Welcome to Shellflow’s documentation!
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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
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Module Index
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Command line options
Syntax
Examples
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TODO
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