BUISCIII/buisciii-tools v2.2.6

Credits

• Alejandro Bernabeu
• Sara Monzón
• Victor Lopez
• Jaime Ozáez

Template fixes and updates

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

Modules

Added enhancements

Fixes

• Fixed drylab_api.py to show a more descriptive message when the resolution ID does not exist #437.

Changed

Removed