RdpHierParser#

Add to module run order:
#BioModule biolockj.module.implicit.parser.r16s.RdpHierParser

Description#

Create taxa tables from the _hierarchicalCount.tsv files output by RDP.

Properties#

Properties are the name=value pairs in the configuration file.

RdpHierParser properties:#

Property	Description
rdp.hierCounts	boolean Set this property to "Y" to use this module instead as the follow-up to the RdpClassifier module. default: null
rdp.minThresholdScore	numeric RdpClassifier will use this property and ignore OTU assignments below this threshold score (0-100) default: 80

General properties applicable to this module:#

Property	Description
cluster.batchCommand	string Terminal command used to submit jobs on the cluster default: null
cluster.jobHeader	string Header written at top of worker scripts default: null
cluster.modules	list List of cluster modules to load at start of worker scripts default: null
cluster.prologue	string To run at the start of every script after loading cluster modules (if any) default: null
cluster.statusCommand	string Terminal command used to check the status of jobs on the cluster default: null
docker.saveContainerOnExit	boolean If Y, docker run command will NOT include the --rm flag default: null
docker.verifyImage	boolean In check dependencies, run a test to verify the docker image. default: null
script.defaultHeader	string Store default script header for MAIN script and locally run WORKER scripts. default: #!/bin/bash
script.numThreads	integer Used to reserve cluster resources and passed to any external application call that accepts a numThreads parameter. default: 8
script.numWorkers	integer Set number of samples to process per script (if parallel processing) default: 1
script.permissions	string Used as chmod permission parameter (ex: 774) default: 770
script.timeout	integer Sets # of minutes before worker scripts times out. default: null

Details#

version: 1.0.0 This module requires that rdp.hierCounts=Y for the RdpClassifier module to make the required output type. As long as rdp.hierCounts is set, this module will automatically be added to the module run order by the RdpClassifier module.
If this module is in the module run order, it adds biolockj.module.classifier.r16s.RdpClassifier as a pre-quisite module.
To use this module without the RDP module, include ModuleOutput[RdpClassifier] in the list of input types:
pipeline.inputTypes=ModuleOutput[RdpClassifier]
When using input from a directory, this module takes exactly one input directory.

This module is an alternative to the default parser, RdpParser. The two parsers produce nearly identical output. The RdpParser module parses the output for each sequence and determines counts for each taxanomic unit. It fills in missing levels so all sequences are counted for all taxanomic levels; this means reads that are unclassified are reported as an OTU with "unclassified" in the name.By contrast, the RdpHierParser module relies on RDP to determine these totals.When using RdpParser the confidence threshold is applied by the parser, when using RdpHierParser the coinfidence threshold is applied by RDP during classification.

Adds modules#

pre-requisite modules
biolockj.module.classifier.r16s.RdpClassifier
post-requisite modules
none found

Docker#

If running in docker, this module will run in a docker container from this image:

biolockjdevteam/biolockj_controller:v1.4.2

This can be modified using the following properties:
RdpHierParser.imageOwner
RdpHierParser.imageName
RdpHierParser.imageTag

Citation#

Module created by Ivory Blakley.