Buisciii-tools

Credits

- [Alejandro Bernabeu](https://github.com/Aberdur)
- [Sara Monzón](https://github.com/saramonzon)
- [Victor Lopez](https://github.com/victor5lm)
- [Jaime Ozáez](https://github.com/jaimeozaezm)

Template fixes and updates

- User added to sftp_user.json [404] (https://github.com/BU-ISCIII/buisciii-tools/pull/404).
- Fix archived path [405](https://github.com/BU-ISCIII/buisciii-tools/pull/405)
- Updated characterization/03-amrfinderplus lablog with summary generator [406](https://github.com/BU-ISCIII/buisciii-tools/pull/406)
- Updated lablog_viralrecon to replace conda by micromamba, and updated the output message from remove_columns_mapping_table.sh [409](https://github.com/BU-ISCIII/buisciii-tools/pull/409)
- Created lablog_bam2fq in viralrecon's template [409](https://github.com/BU-ISCIII/buisciii-tools/pull/409)
- Replaced bu_isciii by buisciii where necessary, and bu_isciii by buisciii-tools in __init__.py [411](https://github.com/BU-ISCIII/buisciii-tools/pull/411)
- Added versions for all dependencies in requirements.txt [411](https://github.com/BU-ISCIII/buisciii-tools/pull/411)
- Implemented a non-interactive mode for running lablog_viralrecon [410](https://github.com/BU-ISCIII/buisciii-tools/pull/410)
- Fixes in several service templates [414](https://github.com/BU-ISCIII/buisciii-tools/pull/414)
- Modified path for temporal files in irma_config.sh [414](https://github.com/BU-ISCIII/buisciii-tools/pull/421)
- Modified field (cut) where extracted flu type information in lablog_irma_results [414](https://github.com/BU-ISCIII/buisciii-tools/pull/421)
- Implemented QC scripts into viralrecon template [422](https://github.com/BU-ISCIII/buisciii-tools/pull/422)
- Fixed minor mistakes in chewBBACA's template [425](https://github.com/BU-ISCIII/buisciii-tools/pull/425).
- Fixed some issues in outbreak services [428](https://github.com/BU-ISCIII/buisciii-tools/pull/428)
- Add micromamba activation comment to viralrecon template lablog and add total_N_count to sgene_metrics script[432](https://github.com/BU-ISCIII/buisciii-tools/pull/432)
- Added last_folder field to plasmidid_assembly service in services.json [434](https://github.com/BU-ISCIII/buisciii-tools/pull/434)
- Fixed bioinfo-doc crashing after resuming [435](https://github.com/BU-ISCIII/buisciii-tools/pull/435)
- Fixed create_summary_report.sh to latest /data/ucct/bi/ layout [436](https://github.com/BU-ISCIII/buisciii-tools/pull/436)
- Changed taxprofiler lablog to skip kaiju, centrifuge and metaphlan [439](https://github.com/BU-ISCIII/buisciii-tools/pull/439)

Modules

Added enhancements

Fixes

- Fixed drylab_api.py to show a more descriptive message when the resolution ID does not exist [437](https://github.com/BU-ISCIII/buisciii-tools/pull/437).

Changed

Removed

Requirements

Credits

- [Victor Lopez](https://github.com/victor5lm)

Template fixes and updates

- Changed mag.md by taxprofiler.md in assets/reports [396](https://github.com/BU-ISCIII/buisciii-tools/pull/396).
- Modified irma_output.md to include only taxprofiler [396](https://github.com/BU-ISCIII/buisciii-tools/pull/396).
- Updated services.json with taxprofiler [396](https://github.com/BU-ISCIII/buisciii-tools/pull/396).
- Created a lablog file for chewbbaca/REFERENCES [396](https://github.com/BU-ISCIII/buisciii-tools/pull/396).
- Updated lablog_irma and renamed ANALYSIS01 folders [396](https://github.com/BU-ISCIII/buisciii-tools/pull/396).
- Updated IRMA template and its files to include RSV [396](https://github.com/BU-ISCIII/buisciii-tools/pull/396).
- Updated chewbbaca results' lablog to include cgMLST_MSA.fasta [396](https://github.com/BU-ISCIII/buisciii-tools/pull/396).
- Updated exometrio and wgstrio results lablogs not to include exomiser's html [396](https://github.com/BU-ISCIII/buisciii-tools/pull/396).
- Created plasmidid's results lablog [396](https://github.com/BU-ISCIII/buisciii-tools/pull/396).
- Updated mtbseq's lablog to remove unnecessary single quotes [396](https://github.com/BU-ISCIII/buisciii-tools/pull/396).
- Fixed snippy's lablog to be better explained and updated its results' lablog [396](https://github.com/BU-ISCIII/buisciii-tools/pull/396).
- Updated version in pyproject.toml and __main__.py [396](https://github.com/BU-ISCIII/buisciii-tools/pull/396).
Modules

Added enhancements

Fixes

Changed

- Replaced setup.py by pyproject.toml [396](https://github.com/BU-ISCIII/buisciii-tools/pull/396).

Removed

- Removed MAG template and replaced it with taxprofiler [396](https://github.com/BU-ISCIII/buisciii-tools/pull/396).

Requirements

Credits

- [Victor Lopez](https://github.com/victor5lm)

Template fixes and updates

- Replaced /data/bi/ by /data/ucct/bi where necessary [385](https://github.com/BU-ISCIII/buisciii-tools/pull/385).
- Removed middle_obx from config files [385](https://github.com/BU-ISCIII/buisciii-tools/pull/385).

Modules

Added enhancements

Fixes

Changed

Removed

Requirements

Credits

Code contributions to the new version:

- [Victor Lopez](https://github.com/victor5lm)
- [Sarai Varona](https://github.com/svarona)

Template fixes and updates

- Updated sftp_user.json, added the locus-tag option for the PROKKA process in the bacass config file and changed new_service.py so that integrity is checked only for the samples of interest [363](https://github.com/BU-ISCIII/buisciii-tools/pull/363).
- Replaced /data/bi/ by /data/ucct/bi/ [380](https://github.com/BU-ISCIII/buisciii-tools/pull/380).
- Updated bacass version in all pertinent files [380](https://github.com/BU-ISCIII/buisciii-tools/pull/380).
- Updated read length variable definition when creating the mapping_illumina.tab file [380](https://github.com/BU-ISCIII/buisciii-tools/pull/380).
- Updated create_irma_stats.sh to include %mapped_reads [380](https://github.com/BU-ISCIII/buisciii-tools/pull/380).
- Changed "Buenas" by "Estimado/a" in email.j2 [380](https://github.com/BU-ISCIII/buisciii-tools/pull/380).

Modules

Added enhancements

Fixes

- Fixed new-service to correctly handle when there are no samples in service [372](https://github.com/BU-ISCIII/buisciii-tools/pull/372). Fixes issue [#371](https://github.com/BU-ISCIII/buisciii-tools/issues/371)

Changed

Removed

Requirements

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

Credits

Template fixes and updates

Modules

Added enhancements

Fixes

Changed

Removed

Requirements

Credits

Code contributions to the new version:

- [Pablo Mata](https://github.com/Shettland)
- [Victor Lopez](https://github.com/victor5lm)

Template fixes and updates

- Updated the fix-permissions module in __main__.py [356](https://github.com/BU-ISCIII/buisciii-tools/pull/356).
- Fixed the singularity cache directory in taxprofiler.config [356](https://github.com/BU-ISCIII/buisciii-tools/pull/356).
- Updated sftp_user.json [356](https://github.com/BU-ISCIII/buisciii-tools/pull/356).
- Fixed viralrecon's lablog and the remove_columns_mapping_table.sh auxiliary script [356](https://github.com/BU-ISCIII/buisciii-tools/pull/356).
- Updated the singularity image in the mtbseq templates [356](https://github.com/BU-ISCIII/buisciii-tools/pull/356).
- Fixed a bug in bioinfo_doc.py [356](https://github.com/BU-ISCIII/buisciii-tools/pull/356).
- Updated new_service.py to check FASTQ integrity via md5sum [356](https://github.com/BU-ISCIII/buisciii-tools/pull/356).

Modules

Added enhancements

- Included a new github action to automatically publish releases to pypi [351](https://github.com/BU-ISCIII/buisciii-tools/pull/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

Credits

Code contributions to the new version:

- [Daniel Valle](https://github.com/Daniel-VM)
- [Sarai Varona](https://github.com/svarona)
- [Victor Lopez](https://github.com/victor5lm)
- [Sergio Olmos](https://github.com/OPSergio)

Template fixes and updates

- Fixed path to blast database and update Emmtyper params [339](https://github.com/BU-ISCIII/buisciii-tools/pull/339)
- Updated sarek version (v3.4.4) in ExomeEB-ExomeTrio-WGSTrio templates [341] (https://github.com/BU-ISCIII/buisciii-tools/pull/341)
- Fixed IRMAs config for amended consensus [325](https://github.com/BU-ISCIII/buisciii-tools/pull/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](https://github.com/BU-ISCIII/buisciii-tools/pull/344).

Modules

Added enhancements

Fixes

Changed

Removed

Requirements