General Architecture

[nicola-calonaci]

• Metadata propagation here
  • Include plugin nf-validation (https://github.com/nextflow-io/nf-validation)
  • Write schema_input.json in assets (e.g. Sarek https://github.com/nf-core/sarek/tree/master/assets)
  • From samplesheet parsing, return a boolean for lifter usage (e.g. https://github.com/nf-core/sarek/blob/master/subworkflows/local/samplesheet_to_channel/main.nf)
• Development of single modules/relying on scripts
• Output management for final assembly
• Reorganise config files:
  • Build config file for each module with publishDir etc. (like https://github.com/nf-core/sarek/blob/master/conf/modules/ascat.config)
    • ensemblevep
    • formatter (subworkflow)
    • QC
      • CNAqc
      • TINC
    • subclonal deconvolution
      • mobster
      • viber
      • pyclone
      • ctree
    • signatures deconvolution
      • sparsesigs
      • sigprofiler
  • Build a config with resources for each module with tag (eg process_medium etc. https://github.com/nf-core/sarek/blob/b5b766d3b4ac89864f2fa07441cdc8844e70a79e/conf/base.config)