[0.2.0] - 2025-01-24

[0.2.0] - 2025-01-24

Adding in proper parameter schema, input available as a sample sheet, and fixing some bugs related to environments

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