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