View source for VirSieve

[[Category:Software]]
[[Category:Biology]]
[[Category:Pipeline]]
[[Category:Software]]
{|<!--CONFIGURATION: REQUIRED-->
|{{#vardefine:app|VirSieve}}
|{{#vardefine:url|https://github.com/Zymo-Research/VirSieve}}
<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
|{{#vardefine:conf|}}           <!--CONFIGURATION-->
|{{#vardefine:exe|1}}            <!--ADDITIONAL INFO-->
|{{#vardefine:job|1}}            <!--JOB SCRIPTS-->
|{{#vardefine:policy|}}         <!--POLICY-->
|{{#vardefine:testing|}}       <!--PROFILING-->
|{{#vardefine:faq|}}             <!--FAQ-->
|{{#vardefine:citation|}}       <!--CITATION-->
|{{#vardefine:installation|}} <!--INSTALLATION-->
|}
<!--BODY-->
<!--Description-->
{{#if: {{#var: url}}|
{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}

Environmental Viral Detection pipeline. Contains VirSieveAlign, VirSieveGATK, VirSieveIVar, and VirSieveVEP applications

<!--Modules-->
==Environment Modules==
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
==System Variables==
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
* HPC_{{uc:{{#var:app}}}}_BIN - installation directory
<!--Configuration-->
{{#if: {{#var: conf}}|==Configuration==
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.
|}}
<!--Run-->
{{#if: {{#var: exe}}|==Additional Information==

Each tool expects to be given a path to a working folder where your configurations, FASTA files, custom references, etc. are located.  To aid with this, UFRC provides a "wrapper script" for each application in the pipeline that can be called with a path pointing to your working directory.  For example, to call VirSieveIVar to process the working directory /blue/groupname/username/virsieve_test/:
 $ module load virseive/20210406
 $ VirSieveIVar /blue/groupname/username/virsieve_test/

Each tool also has the ability to set non-default options via environment variables.  Since we are running these tools within Singularity containers, you will need to prefix those environment variables with "SINGULARITYENV_" if you want to use them as overrides.  For example, VirSieveIVar allows for a custom reference BED file by setting the PRIMERBED environment variable.  To use "mycustom.bed" as a custom BED file in HPG, you would:
 $ module load virsieve/20210406
 $ export SINGULARITYENV_PRIMERBED=/path/to/mycustom.bed
 $ VirSieveIVar /blue/groupname/username/virsieve_test/

The expected working directory structure and lists of the available environment variables for each tool can be found on that tool's page:<br/>

https://www.github.com/Zymo-Research/VirSieveAlign<br/>
https://www.github.com/Zymo-Research/VirSieveGATK<br/>
https://www.github.com/Zymo-Research/VirSieveIVar<br/>
https://www.github.com/Zymo-Research/VirSieveVEP<br/>

|}}
<!--Job Scripts-->
{{#if: {{#var: job}}|==Job Script Examples==
<div class="mw-collapsible mw-collapsed" style="width:70%; padding: 5px; border: 1px solid gray;">
''Expand this section to view script example.''
<div class="mw-collapsible-content" style="padding: 5px;">
<pre>
#!/bin/bash
#SBATCH --job-name=virsieve_test
#SBATCH --mail-type=NONE
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=32
#SBATCH --mem-per-cpu=4gb
#SBATCH --time=24:00:00
#SBATCH --output=virsieve_test.log

TEST_PWD=/data/apps/tests/virsieve
TEST_SAMPLEDIR=${TEST_PWD}/sample_data
TEST_WORKDIR=${TEST_PWD}/virsieve_test

cd ${TEST_PWD}
module load virsieve

# Remove any previous test results, create a working directory, and copy
# initial test reads into the expected position in working directory
if [ -d ${TEST_WORKDIR} ]; then rm -rf ${TEST_WORKDIR}/; fi
mkdir -p ${TEST_WORKDIR}/rawFASTQ
cp ${TEST_SAMPLEDIR}/*.gz ${TEST_WORKDIR}/rawFASTQ

echo "Starting test run at $(date) on $(hostname)..."

# Run VirSieveAlign (rawFASTQ/ --> processedFASTQ/, mergedBAM/, rawBAM/)
VirSieveAlign ${TEST_WORKDIR}

# Run VirSieveIVar (mergedBAM/ --> primerTrimBAM/)
# export SINGULARITYENV_PRIMERBED=/path/to/mycustom.bed
VirSieveIVar ${TEST_WORKDIR}

# Run VirSieveGATK (primerTrimBAM/ --> filteredVCF/, alignmentArtifactFilteredVCF/, etc.)
VirSieveGATK ${TEST_WORKDIR}

# Run VirSieveVEP (filteredVCF/, alignmentArtifactFilteredVCF/ --> vepOutputs/, results/)
VirSieveVEP ${TEST_WORKDIR}

# There should be some files in the results/ directory
echo "There should be some results listed below:"
find ${TEST_WORKDIR}/results/ -type f ! -empty -ls

echo "Test complete at $(date)."
</pre>
</div>
</div>
|}}
<!--Policy-->
{{#if: {{#var: policy}}|==Usage Policy==

WRITE USAGE POLICY HERE (Licensing, usage, access).

|}}
<!--Performance-->
{{#if: {{#var: testing}}|==Performance==

WRITE_PERFORMANCE_TESTING_RESULTS_HERE

|}}
<!--Faq-->
{{#if: {{#var: faq}}|==FAQ==
*'''Q:''' **'''A:'''|}}
<!--Citation-->
{{#if: {{#var: citation}}|==Citation==
If you publish research that uses {{#var:app}} you have to cite it as follows:|}}
<!--Installation-->
{{#if: {{#var: installation}}|==Installation==
See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
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