Releases: BU-ISCIII/buisciii-tools
Releases · BU-ISCIII/buisciii-tools
BUISCIII/buisciii-tools v2.2.2
Credits
Code contributions to the new version:
Template fixes and updates
- Updated the fix-permissions module in main.py #356.
- Fixed the singularity cache directory in taxprofiler.config #356.
- Updated sftp_user.json #356.
- Fixed viralrecon's lablog and the remove_columns_mapping_table.sh auxiliary script #356.
- Updated the singularity image in the mtbseq templates #356.
- Fixed a bug in bioinfo_doc.py #356.
- Updated new_service.py to check FASTQ integrity via md5sum #356.
Modules
Added enhancements
- Included a new github action to automatically publish releases to pypi #351
Fixes
Changed
Removed
BUISCIII/buisciii-tools v2.2.1
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] (#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
BUISCIII/buisciii-tools v2.2.0
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] (#265)
- Added MAG tempalte and removed MAG from other templates #288
- Added amrfinderplus to characterization template. [#289] (#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
--devoption, 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
BUISCIII/buisciii-tools v2.1.0
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
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:
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:
Template fixes and updates
- Added new line in
buisciii_tools/bu_isciii/templates/viralrecon/ANALYSIS/lablog_viralrecon, in order to automatically renameANALYSIS0X_MAGdirectory with the current date. - Introduced handling of flu-C in
buisciii_tools/bu_isciii/templates/IRMA/ANALYSIS/ANALYSIS01_FLU_IRMA/04-irma/lablogandcreate_irma_stats.sh - Small changes to
buisciii_tools/bu_isciii/templates/viralrecon/RESULTS/viralrecon_resultsfor 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_ONLYto exometrio'sexomiser_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