Meta issue for Milestone 1.0.0

[maxulysse]

Tasks

• Move assets in nf-core/references-assets from assets/ into ./
  • Update path in nextflow.config on the pipeline side
• Deal with igenomes_base when generating published files in nf-core/references-assets
• Differentiate the source files and the published files
• Flat structure
• Create a subworkflow in nf-core/modules to store schema and functions
• Add to schema all items from rnaseq #99
• Add to schema all items from sarek
• Add tools from rnaseq #16
• Add all tools from sarek
• Refine definition and syntax for all elements
• More meaningful name for field in input_schema.json, especially for the meta data #65
• Describe and version the schema specs