2_Install.md

• Introduction: Quick Start, Tutorial, Flowchart, Outputs structure
• Install: Dependencies, Containers, References, Test datasets
• Inputs: Data, Design, Parameters
• 1. Preprocessing: ATAC reads, ATAC peaks, mRNA
• 2. Differential Analysis: ATAC, mRNA, Split
• 3. Enrichment Analysis: Enrichment, Figures, Tables

This section covers the Installation of Cactus, including:

• The installation of the two dependencies: Nextflow and a tools manager (Docker or Singularity containers or conda or Mamba virtual environments)
• The containers / virtual environments used by Cactus, their origins and their sizes
• The species-specific references used by Cactus, their sizes, how these files were created and details on the CHIP-Seq datasets
• The test datasets that can optionally be downloaded to test Cactus in each of the 4 supported species, their sizes, details on their origins and on the samples