Example input and output files for the virus variant caller pipeline

<p><code>example_config_files.zip</code>: reference annotations for HSV-1 strain 17 and config files describing the input files.</p> <p><code>example_bam_files.zip:</code> alignment files (in BAM format) for two replicates each of the&nbsp; ICP0 and vhs knockout mutants.</p> <p><code>example_fastq_files.zip</code>: read sequences (in FASTQ format) for two replicates each of the&nbsp; ICP0 and vhs knockout mutants.</p> <p><code>example_output.zip</code>: resulting output files</p> <p>&nbsp;</p> <p>After downloading and unpacking the zip-archives,&nbsp;<strong>adjust the constants in the Watchdog workflow</strong> as follows:</p> <p><code>&lt;const name="REFERENCE"&gt;/path/to/chrHsv1_s17.fa&lt;/const&gt;</code><br><code>&lt;const name="REFERENCE_SNPS"&gt;/path/to/reference_snps.txt&lt;/const&gt;</code><br><code>&lt;const name="CONFIG"&gt;/path/to/config_strains_HSV1.txt&lt;/const&gt;</code><br><code>&lt;const name="GTF"&gt;/path/to/HSV1_Annotation_chrHsv1_s17.gtf&lt;/const&gt;</code><br><code>&lt;const name="samples"&gt;/path/to/example_samples.txt&lt;/const&gt;</code><br><code>&lt;const name="replicates"&gt;/path/to/example_replicates.txt&lt;/const&gt;</code></p> <p>where <code>/path/to/</code> is the directory the content of the archive zip-archives is located in.</p> <p>Furthermore, change <code>/path/to/</code> in the <code>example_replicates.txt</code>&nbsp; and <code>example_samples.txt</code> files to the directory the content of the archive zip-archives is located in.</p>