Welcome to Shellflow’s documentation!

Contents:

• Getting Started
  • Before starting tutorial
  • 1st step: mapping
  • 2nd step: check status
  • 3rd step: add more commands
  • 4th step: use variable
  • 5th step: use loop
  • 6th step: map all FASTQ in a directory
• Command line options
  • run
  • dot
  • viewlog
  • flowscript
• Syntax
  • Input files
  • Output files
  • Varaible
  • Loop
  • if
• Examples
  • Build C program
  • Prepare hs37d5 index file
  • Analyze simulated FASTQ with GATK
• Flowscript
  • Syntax
  • Built-in functions
• Configuration
  • Command
  • Configuration Example
• TODO
• Backup

Indices and tables

• Index
• Module Index
• Search Page