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Merge changes on dev into public_dev ahead of preparation for release 2.0 #143

Merged
merged 18 commits into from
Oct 2, 2024
Merged

Merge changes on dev into public_dev ahead of preparation for release 2.0 #143

merged 18 commits into from
Oct 2, 2024

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BethYates
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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>).
  • 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).

tkchafin and others added 15 commits July 5, 2024 13:23
@tkchafin
conditional writing of assembly statistics fields
1271da7
@tkchafin
styling and linting
8100c39
@tkchafin
script now writes nan for value missing from ncbi datasets output
9937493
@tkchafin
linting
6d0763e
@tkchafin
bump version to 1.2.1
25ab1f7
@tkchafin @muffato
Update CITATION.cff
4e5ec7d 
Co-authored-by: Matthieu Muffato <[email protected]>
@tkchafin @muffato
Update bin/create_table.py
e12d883 
Co-authored-by: Matthieu Muffato <[email protected]>
@muffato
Merge pull request #127 from tkchafin/1.2.1
028ddae 
Patch 1.2.1: Fix issue where pipeline fails on missing fields from NCBI datasets JSON
@muffato
Missing release names
8c6aa38
@muffato
Swapped name and surname
aab6b75
@muffato
Update the author list
64d9c7c
@muffato
Obey use_work_dir_as_temp but don't run Busco in scratch mode for lar…
ecb1228 
…ge genomes as it takes too much space on /tmp
@muffato
Changed the date, the release will happen today
878921e
@muffato
Merge pull request #139 from sanger-tol/patch
2208ff8 
Switch back to `scratch=false` for large genomes
@BethYates
Merge branch 'dev' into merge_dev
be630e2
@github-actions GitHub Actions
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github-actions bot commented Oct 1, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit eb89d32

+| ✅ 131 tests passed       |+
#| ❔  21 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

❔ Tests ignored:

  • files_exist - File is ignored: assets/nf-core-genomenote_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-genomenote_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-genomenote_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
  • files_exist - File is ignored: conf/igenomes.config
  • 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 does not exist: .github/ISSUE_TEMPLATE/config.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File does not exist: assets/nf-core-genomenote_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-genomenote_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-genomenote_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • actions_ci - actions_ci
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/genomenote/genomenote/.github/workflows/awstest.yml
  • template_strings - template_strings

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2024-10-01 13:25:52

@github-actions GitHub Actions
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github-actions bot commented Oct 1, 2024

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!

@BethYates BethYates merged commit ef1c8dc into public_dev Oct 2, 2024
6 checks passed
@BethYates BethYates deleted the merge_dev branch October 2, 2024 09:15
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3 participants
@BethYates @muffato @tkchafin