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Add in IRIDA Next requirements #6

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Add in IRIDA Next requirements #6

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DarianHole
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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 (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • 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).

@github-actions GitHub Actions
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github-actions bot commented Feb 7, 2025

nf-core pipelines lint overall result: Failed ❌

Posted for pipeline commit 58781e2

+| ✅  76 tests passed       |+
#| ❔  32 tests were ignored |#
!| ❗  17 tests had warnings |!
-| ❌   3 tests failed       |-

❌ Test failures:

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required
  • 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
  • schema_lint - Schema $id should be https://raw.githubusercontent.com/phac-nml/viralassembly/master/nextflow_schema.json
    Found https://raw.githubusercontent.com/phac-nml/viralassembly/main/nextflow_schema.json
  • schema_lint - Parameter input is not defined in the correct subschema (input_output_options)
  • system_exit - System.exit in format_input.nf: System.exit(1) [line 51]
  • system_exit - System.exit in NfcoreSchema.groovy: System.exit(1) [line 180]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 83]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 90]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 97]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 100]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 105]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 111]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 114]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 118]
  • schema_description - No description provided in schema for parameter: show_hidden_params

❔ Tests ignored:

  • files_exist - File is ignored: CODE_OF_CONDUCT.md
  • 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
  • files_exist - File is ignored: assets/multiqc_config.yml
  • files_exist - File is ignored: assets/nf-core-viralassembly_logo_light.png
  • files_exist - File is ignored: conf/igenomes.config
  • files_exist - File is ignored: conf/igenomes_ignored.config
  • files_exist - File is ignored: docs/images/nf-core-viralassembly_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-viralassembly_logo_dark.png
  • files_exist - File is ignored: lib/NfcoreTemplate.groovy
  • files_exist - File is ignored: lib/Utils.groovy
  • files_exist - File is ignored: lib/WorkflowMain.groovy
  • files_exist - File is ignored: lib/nfcore_external_java_deps.jar
  • nextflow_config - nextflow_config
  • files_unchanged - File does not exist: .gitattributes
  • files_unchanged - File does not exist: CODE_OF_CONDUCT.md
  • files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.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: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/linting_comment.yml
  • files_unchanged - File does not exist: assets/nf-core-viralassembly_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-viralassembly_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-viralassembly_logo_dark.png
  • files_unchanged - File ignored due to lint config: docs/README.md
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/viralassembly/viralassembly/.github/workflows/awstest.yml
  • actions_awsfulltest - actions_awsfulltest
  • pipeline_name_conventions - pipeline_name_conventions
  • multiqc_config - multiqc_config

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2025-02-07 17:33:15

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@DarianHole