This is a snakemake workflow to get copy number calls from low-pass whole genome sequencing. It aligns fastq files, performs some QC and then runs QDNAseq.
- Marc Williams (@marcjwilliams1)
If you simply want to use this workflow, download and extract the latest release. If you intend to modify and further extend this workflow or want to work under version control, fork this repository as outlined in Advanced. The latter way is recommended.
Configure the workflow according to your needs via editing the file config.yaml.
Make sure you have snakemake installed on your hpc. If running on apocrita (QMUL hpc) you may need to install it in an environment. eg I run the following to activate an environment with snakemake installed.
source /data/home/hfx042/bin/snakemake/bin/activate
You can then run a dry-run to check all rules have correct dependencies:
snakemake -n
Finally to run the workflow using the job scheduling on apocrita you can use the following:
snakemake --jobs 75 \
--cluster-config cluster.yaml \
--cluster "qsub -cwd -l h_rt={cluster.time} -l h_vmem={cluster.mem} -pe smp {threads} -o {cluster.output} -j y -N {cluster.name}"
If you're using a different HPC you may need to change this command and the cluster configuration file cluster.yaml.