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bu-isciii tools Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[2.2.Xdev] - 2024-0X-XX : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.2.X

Credits

Code contributions to the new version:

Template fixes and updates

Modules

Added enhancements

Fixes

Changed

Removed

Requirements

[2.X.1hot] - 2024-0X-0X : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.X.1

Credits

Code contributions to the hotfix:

Template fixes and updates

Modules

Added enhancements

Fixes

Changed

Removed

Requirements

[2.1.0] - 2024-04-19 : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.1.0

Credits

Code contributions to the new version:

Template fixes and updates

  • Added blast_nt template to services.json #208
  • Included new user to sftp_user.json
  • Included a missing sed inside IRMA's 04-irma/lablog #213
  • Changed singularity mount options in Viralrecon template to fix errors with Nextflow v23.10.0
  • excel_generator.py reverted to last state, now lineage tables are merged when argument -l is given
  • Adapted viralrecon_results lablog to new excel_generator.py argument
  • IRMA/RESULTS now creates a summary of the different types of flu found in irma_stats.txt
  • Updated IRMA to v1.1.4 date 02-2024 and reduced threads to 16
  • IRMA 04-irma/lablog now creates B and C dirs only if those flu-types are present
  • Fixed characterization template #220
  • Created Chewbbaca template #230

Modules

Added enhancements

  • #207 - Bioinfo-doc updates: email password can be given in buisciii_config.yml and delivery notes in a text file

Fixes

  • Added missing url for service assembly_annotation in module list
  • Autoclean-sftp refined folder name parsing with regex label adjustment
  • Autoclean_sftp does not crash anymore. New argument from 'utils.prompt_yn_question()' in v2.0.0 was missing: 'dflt'
  • Bioinfo-doc now sends email correctly to multiple CCs

Changed

Removed

  • Removed empty strings from services.json

Requirements

[2.0.0] - 2024-03-01 : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.0.0

Credits

Code contributions to the release:

Template fixes and updates

  • Added templates:
    • freebayes

Modules

Added enhancements

  • Added credential parameters: --api_user, --api_password and --cred_file
  • Make modules to create folder's paths automatically from DB
  • Added finish module
  • Added json files: sftp_user.json
  • Added delivery jinja templates
  • Added IRMA template to services.json
  • Scratch module now executes rsync using SLURM's srun

Fixes

Changed

  • Fixed API requests to fit in the new database format
  • Updated README

Removed

Requirements

  • Added PyYAML

[1.0.1] - 2024-02-01 : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/1.0.1

Credits

Code contributions to the hotfix:

Template fixes and updates

  • Added new line in buisciii_tools/bu_isciii/templates/viralrecon/ANALYSIS/lablog_viralrecon, in order to automatically rename ANALYSIS0X_MAG directory with the current date.
  • Introduced handling of flu-C in buisciii_tools/bu_isciii/templates/IRMA/ANALYSIS/ANALYSIS01_FLU_IRMA/04-irma/ lablog and create_irma_stats.sh
  • Small changes to buisciii_tools/bu_isciii/templates/viralrecon/RESULTS/viralrecon_results for blast and new excel_generator.py
  • Introduced better error handling in excel_generator.py. Now it can also be used for single files
  • Brought back PASS_ONLY to exometrio's exomiser_configfile.yml
  • #187 - Added new template for bacterial assembly. Allowing for short, long and hybrid assembly.
  • #190 - renamed some variables in create-summary_report from viralrecon template as their name was misleading and fixed a small typo in regex finding in excel_generator.py
  • #192 - Small changes in excel_generator.py to automatically merge pangolin/nextclade tables when more than 1 reference is found

Modules

Added enhancements

  • Added CHANGELOG
  • Added template for Pull Request
  • Added Contributing guidelines
  • Added github action to sync branches

Fixes

Changed

Removed

Requirements

[1.0.0] - 2024-01-08 : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/1.0.0

Credits

Code contributions to the inital release: