This is a very simple pipeline to map WES data to KIR reference genes using kir-mapper. This pipeline only implements the map step, because it is the most time intensive of all kir-mapper steps and it needs to be executed on each sample. The other steps (ncopy, genotype and haplotype) are executed on the whole sample set so they can be executed manually afterwords.

Requirements

• Nextflow
• Docker or Singularity

Usage

Make sure to have the wes samples in the wes folder and the kir reference database in kir-mapper_db_latest (Check kir-mapper documentation to see how to download).

nextflow run nmendozam/kir-mapper -r main

If you don't have a nextflow configuration with docker activated. You can run the pipeline with the -with-docker flag:

nextflow run nmendozam/kir-mapper -r main -with-docker

Output

The output will be in the output/map folder.