Rcwl and Case Study
Preface
0.1
R package installation
0.2
System requirements
0.3
Docker
0.4
Structure of the book
0.5
R session information
1
Introduction
2
Get started
3
Wrap command line tools
3.1
Input Parameters
3.1.1
Essential Input parameters
3.1.2
Array Inputs
3.2
Output Parameters
3.2.1
Capturing Output
3.2.2
Array Outputs
3.2.3
Standard output
4
Writing Pipeline
4.1
Scattering pipeline
4.2
Pipeline plot
5
Tool/pipeline execution
5.1
Running Tools in Docker
5.2
Running Tools in Cluster server
5.3
Web Application
5.3.1
cwlProcess example
5.3.2
cwlProcess to Shiny App
6
RcwlPipelines
6.1
Rcwl recipes and CWL scripts
6.2
RcwlPipelines core functions
6.2.1
cwlUpdate
6.2.2
cwlSearch
6.2.3
cwlLoad
6.3
Tool/pipeline customization
6.4
Build a pipeline
7
DNAseq alignment
8
DNAseq variant calling
9
Bulk RNAseq
9.1
Prepare data
9.2
Submit parallel jobs
9.3
QC Summary
9.4
Abundances summary
9.5
transcriptome quantification
9.5.1
Kallisto
9.5.2
salmon
10
single cell RNAseq
11
miRNA
11.0.1
Reference index
11.0.2
Run miRDeep2 pipeline
References
Published with bookdown
Bioinformatics tools and pipelines using R and CWL
Chapter 8
DNAseq variant calling
to be added.