LogTransformTaxaTables#
Add to module run order:
#BioModule biolockj.module.report.taxa.LogTransformTaxaTables
Description#
Log-transform the raw taxa counts on Log10 or Log-e scales.
Properties#
Properties are the name=value
pairs in the configuration file.
LogTransformTaxaTables 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 |
report.logBase | string Options: 10,e,null. If e, use natural log (base e); if 10, use log base 10; if not set, counts will not be converted to a log scale. default: 10 |
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: 0.0.0 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
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:
LogTransformTaxaTables.imageOwner
LogTransformTaxaTables.imageName
LogTransformTaxaTables.imageTag
Citation#
Module developed by Mike Sioda
BioLockJ v1.4.2