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New Full Test Config #11

Merged
merged 10 commits into from
May 10, 2024
Merged

New Full Test Config #11

merged 10 commits into from
May 10, 2024

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BWMac
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@BWMac BWMac commented May 8, 2024 •
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This PR updates the test_full profile configuration to include all supported file types for DCQC. This was used for testing in this py-dcqc PR. All files included in the test_full manifest are hosted here on Synapse and the DPE team has Administrator access to the location.

While working through the PR requirements, the nf-core lint tool made updates to some of its configuration as well.

I also added the DPE team as CODEOWNERS.

PR checklist

  • This comment contains a description of changes (with reason).
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).

@swarmia Swarmia
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swarmia bot commented May 8, 2024

✅  Linked to Story ORCA-256 · [SPIKE] How do we want to return all the different failure reasons in DCQC
➡️  Part of Epic ORCA-250 · DCQC Failure Reasons
➡️  Part of IBCDPE-502 · DCQC

@BWMac BWMac changed the title Bwmac/orca 256/failure prototyping New Test Suite May 8, 2024
@BWMac BWMac changed the title New Test Suite New Full Test Config May 8, 2024
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github-actions bot commented May 8, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 43f73d2

+| ✅ 127 tests passed       |+
#| ❔  12 tests were ignored |#
!| ❗  20 tests had warnings |!
-| ❌  15 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
  • nextflow_config - Config variable not found: params.validationShowHiddenParams
  • nextflow_config - Config variable not found: params.validationSchemaIgnoreParams
  • nextflow_config - Config default value incorrect: params.tracedir is set as ${params.outdir}/pipeline_info in nextflow_schema.json but is results/pipeline_info in nextflow.config.
  • files_unchanged - .github/CONTRIBUTING.md does not match the template
  • files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml 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
  • schema_params - Param schema_ignore_params from nextflow config not found in nextflow_schema.json
  • multiqc_config - assets/multiqc_config.yml not found.

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • nextflow_config - Config manifest.version should end in dev: 0.1
  • 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: Write a 1-2 sentence summary of what data the pipeline is for and what it does
  • pipeline_todos - TODO string in README.md: Add full-sized test dataset and amend the paragraph below if applicable
  • 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: Update the example "typical command" below used to run the pipeline
  • 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 output.md: Write this documentation describing your workflow's output
  • 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 WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
  • pipeline_name_conventions - Naming does not adhere to nf-core conventions: Contains non alphanumeric characters
  • schema_lint - Schema $id should be https://raw.githubusercontent.com/sage-bionetworks-workflows/nf-dcqc/master/nextflow_schema.json
    Found https://raw.githubusercontent.com/sage/dcqc/master/nextflow_schema.json
  • system_exit - System.exit in WorkflowDcqc.groovy: // System.exit(1) [line 18]
  • system_exit - System.exit in WorkflowDcqc.groovy: System.exit(1) [line 74]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 85]
  • 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-dcqc_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-dcqc_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-dcqc_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 does not exist: CODE_OF_CONDUCT.md
  • files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/nf-dcqc/nf-dcqc/.github/workflows/awstest.yml

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-05-09 17:30:18

@BWMac BWMac mentioned this pull request May 8, 2024
Merged
@BWMac BWMac marked this pull request as ready for review May 9, 2024 17:30
@BWMac BWMac requested a review from a team May 9, 2024 17:30
BryanFauble
BryanFauble approved these changes May 9, 2024
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LGTM!

@BWMac BWMac merged commit 807baab into main May 10, 2024
5 of 7 checks passed
@BWMac BWMac deleted the bwmac/orca-256/failure_prototyping branch May 10, 2024 15:24
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