Automated benchmarking of recombination detection methods
(Note: many things are hardcoded)
Nextflow 22.10 (DSL1-compatible)
conda
# Download repo
git clone https://github.com/fredjaya/rec-bench.git
# Generate p-value table for 3SEQ
bin/3seq_elf -gen-p bin/p700 700
Install openrdp according to If Nextflow doesn't appear to create the conda environment properly. Create manually.
conda env create -f environment.yml
conda activate fredjaya-rec-bench-0.1.0
nextflow run sim.nf \
--mode scalability \
--seq data/FP7_patient_037_allseqs.fasta \
--xml data/neutral.xml \
--out `pwd`