NormalizeByReadsPerMillion#

Add to module run order:
#BioModule biolockj.module.report.taxa.NormalizeByReadsPerMillion

Description#

new counts = counts / (total counts in sample / 1 million)

Properties#

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

NormalizeByReadsPerMillion properties:#

none

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 Represent each count value in the table as: counts / (total counts in sample / 1 million)
If report log base is not null, LogTransformTaxaTables is added as a post-requisite to do the log transformation and AddPseudoCount is added as a pre-requisite before normalization to avoid taking the log of 0.
If the pipeline input does not include at least one taxa table, then the BuildTaxaTables class is added by this module as a pre-requisite.

Adds modules#

pre-requisite modules
pipeline-dependent
post-requisite modules
biolockj.module.report.taxa.LogTransformTaxaTables

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:
NormalizeByReadsPerMillion.imageOwner
NormalizeByReadsPerMillion.imageName
NormalizeByReadsPerMillion.imageTag

Citation#

Module developed by Ivory Blakley.