illumina

#!/bin/bash


bam="$1"
[[ -z "$1" ]] && { echo "Parameter 1 is empty" 1>&2; exit 1; }
peaks="$2"
[[ -z "$2" ]] && { echo "Parameter 2 is empty" 1>&2; exit 1; }
genome="$3"
[[ -z "$3" ]] && { echo "Parameter 3 is empty" 1>&2; exit 1; }
output_dir="$4"
[[ -z "$4" ]] && { echo "Parameter 4 is empty" 1>&2; exit 1; }
config="$6"
[[ -z "$6" ]] && { config="configs/configManta.py.ini" && echo "Path to config file was not specified. Using '$config'." 1>&2; }
if [ ! -f  "$config" ]; then
	echo "The mamta config file ($config) could not be found. Check that it exists." 1>&2; exit 1;
fi
manta_dir="$7"
if [[ -z "$7" ]]; then
	echo "Manta directory not specified. Attempting to retrieve from conda env..." 1>&2
	if [[ -z "$CONDA_PREFIX" ]]; then
		echo "Error: not running in conda env" 1>&2; exit 1;
	else
		manta_dir="$(ls "$CONDA_PREFIX"/share | grep 'manta' | head -n1)"
		if [[ -z "$manta_dir" ]]; then
			echo "Error: coudn't find manta in conda env" 1>&2; exit 1;
		fi
		manta_dir="$CONDA_PREFIX"/share/"$manta_dir"
	fi
else
	manta_dir="$7"
fi
echo "Using manta dir: $manta_dir" 1>&2


rm -rf "$output_dir"/results "$output_dir"/workspace "$output_dir"/workflow* "$output_dir"/runWorkflow*

# bgzip compress and index the bed file
bgzip -f "$peaks" -c > "$output_dir/peaks.bed.gz" && tabix -p bed -f "$output_dir/peaks.bed.gz"

"$manta_dir"/bin/configManta.py --exome --bam "$bam" --referenceFasta "$genome" --callRegions "$output_dir/peaks.bed.gz" --runDir "$output_dir" --config "$config"

"$output_dir"/runWorkflow.py -j 24 && \
bgzip -d "$output_dir"/results/variants/diploidSV.vcf.gz