G-CAT Workflow

G-CAT Workflow is a cancer genome and RNA sequencing data analysis pipeline that efficiently detects genomic variants and transcriptomic changes. Users can run G-CAT Workflow with ease of use in the supercomputer and also can run it on other high-performance computers.

Manual

https://github.com/ncc-ccat-gap/GCATWorkflow

For developers, https://github.com/ncc-ccat-gap/GCATWorkflow/wiki

Setup

0. Precondition

Make DRMAA and singularity available beforehand.

1. Install

git clone https://github.com/ncc-ccat-gap/GCATWorkflow.git
cd GCATWorkflow
python setup.py install

2. Pull container images

For example,

singularity pull docker://genomon/bwa_alignment:0.2.0

3. Edit config file

Edit image options, to pulled .sif.
And edit paths of reference files.

vi ./tests/gcat.cfg

4. Edit sample.csv

Edit paths of sequence files.

vi ./tests/sample.csv

How to use

1. Configure

case with germline mode

gcat_workflow germline ./tests/sample.csv ${output_dir} ./tests/gcat.cfg

2. snakemake

cd ${output_dir}
snakemake --cores 4 -k

case, dry-run

snakemake -n

case, re-run (force all)

snakemake --forceall