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Develop merge for 2.2.1 release #345

Merged
merged 19 commits into from
Oct 1, 2024
Merged

Develop merge for 2.2.1 release #345

merged 19 commits into from
Oct 1, 2024

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victor5lm
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PR checklist

  • Merge develop branch into main, preparing for release of version 2.2.1
  • 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 19 commits September 12, 2024 12:51
@github-actions @saramonzon
@Shettland @victor5lm
Merge changes from main into hotfix (#195) (#337)
7839afa 
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]>
@Daniel-VM
fixed path database and update emmtyper params
21eac2f
@Daniel-VM
update changelog #339
34ac552
@OPSergio
update sarek version in exomeeb (#341)
3a5b571 
* update sarek version in exomeeb

* Updated sarek version (v3.4.4) in ExomeEB-ExomeTrio-WGSTrio templates

* Current version Nextflow
@svarona
Created code to generate amended consensus without ambiguities but ma…
84809b1 
…sked
@svarona
Updated changelog
bd85c05
@svarona
Fixd changelog
b584e75
@svarona
Created postprocessing script for amended files
bc1a72f
@svarona
included postprocessing script in lablog
1b59d9a
@svarona
Shortened code to look better
ac6f23e
@victor5lm
Updated the 03-annotation/lablogs in exomeeb, exometrio and wgstrio s…
89469fd 
…ervices to have all the necessary -bind routes
@victor5lm
Updated bioinfo_doc.py to allow more options when creating the delive…
14bd968 
…ry email
@victor5lm
Updated excel_generator.py to be more informative
db6aa19
@victor5lm
Updated sftp_user.json
7038b86
@victor5lm
Updated 03-MTBSeq/lablog to handle the first sample name appropriately
99edee6
@victor5lm
Fixed linting mistakes
baa1925
@victor5lm
Updated CHANGELOG.md
1ce7956
@victor5lm
Updated setup.py
a104991
@victor5lm
Updated __main__.py
96a7db8
@victor5lm victor5lm marked this pull request as ready for review October 1, 2024 11:13
svarona
svarona approved these changes Oct 1, 2024
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@svarona svarona left a comment

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LGTM!

@victor5lm victor5lm merged commit 3c20883 into main Oct 1, 2024
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@svarona svarona svarona approved these changes

@saramonzon saramonzon saramonzon approved these changes

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5 participants
@victor5lm @saramonzon @svarona @Daniel-VM @OPSergio