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Release 2.1.0 from develop. #239

Merged
merged 40 commits into from
Apr 19, 2024
Merged

Release 2.1.0 from develop. #239

merged 40 commits into from
Apr 19, 2024

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Shettland
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PR checklist

  • This new release changes previous version 2.0.0 to 2.1.0
  • 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

Shettland and others added 30 commits March 5, 2024 14:28
@Shettland
Bumped new version and included mail_password into yaml for bioinfo-doc
16554b9
@Shettland
Included blast template
28030e2
@Shettland
Included default CC and option to use text file for delivery notes
0a02b2a
@Shettland
Bioinfo-doc updates; linting
d173457
@Shettland
Updated CHANGELOG.md
be88b6b
@Shettland
Updated CHANGELOG.md. v2
7785353
@Shettland
Updated CHANGELOG.md. v3
e540731
@Shettland @saramonzon
Small fix in autoclean_sftp, dflt missing
5302f61
@Shettland @saramonzon
Small fix to correctly attach multiple CCs
692fea9
@Shettland @saramonzon
Included new user in sftp_user.json
5161295
@Shettland @saramonzon
excel_generator.py reverted, argument -l included
2a742f9
@Shettland @saramonzon
Adapted viralrecon_results lablog to new excel_generator, also commen…
7c63796 
…ted a solution for complex services
@Shettland @saramonzon
Updated changelog
6d879d2
@Shettland @saramonzon
excel_generator.py reverted, -l included. Linting
c746d4f
@Daniel-VM @saramonzon
updated regex
313d117
@Daniel-VM @saramonzon
added missing url
dfe3e6a
@Daniel-VM @saramonzon
update change log
308c593
@Shettland @saramonzon
Removed empty strings from folders to clean as they were leading to t…
f7cbfc3 
…he deletion of everything
@Shettland @saramonzon
Fixed a missing sed in _03_post_processing step
0eff368
@Shettland @saramonzon
Included line to create a summary of flu types from irma_stats.txt
e955a25
@Shettland @saramonzon
Fixed missing strings in services.json, updated CHANGELOG
588f1d1
@Shettland @saramonzon
Updated IRMA location and reduced threads to 16
269cea2
@Shettland @saramonzon
Updated IRMA location and reduced threads to 16. Updated CHANGELOG
aa4e1ec
@Shettland @saramonzon
Updated IRMA version. Updated CHANGELOG
640fe87
@Shettland @saramonzon
IRMA: Create C-B dirs only if those flu types are present
db77078
@Shettland @saramonzon
Fixed singularity mount problem in nextflow v23.10.0
b4cc501
@Shettland @saramonzon
Commented auxiliar code
01c6d81
@Shettland @saramonzon
Fixed singularity mount problem in nextflow v23.10.0 in viralrecon te…
b93da68 
…mplate. Updated CHANGELOG
@svarona @saramonzon
Fixed paths to trimmed reads
8641e7a
@svarona @saramonzon
added ampersand to srun
e0a87be
@saramonzon saramonzon merged commit 0fdd4a1 into main Apr 19, 2024
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@Daniel-VM Daniel-VM Daniel-VM approved these changes

@saramonzon saramonzon saramonzon approved these changes

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4 participants
@Shettland @saramonzon @Daniel-VM @svarona