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#!/bin/sh

# folder, input path within foler, output path within folder

# directory, reads within directory, output file

echo $@

echo "dir: $1"

echo "reads: $2"

echo "3 $3"

docker run --rm -it -u=`id -u`:`id -g` -v $1:/data ${GRAPHMAP_IMAGE:-"nmiculinic/graphmap"} align -r /data/ref.fasta -d /data/$2 -o /data/$3 --extcigar

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