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Update input_assure.py for locidex:0.2.3 mlst.json report support #20

Merged
merged 4 commits into from
Aug 23, 2024
Merged

Update input_assure.py for locidex:0.2.3 mlst.json report support #20

merged 4 commits into from
Aug 23, 2024

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kylacochrane
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@kylacochrane kylacochrane commented Aug 23, 2024 •
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This PR:

  1. Upgrades the locidex/merge module to version 0.2.3.

  2. To maintain compatibility, the input_assure module and corresponding python script have been updated to handle the new mlst.json format. The test data has also been updated accordingly.

New mlst.json formatting:
image

  1. Container directives have been revised to meet phac-nml/pipeline standards, as outlined in the Module Software Requirements and Container Registries, by utilizing the extension setting process.ext.override_configured_container_registry.
  • 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>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • CHANGELOG.md is updated.

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github-actions bot commented Aug 23, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 1b9b1ed

+| ✅ 145 tests passed       |+
#| ❔  22 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 0.2.0
  • schema_lint - Schema $id should be https://raw.githubusercontent.com/phac-nml/gasnomenclature/master/nextflow_schema.json
    Found https://raw.githubusercontent.com/phac-nml/gasnomenclature/main/nextflow_schema.json

❔ Tests ignored:

  • files_exist - File is ignored: assets/nf-core-gasnomenclature_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-gasnomenclature_logo_dark.png
  • files_exist - File is ignored: docs/images/nf-core-gasnomenclature_logo_light.png
  • 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: 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 ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • files_unchanged - File does not exist: assets/nf-core-gasnomenclature_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-gasnomenclature_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-gasnomenclature_logo_dark.png
  • files_unchanged - File ignored due to lint config: docs/README.md
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/gasnomenclature/gasnomenclature/.github/workflows/awstest.yml
  • actions_awsfulltest - actions_awsfulltest
  • pipeline_name_conventions - pipeline_name_conventions

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-08-23 14:01:36

@kylacochrane kylacochrane marked this pull request as ready for review August 23, 2024 14:56
apetkau
apetkau approved these changes Aug 23, 2024
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This looks great. Thanks so much for all your work on this Kyla 😄

@kylacochrane kylacochrane merged commit fe9511c into dev Aug 23, 2024
4 checks passed
@kylacochrane kylacochrane deleted the update/input_assure branch September 11, 2024 15:15
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@apetkau apetkau apetkau approved these changes

@sgsutcliffe sgsutcliffe Awaiting requested review from sgsutcliffe

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@kylacochrane @apetkau