Hastings RD WGS

Clinical Genomics Uppsala rare disease pipeline for Twist2.0 whole exome sequence data.

https://hastings-rd-wes.readthedocs.io/en/latest/

This ReadMe is only a brief introduction, please refer to ReadTheDocs for the latest documentation and a more detailed description of the pipeline.

❗ Dependencies

In order to use this module, the following dependencies are required:

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🚀 Usage

To use this run this pipeline the requirements in requirements.txt must be installed. It is most straightforward to install the requirements inside a python virtual environment created with the python venv module. The sample.tsv, units.tsv, resources.yaml, and config.yaml files need to be available in the config directory (or otherwise specified in config.yaml). You always need to specify the config-file either in the profile yaml file or in the snakemake command. To run the pipeline:

Running the pipeline on CPU:

module load slurm-drmaa
module load singularity/3.11.0

python3.9 -m venv venv
source venv/bin/activate
pip install -r requirements.txt

pipeline_path=/path/to/pipeline

snakemake  --profile ${pipeline_path}/profiles/slurm/ -s ${pipeline_path}/workflow/Snakefile --prioritize prealignment_fastp_pe \
 -p  --configfiles config/config.yaml config/config_exomedepth_nextseq.yaml --config aligner=bwa_cpu snp_caller=deepvariant_cpu

Exomedepth reference creation

To create a reference for exomedepth based on the samples in the samples_ref.tsv and units_ref.tsv a config_reference.yaml must be specified in the command:

snakemake  --profile ${pipeline_path}/profiles/slurm/ -s ${pipeline_path}/workflow/Snakefile --prioritize prealignment_fastp_pe \
 -p  --configfiles config/config.yaml config/config_reference.yaml --config aligner=bwa_cpu snp_caller=deepvariant_cpu --notemp -n

✅ Testing

The workflow repository contains a dry run test of the pipeline in .tests/integration which can be run like so:

$ cd .tests/integration
$ snakemake -n -s ../../workflow/Snakefile --configfile config/config.yaml