bin/minimap2-index @ 2e41ef790dc8

#!/usr/bin/env bash

set -euo pipefail

# minimap2-index \
#     /nfs/turbo/boylelab/slosh/reference-genomes/hg38_no_alt/seq/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna \
#     map-ont/ \
#     -x map-ont
reference="$1"
shift
output_dir="$1"
shift

# remaining opts are e.g. -x ont

minimap="/nfs/turbo/boylelab/slosh/software/minimap2-2.30_x64-linux/minimap2"

mkdir -p "$output_dir"

{
    echo Minimap version: "$("$minimap" --version)"

    echo Indexing command: " "
    echo \
    "$minimap" -t 8 -d "$output_dir/index.mmi" "$reference" "$@"

    echo
    echo Output:
    "$minimap" -t 8 -d "$output_dir/index.mmi" "$reference" "$@"
} >> "$output_dir"/README.txt 2>&1