#!/bin/bash
# An example setup script to generate slurm scripts for running RUFUS in windowed mode

SLURM_ACCOUNT=
SLURM_PARTITION=
EMAIL=
SIF=/path/to/container.sif
KMER_DEPTH=5
SUBJECT=/path/to/subject.cram
CONTROL1=/path/to/control_1.cram
CONTROL2=/path/to/control_2.cram
REF=/path/to/ref.fa

singularity exec $SIF bash /opt/RUFUS/singularity/setup_slurm.sh -d "$DATA_DIR" -s "$SUBJECT" -c "$CONTROL1","$CONTROL2" -r "$REF" -a "$SLURM_ACCOUNT" -p "$SLURM_PARTITION" -e "$EMAIL" -y $SIF -l 1000 -w 1000 -m $KMER_DEPTH