phac-nml/LegioVue: Changelog

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

0.2.0 - 2025-01-24

`Added`

nf-schema plugin and associated functions
- Schemas
- Param summary, param help, version
- samplesheetToList
params.input <CSV> to allow input samplesheets
iridanext plugin
nf-prov plugin
Required nf-core files
CI tests and linting
Added in quality parameters to allow more user freedom:
- max_contigs
- min_align_percent
- min_reads_warn
- min_n50_score
- max_n50_score

`Changed`

Final quality metrics output is a CSV now to work with IRIDA next
Logic for input data
Logic for skipping specific modules
- Allowed to skip el_gato ST
- Allowed to skip el_gato allele plotting
All process publishDir now in the modules.conf file
Container for allele plotting
Adjusted default warn and fail parameters for quality module based on testing
- min_reads to 60,000 from 150,000

`Updated`

Usage and README docs for the input adjustments

0.1.0 - Beta-Test-2024-11-29

`Added`

LegioVue pipeline created and initial beta code added