Version v0.4.0

For zenodo

minor update - v0.3.78

• Added bbduk trimming to single end mode
• Added minion module to IRMA RSV
• Fixed issue with IRMA not running in single mode
• Fixed issue with standard trimming not working (primer names were wrong)
• Coded a check if the files are empty stop and through a helpful message

minor update - v0.3.77

Fixed small snakemake issues with new adapters.
Fixed autoinstall issue.

v0.3.76

Full Changelog: v0.3.75...v0.3.76

Minor update - version 0.3.5

v0.3.5

• Added new trimming method (bbduk) for tiling experiment
• Added new adapters for tiling
• Removed R dependency stringr and stringi #7

Minor update - version 0.3.2

• Automatic Installation script included

Minor update - version 0.3.1

• Removed code trying to detect new github version, doesn't work when downloading releases.
• updated FLU init.sh to correct settings ("default whocc" settings")
• wfi_config.yaml includes file patterns for different sequences, currently experimental!
• Pipeline now outputs a status folder, this should allow for better recovery if the pipeline fails
• Updated some file wrangling scripts to actually work

wfi-snakemake - version 0.3

• Summary reports are generated including text report and combined depth plot
• Updated minimum depth cutoff for calling SNVs and indels (now 5% and 8% respectively)
• Added new module for RSV organism
  • Note: RSV-secondary requires further testing
  • Note: minimap2 modules are present but not integrated in pipeline (planned for future releases)
• Reworked pattern matching for sample names: {sample}_{lane}_{pair}_{run}.fastq.gz
• Added option to change file pattern matching
• Removed read trimming step completely - IRMA does read filtering and trimming internally
• Added primer filtering with cutadapt for FLU and RSV
• Added QC tables as part of the output