BUISCIII/buisciii-tools v2.2.7

Credits

• Jaime Ozáez
• Alejandro Bernabeu
• Sergio Olmos
• Victor Lopez
• Sarai Varona

Template fixes and updates

• Fixed bug in 08_create_quality_control_summary.sh (viralrecon template) #447.
• Updated services.json file in order to properly delete folders and files when running clean module #451.
• Add assets for Updating Lineage-Defining Mutations from outbreak-info #452
• Fix get_percentage_LDM.py to Use Versioned CSV File#453.
• Moved lablog_bam2fq.sh to RAW/** to centralize BAM-to-FASTQ processing #455
• Updated _01_bam2fq.sh to correctly detect all BAM files in RAW/ #455
• Refactored _02_pgzip.sh to compress .fastq files and remove uncompressed versions #455
• Created _03_symlink.sh to manage symbolic links in ANALYSIS/00-reads/, preventing broken links #455
• Removed single quotes from sftp_copy in configuration.json #458
• Fixed and enhanced some issues for lablog_viralrecon #461
• Update sftp_users.json with new user for e.abascal #464
• Update sample handling in get_percentage_LDM #465
• Added _02_filter_results.sh script to pikavirus template #466
• Changed short_obx for middle_idx in 02-clean.sh #468
• Update exometrio lablog to Handle Fourth Individual #469
• Update get_percentage_LDM.py to read sample column as string #470
• Updated ivar varsion in viralrecon template to makwe it work with IonTorrent data #471
• Update get_percentage_LDM.py to Handle Cases with No Lineage Found in outbreak.info CSV #473
• Added autorun.sh script for automation of multiple sbatch running in viralrecon pipeline #474
• Modified clean.py in order to properly delete exact matching-name folders and files #476
• Added information on the period of permanence of the results in the sftp folder in email template #477

Modules

Added enhancements

Fixes

Changed

Removed

Requirements