BUISCIII/buisciii-tools v2.2.11

Credits

• Juan Ledesma
• Victor Lopez
• Jaime Ozáez

Template fixes and updates

• Added micromamba environment PikaVirus_dev_2.6 to file hpc_slurm_pikavirus.config #535.
• Changed analysis_date in create_summary_report.sh to take properly dates from RSV services when using viralrecon #540.
• Fixed date formats for IRMA's template and excel_generator.py #549.
• Fixed the way whether samples are paired or single-end is detected #550.
• Removed pseudo_aligner parameter from RNASeq's lablog and added all missing symlinks in its RESULTS's lablog #552.
• Updated scratch.py and main.py to properly handle custom paths and temporary directories #555.
• Updated create_summary_report.sh to transform negative values into 0 #556.
• Updated the assembly stats script to handle files in RAW properly and when quast results are not available for any sample #557.

Modules

• Fixed clean module to handle subpaths stated in services.json #543.
• Fixed bioinfo_doc module to be able to indicate type (service_info or delivery) via CLI #558.
• Fixed the bioinfo_doc module to properly ask for email text notes and the scratch module to use proper scratch_tmp_path #559.

Added enhancements

• Added new script to download multiple SRA entries in fastq format when necessary #551.

Fixes

Changed

• Modified bu-isciii > buisciii for all commands in README text #548.

Removed