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Develop merge for 2.2.2 release #358

Merged
merged 18 commits into from
Oct 29, 2024
Merged

Develop merge for 2.2.2 release #358

merged 18 commits into from
Oct 29, 2024

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victor5lm
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PR checklist

  • Merge develop branch into main, preparing for release of version 2.2.2
  • Make sure your code lints (black and flake8).
  • If a new tamplate was added make sure:
    • Template's schema is added in templates/services.json.
    • Template's pipeline's documentation in assets/reports/md/template.md is added.
    • Results Documentation in assets/reports/results/template.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).
  • If you know a new user was added to the SFTP, make sure you added it to templates/sftp_user.json

github-actions bot and others added 18 commits October 1, 2024 13:36
@github-actions @saramonzon
@Shettland @victor5lm
Merge changes from main into hotfix (#195) (#346)
fdf6d29 
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Sara Monzón <[email protected]>
Co-authored-by: Pablo Mata <[email protected]>
Co-authored-by: Víctor López <[email protected]>
@Shettland
Included actions to publish release to pypi
e695d0e
@Shettland
Updated CHANGELOG
c34e98a
@Shettland
Updated new pip instructions
7e1b4af
@victor5lm
Updated the fix-permissions module in __main__.py
e53ee65
@victor5lm
Updated taxprofiler.config
a454e5a
@victor5lm
Updated sftp_user.json
dd1fa02
@victor5lm
Fixed viralrecon's lablog and remove_columns script
6cd5112
@victor5lm
Updated mtbseq templates
7c0522c
@victor5lm
Updated bioinfo_doc.py to handle the Unable to send e-mail error message
7db149e
@victor5lm
Updated new_service.py to check FASTQ integrity
ced57ba
@victor5lm
Updated CHANGELOG.md, setup.py and __main__.py
8a24621
@victor5lm
Fixed some linting mistakes in new_service.py
04615c7
@victor5lm
Ran black on new_service.py
cb6a877
@victor5lm
Removed an extra comma from sftp_user.json
7a529bf
@victor5lm
Removed conda env line from viralrecon's results lablog
34f9590
@victor5lm
Substituted /srv/fastq_repo by its variable name
b5317ad
@victor5lm
Ran black on new_service.py
4d4da2e
@victor5lm victor5lm marked this pull request as ready for review October 29, 2024 09:29
Shettland
Shettland approved these changes Oct 29, 2024
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@Shettland Shettland left a comment

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LGTM!

@victor5lm victor5lm merged commit 86556c4 into main Oct 29, 2024
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@Shettland Shettland Shettland approved these changes

@saramonzon saramonzon saramonzon approved these changes

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3 participants
@victor5lm @saramonzon @Shettland