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antismash to gff conversion #2

Merged
merged 6 commits into from
Dec 8, 2023
Merged

antismash to gff conversion #2

merged 6 commits into from
Dec 8, 2023

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mberacochea
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@mberacochea mberacochea requested a review from tgurbich December 7, 2023 16:43
@mberacochea mberacochea self-assigned this Dec 7, 2023
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github-actions bot commented Dec 7, 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 7, 2023 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 9d4bde2

+| ✅ 119 tests passed       |+
#| ❔  25 tests were ignored |#
!| ❗  12 tests had warnings |!
-| ❌   4 tests failed       |-

❌ Test failures:

  • files_exist - File must be removed: pipeline_template.yml
  • files_unchanged - .github/workflows/linting.yml does not match the template
  • files_unchanged - lib/NfcoreTemplate.groovy does not match the template
  • schema_params - Default value for param antismash_db invalid: Not in pipeline parameters. Check nextflow.config.

❗ Test warnings:

  • 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
  • schema_params - Schema param antismash_db not found from nextflow config
  • 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

❔ 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 09:14:54

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

@tgurbich tgurbich merged commit 18549fe into extend-annotations Dec 8, 2023
0 of 6 checks passed
@tgurbich tgurbich deleted the feature/antismash-gff branch December 8, 2023 10:07
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@tgurbich tgurbich tgurbich approved these changes

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@mberacochea mberacochea

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@mberacochea @tgurbich