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.