The QC pipeline of MoBa genotypes is organized in different modules built using SnakeMake. The pipeline is executed on the HUNT Cloud system using Linux Ubuntu as operating system and conda to manage environments. The pipeline is not tested and not intended to work on other platforms.
- bin: this folder contains executables used throughout the pipeline.
- docs: this folder contains documentation generated by the QC pipeline.
- env: this folder contains specification for the environment used for the execution of the pipeline.
- resources: this folder contains resources used in the pipeline.
- snakefiles: this folder contains the SnakeMake files for the pipeline.
Prior to execution, make sure that SnakeMake and conda or equivalent are installed. Clone the repository, and install the conda environment specified in snp_qc.yaml. Then, activate the environment using snakemake activate snp_qc.
To execute the pipeline, navigate to the snakefiles folder and run snakemake --snakefile Snakefile --use-conda. You can set the number of cores using the --cores n option, and rerun incomplete rules using the --rerun-incomplete option.
- Batch details contains information on the different batches.
- General configuration contains general parameters and paths.
- Rules lists all the rules implemented in the different modules.
- Variables general variables used in the pipelines including paths and the list of batches to process.
For HRC verification tool install ReadKey for perl sudo apt install libterm-readkey-perl