RarefyOtuCounts#

Add to module run order:
#BioModule biolockj.module.report.otu.RarefyOtuCounts

Description#

Applies a mean iterative post-OTU classification rarefication algorithm so that each output sample will have approximately the same number of OTUs.

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

Property	Description
rarefyOtuCounts.iterations	integer (positive integer) the number of iterations to randomly select the rarefyOtuCounts.quantile of OTUs default: 10
rarefyOtuCounts.lowAbundantCutoff	numeric (positive double) minimum percentage of samples that must contain an OTU. default: 0.01
rarefyOtuCounts.quantile	numeric Quantile for rarefication. The number of OTUs/sample are ordered, all samples with more OTUs than the quantile sample are subselected without replacement until they have the same number of OTUs as the quantile sample default: 0.5
rarefyOtuCounts.rmLowSamples	boolean Options: Y/N. If Y, all samples below the rarefyOtuCounts.quantile quantile sample are removed default: null

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

version: 0.0.0 none

pre-requisite modules
none found
post-requisite modules
none found

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:
RarefyOtuCounts.imageOwner
RarefyOtuCounts.imageName
RarefyOtuCounts.imageTag

Module developed by Mike Sioda
BioLockJ v1.4.2