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Quick Start

  1. Create a folder for your project (e.g. yourproject)

  2. Prepare a tab-separated table of phenotypes and eventually covariates (see the input section).

  3. Prepare and configure the required input data for step 2, usually an imputed or sequencing dataset, and step 1, usually a QCed and pruned dataset. You can eventually prepare also a set of files for LD computation, suggested if you want to run loci clumping when analyzing a large dataset with > 100k samples.

  4. If you want to perform a multi-models or multi-projects execution, prepare the models table or projects table to describe your analyses.

  5. If you want to perform conditional or interaction analysis, prepare the additional genotype dataset and eventually conditional variant list as described in the conditional analysis section.

  6. Prepare the necessary config files, using the templates provided in the templates folder:

  7. A config file describing settings and inputs for your project.
  8. A config file to define the profile for your computational environment.

  9. Optionally, you can also add configuration to enable execution monitoring using Nextflow Tower

  10. Invoke the pipeline using nextflow run HTGenomeAnalysisUnit/nf-pipeline-regenie

Usually, you want to prepare a script to submit the pipeline in your project folder. In this example we use sbatch submission system, but this can be adapted to any scheduler. myprofile corresponds to a profile you created for your computational environment:

#!/bin/bash
#SBATCH --job-name nf-regenie
#SBATCH --output nf-regenie_master_%A.log
#SBATCH --partition cpuq
#SBATCH --cpus-per-task 1
#SBATCH --mem 8G
#SBATCH --time 1-00:00:00

module load nextflow/22.10.1 singularity/3.8.5

export NXF_OPTS="-Xms1G -Xmx8G" 
nextflow run HTGenomeAnalysisUnit/nf-pipeline-regenie \
   -profile singularity,myprofile -c your_project.conf

Alternatively, you can clone the latest pipeline version using

git clone --depth 1 https://github.com/HTGenomeAnalysisUnit/nf-pipeline-regenie.git

This will create a new folder called nf-pipeline-regenie in the current folder containing all the pipeline files.

You can eventually chose a specific version of the pipeline using the --branch option

git clone --depth 1 --branch v1.8 https://github.com/HTGenomeAnalysisUnit/nf-pipeline-regenie.git