quilt-nf: A Nextflow pipeline for haplotype reconstruction using low-coverage whole-genome sequencing data

Execution:

On the JAX HPC, from within the quilt-nf directory:

sbatch run_scripts/quilt_DO.sh [run name]

A prospective user can write their own run script using the following template:

#!/bin/bash
#SBATCH --mail-user={USER.EMAIL}
#SBATCH --job-name=QUILT-NF
#SBATCH --mail-type=END,FAIL
#SBATCH -p compute
#SBATCH -q batch
#SBATCH -t 72:00:00
#SBATCH --mem=1G
#SBATCH --ntasks=1

cd $SLURM_SUBMIT_DIR

# LOAD NEXTFLOW
module use --append /projects/omics_share/meta/modules
module load nextflow

# RUN PIPELINE
nextflow main.nf \
--workflow quilt \
-profile sumner2 \
--sample_folder '{PATH TO DIRECTORY CONTAINTING FASTQ FILES}' \
--gen_org mouse \
--pubdir '{PATH TO DESIRED RESULTS DIRECTORY' \
--extension 'fastq.gz' \ # this is the typical file extension, but see run_scripts/quilt_DO_ddRADseq.sh for alternative example
--pattern="*_R{1,2}*" \ # see above comment
--library_type "seqwell" \ # see above comment
--run_name $1 \
-w '{PATH TO DESIRED NEXTFLOW WORK DIRECTORY}' \ # on JAX, use /flashscratch/{USER} or /flashscratch/{OTHER}
--downsample_to_cov '{PATH TO .CSV WITH COVERAGE VALUES TO DOWNSAMPLE TO}' \
--bin_shuffling_file '{PATH TO .CSV WITH QUILT BIN SHUFFLE RADIUS VALUES}' \
--cross_type 'do' \
--ref_file_dir '{PATH TO DIRECTORY WITH REFERENCE HAPLOTYPE FILES}' \
--covar_file '{PATH TO R/QTL2 COVAR FILE}' \
--comment "This script will run haplotype inference on DO lcWGS data" \
-resume