📄️ Getting Started
Install necessary dependencies
📄️ Preparing Input Files
To harmonise GWAS summary statistics data, the pipeline requires two input files for each dataset:
📄️ Preparing Reference Files
A reference file is a dataset that contains detailed information about known genetic variants, including at least their genomic positions, reference alleles, and alternative alleles. These reference files are crucial for variant harmonisation, as they determine both whether and how your variants will be harmonised.
📄️ Preparing the Executor
Nextflow supports running pipelines on a variety of execution environments, including local machines, HPC systems, and cloud platforms. The default executor for this pipeline is SLURM, but you can easily switch between different environments by modifying the executor settings in the executor.config file.
📄️ Harmonising a single sumstat
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📄️ Harmonising a large number of sumstats
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