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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.X.Xdev] - 2024-0X-XX : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.X.X

Credits

Code contributions to the new version:

Template fixes and updates

Modules

Added enhancements

  • Included a new github action to automatically publish releases to pypi #351

Fixes

Changed

Removed

Requirements

[2.X.Xhot] - 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

[2.2.1] - 2024-10-01 : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.2.1

Credits

Code contributions to the new version:

Template fixes and updates

  • Fixed path to blast database and update Emmtyper params #339
  • Updated sarek version (v3.4.4) in ExomeEB-ExomeTrio-WGSTrio templates [#341] (BU-ISCIII#341)
  • Fixed IRMAs config for amended consensus #325.
  • Improved excel_generator.py and bioinfo_doc.py email creation function, and updated sftp_user.json, setup.py, main.py and some lablogs #344.

Modules

Added enhancements

Fixes

Changed

Removed

Requirements

[2.2.0] - 2024-09-12 : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.2.0

Credits

Code contributions to the new version:

Template fixes and updates

  • Updated documentation and results markdown for viralrecon, pikavirus and MAG #247
  • Added documentation and results markdown for RNAseq #248
  • Added documentation both output and results for plasmidID#258
  • Added markdown of assembly analysis procedure #244
  • Added output and results markdowns for ExomeEB, ExomeTrio and WGStrio #249
  • Added markdown of assembly results folder #250
  • Updated lablog results filenames where necessary (IRMA, seekndestroy, viralrecon and genomeev) #253
  • Added output and results markdowns for cgMLST/wgMLST #255
  • Added markdown for IRMA #256
  • Included RESULTS/lablog for exomeeb, exometrio and wgstrio templates and updated files to clean #260
  • Changed scratch copy queue to middle_obx
  • Included missing folders in wgstrio template
  • Changed exomiser-html-description to png format and fixed location of irma-sarek markdowns #261
  • Updated configuration.json so that either idx or obx is used in case one of these queues is full #263
  • Updated lablog_viralrecon script for the automation of the setup of viralrecon services. #264
  • Included MULTIQC v.1.19 in viralrecon.config to fix error with string and numeric samples #267
  • Updated MTBSeq template to fit bacass pipeline. #268
  • IRMA template modified in order to avoid average overload.
  • Added "01" to results folder creation in assembly template.
  • Some prompt answers limited to 1 character in lablog_viralrecon.
  • Created lablog_mtbseq_results. #270
  • PR #271. Closes #235, #228 and #196
  • Included annotated tab description in exome-trios markdowns #273
  • Installed all necessary singularity images and modified all templates so that, instead of using conda environments or loaded modules, the corresponding singularity images are used #272
  • Updated sarek version in exomeeb, exometrio and wgstrio templates #277
  • Extension file of all_samples_virus_table_filtered (from csv to tsv) in lablog_viralrecon_results changed #278
  • Fixed singularity-images path when updating pangolin database in lablog_viralrecon. Added line break after prompted input. #282
  • Updated characterization and snippy templates to fit bacass pipeline. Corrected path in 05-iqtree in snippy template. #283
  • Included multiqc_report.html in RESULTS folder in every service, where necessary [#265] (BU-ISCIII#265)
  • Added MAG tempalte and removed MAG from other templates #288
  • Added amrfinderplus to characterization template. [#289] (BU-ISCIII#289)
  • Updated all files so that paths referring to /pipelines/ are updated according to the new structure #287
  • Updated assembly, ariba, snippy, amrfinderplus and iqtree templates, removed genomeev and mtbseq_assembly templates and updated services.json #295
  • Changed viralrecon's lablog so that references are available within refgenie #296
  • Updated services.json, mtbseq's lablog, viralrecon's lablog and assembly's config file #299
  • Added lablog to automate gene characterization with emmtyper, including unzipping assemblies. #300
  • Fixed 99-stats (MAG) template. #301
  • Created a python script to process IRMA's results and create a standard vcf file against reference. #304
  • Fixed IRMA's lablog so that the sequences of the samples are not displayed several times neither in the .txt files of each influenza type nor in all_samples_completo.txt #305
  • Modified bioinfo_doc.py so that new lines in the delivery message are applied in the email #307
  • Added several improvements in lablog_viralrecon (created log files, modified check_references function behaviour, enabled config files regeneration) #306
  • Fixed bug when lablog_viralrecon tries to download references that don't belong to any family. #310
  • Added mvmoneo to SFTP users. #317
  • Added scripts for time series RNAseq and updated differential expression code for differentially expressed transcripts #316.
  • Added bbaladron to SFTP users #316.
  • Added new template for comprehensive taxonomy profiling using the nf-core/taxprofiler pipeline #320.
  • Added full execution support for the MAG template #321.
  • Added labels to services.json and updated bioinfo_doc.py and jinja_template_delivery.j2 so that software versions data is displayed in the delivery pdf #330.
  • Updated several templates (singularity images, outdated paths, improvements, etc) #331
  • Added permissions fixing after running scratch_copy, as well as a new fix-permissions module in the tools #332.
  • Updated MAG lablogs and utils.py #334.
  • Updated some files (setup.py, main.py, README, etc) for the 2.2.0 release #335.

Modules

Added enhancements

  • PR #274: added --dev option, configuration dev and test folder structure.
  • PR #276: wkhtmlpdf does not need absolute path to executable. Added better error handling when executable does not exists.
  • PR #288 Allowed to handle more than one service at a time, related to issue #217

Fixes

  • Fixed archive module. Updated correct header for scout tsv #258.
  • Fixed clean module. Corrected purge_files function. Renaming stage moved from clean to rename_nocopy option. Updated services.json file with correct paths for some services. #280
  • Fixed autoclean-sftp function. #281
  • Fixed bioinfo_doc.py. Modified it so that this module creates a .pdf file including new-line characters, without merging lines into one single line #259.
  • PR #288 Fixed updating service's state to in_progress multiple times, related with issue #285
  • Review and update of services.json for files and folders cleaning #318.

Changed

  • Forcing python lint to success if no .py files are in PR #279

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: