File: workflow.sh

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#!/bin/bash

#Set the inputReads and reference -- change at your leisure
inputReads=filtered_subreads.fastq
reference=lambda_modified.fasta

echo "PIEMapping"
Honey.py pie $inputReads $reference

echo "Sam To Bam"
sam2bam $reference mapping.tails.sam

echo "Calling Tails"
Honey.py tails mappingFinal.bam --reference $reference

echo "Calling Spots"
Honey.py spots mappingFinal.bam