BUISCIII/buisciii-tools v2.1.0

Credits

Code contributions to the new version:

• Sarai Varona
• Pablo Mata
• Daniel Valle

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

BUISCIII/buisciii-tools v2.0.0

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

Credits

Code contributions to the release:

• Sara Monzón
• Sarai Varona
• Pablo Mata
• Guillermo Gorines

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

BU-ISCIII/buisciii-tools v1.0.1

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

Credits

Code contributions to the hotfix:

• Pablo Mata
• Jaime Ozaez
• Sara Monzón
• Sarai Varona
• Daniel Valle

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

BU-ISCIII/buisciii-tools v1.0.0

[1.0.0] - 2024-01-08

Initial release of BU-ISCIII/buisciii-tools.

BU-ISCIII provides a serie or services in its portfolio for supporting bioinformatics analysis to the labs in the Institute of Health Carlos III. bu-isciii tools is a set of helper tools for management of these bioinformatics analysis together with the LIMS (iSkyLIMS)

If you want to install the latest code in the repository:

conda create -n buisciii-tools pip
pip install --force-reinstall --upgrade git+https://github.com/bu-isciii/buisciii-tools.git@main