Nextflow pipeline for running SNPmatch

Installation

This pipeline itself needs no installation - NextFlow will automatically fetch it from GitHub rbpisupati/nf-snpmatch

git clone https://github.com/rbpisupati/nf-snpmatch.git

You need to have SNPmatch installed in your system. Please visit (https://github.com/Gregor-Mendel-Institute/SNPmatch.git) for detailed instructions on installing SNPmatch.

Running the pipeline

Genotyping inbred lines

nextflow run main.nf --func "inbred" --input "*.vcf" --outdir "snpmatch" --db "hdf5" --db_acc "hdf5_acc"
## or run cross genotyper
nextflow run main.nf --func "cross" --input "*.vcf" --outdir "snpmatch" --db "hdf5" --db_acc "hdf5_acc"

Genotyping crosses in windows given parents

nextflow run genocross.nf --input "*.vcf" --parents "6191x6046" --window 300000 --outdir "snpmatch" --db "hdf5_path" --db_acc "hdf5_acc_path"

Input, parents, outdir are required arguments.

Configuration

The pipeline is written mainly to run SNPmatch on GMI HPC mendel which is PBS system. Please change config file accordingly to run it on your system.

Credits

• Rahul Pisupati (rahul.pisupati[at]gmi.oeaw.ac.at)

Citation

Cite the paper below if you use SNPmatch tool. Pisupati, R. et al.. Verification of Arabidopsis stock collections using SNPmatch, a tool for genotyping high-plexed samples. Nature Scientific Data 4, 170184 (2017). doi:10.1038/sdata.2017.184