSOFTWAREVERSIONS, but the corresponding process is not present in any of the Nextflow scripts.
  • modules_config - conf/modules.config contains withName:CUSTOM_DUMPSOFTWAREVERSIONS, but the corresponding process is not present in any of the Nextflow scripts.

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 1.0.0
  • 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: Remove this line if you don't need a FASTA file
  • pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
  • pipeline_todos - TODO string in README.md: TODO nf-core:
  • 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 README.md: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
  • pipeline_todos - TODO string in README.md: update the following command to include all required parameters for a minimal example
  • 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 README.md: Add bibliography of tools and data used in your pipeline
  • 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!
  • 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 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.
  • pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
  • 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 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_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
  • nfcore_yml - nf-core version not set in .nf-core.yml

❔ Tests ignored:

  • files_exist - File is ignored: CODE_OF_CONDUCT.md
  • files_exist - File is ignored: assets/nf-core-neoantigenpipeline_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-neoantigenpipeline_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-neoantigenpipeline_logo_dark.png
  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • files_unchanged - File ignored due to lint config: CODE_OF_CONDUCT.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
  • files_unchanged - File ignored due to lint config: assets/nf-core-neoantigenpipeline_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-neoantigenpipeline_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-neoantigenpipeline_logo_dark.png
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/NeoAntigen-Pipeline/NeoAntigen-Pipeline/.github/workflows/awstest.yml

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-07-08 14:46:41

@nikhil
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nikhil commented Jul 29, 2024

Figured it out! It was an inconsistency issue with capitalization between the call and the github name of the pipeline

@nikhil nikhil closed this Jul 29, 2024
@nikhil nikhil deleted the hotfix/fix_pipeline_download_test branch July 29, 2024 19:06
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