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Feature/gff post processing split cds #3

Merged
merged 10 commits into from
Dec 8, 2023
Merged

Feature/gff post processing split cds #3

merged 10 commits into from
Dec 8, 2023

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mberacochea
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@mberacochea mberacochea requested a review from tgurbich December 8, 2023 11:04
@mberacochea mberacochea self-assigned this Dec 8, 2023
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github-actions bot commented Dec 8, 2023

Python linting (black) is failing

To keep the code consistent with lots of contributors, we run automated code consistency checks.
To fix this CI test, please run:

  • Install black: pip install black
  • Fix formatting errors in your pipeline: black .

Once you push these changes the test should pass, and you can hide this comment 👍

We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!

Thanks again for your contribution!

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github-actions bot commented Dec 8, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit bd873c2

+| ✅ 123 tests passed       |+
#| ❔  25 tests were ignored |#
!| ❗  12 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • schema_description - No description provided in schema for parameter: interproscan_db
  • schema_description - No description provided in schema for parameter: eggnong_diamond_db
  • schema_description - No description provided in schema for parameter: eggnog_db
  • schema_description - No description provided in schema for parameter: eggnong_data_dir
  • schema_description - No description provided in schema for parameter: rfam_rrna_models
  • schema_description - No description provided in schema for parameter: rfam_ncrna_models
  • schema_description - No description provided in schema for parameter: amrfinder_plus_db
  • schema_description - No description provided in schema for parameter: defense_finder_db
  • schema_description - No description provided in schema for parameter: antismash_db
  • schema_description - No description provided in schema for parameter: dbcan_db

❔ Tests ignored:

  • files_exist - File is ignored: CODE_OF_CONDUCT.md
  • files_exist - File is ignored: assets/nf-core-mettannotator_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-mettannotator_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-mettannotator_logo_dark.png
  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
  • files_exist - File is ignored: conf/test_full.config
  • files_exist - File is ignored: docs/output.md
  • files_exist - File is ignored: docs/README.md
  • files_exist - File is ignored: docs/README.md
  • files_exist - File is ignored: docs/usage.md
  • files_exist - File is ignored: conf/igenomes.config
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: ci.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: LICENSE or LICENSE.md or LICENCE or LICENCE.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-mettannotator_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-mettannotator_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-mettannotator_logo_dark.png
  • files_unchanged - File does not exist: docs/README.md
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/mettannotator/mettannotator/.github/workflows/awstest.yml

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-12-08 14:11:52

tgurbich
tgurbich approved these changes Dec 8, 2023
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Thank you!

@tgurbich tgurbich merged commit abd9e22 into extend-annotations Dec 8, 2023
1 of 6 checks passed
@tgurbich tgurbich deleted the feature/gff_post_processing_split_cds branch December 8, 2023 14:19
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@tgurbich tgurbich tgurbich approved these changes

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@mberacochea @tgurbich