To run this pipeline Snakemake is required.

for easy installation you need (mini)conda.

Miniconda installation from folder where you want to install miniconda:

cd </path/to/files/dir/>
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh

follow the instructions of the installation process, give the location where you want miniconda to be installed and answer YES to add miniconda to your path.

go to the directory where the analysis need to be performed

cd </path/to/analysis/dir>
git clone https://github.com/tgac-vumc/WES-snake.git
cd WES-snake

install the snakemake environment,

conda env create --name snakemake --file snakemake.yaml

activate the snakemake environment

source activate snakemake

Setup your files correctly: - Place (links to) fastq files in the fastq directory one directory up from the WES-snake folder.
- Change the matching_samples.tsv file with your sample Normal_samples
- Change the configfile with the correct paths to the reference files and check if the correct manifest files are present

go to WES-snake directory and start snakemake.

snakemake --use-conda

Useful snakemake options

-j , --cores, --jobs : Use at most N cores in parallel (default: 1). If N is omitted, the limit is set to the number of available cores.
-n , --dryrun : Do not execute anything. but show rules which are planned to be performed.
-k , --keep-going : Go on with independent jobs if a job fails.
-f , --force : Force the execution of the selected target or the first rule regardless of already created output.
-U , --until : Runs the pipeline until it reaches the specified rules or files. Only runs jobs that are dependencies of the specified rule or files, does not run sibling DAGs.
-T , --timestamp : Add a timestamp to all logging output

for all options go to http://snakemake.readthedocs.io/en/stable/executable.html#all-options