Example input and output files for the virus variant caller pipeline

example_input.zip: reference annotations for HSV-1 strain 17 and alignment files (in BAM format) and read sequences (in FASTQ format) for two replicates each of the ICP0 and vhs knockout mutants. After downloading and unpacking the zip-archive, adjust the constants in the Watchdog workflow as follows: <const name="REFERENCE">/path/to/chrHsv1_s17.fa</const><const name="REFERENCE_SNPS">/path/to/reference_snps.txt</const><const name="CONFIG">/path/to/config_strains_HSV1.txt</const><const name="GTF">/path/to/HSV1_Annotation_chrHsv1_s17.gtf</const><const name="samples">/path/to/example_samples.txt</const><const name="replicates">/path/to/example_replicates.txt</const> where /path/to/ is the directory the content of the archive zip-archive is located in. example_output.zip: resulting output files