microarray-eval-nf

A nextflow pipeline to test imputation quality of simulated microarrays.

Development

git clone https://github.com/seppinho/microarray-eval-nf
cd microarray-eval-nf
docker build -t genepi/microarray-eval:latest . # don't ignore the dot

Run Chip Simulation

This command simulates array data from sequencing data. For each strand file included, an array will be created.

nextflow run main.nf -c tests/simulate_hg19.config -profile development

Run RSQ Calculation

This command calculates the RSQ between sequencing data and imputed data.

nextflow run main.nf -c tests/calc_rsq_hg19.config -profile development

Run Tests

./nf-test test