AddMetadataToTaxaTables#

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

Description#

Map metadata onto taxa tables using sample ID.

Properties#

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

AddMetadataToTaxaTables 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
metadata.columnDelim	string defines how metadata columns are separated; Typically files are tab or comma separated. default: \t
metadata.commentChar	string metadata file comment indicator; Empty string is a valid option indicating no comments in metadata file. default: null
metadata.filePath	file path If absolute file path, use file as metadata. If directory path, must find exactly 1 file within, to use as metadata. default: null
metadata.nullValue	string metadata cells with this value will be treated as empty default: NA
report.taxonomyLevels	list Options: domain,phylum,class,order,family,genus,species. Generate reports for listed taxonomy levels default: phylum,class,order,family,genus
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 The output of this module will have a row for each sample (just like the metadata and the taxa tables) and columns for data AND metadata.
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:
AddMetadataToTaxaTables.imageOwner
AddMetadataToTaxaTables.imageName
AddMetadataToTaxaTables.imageTag

Citation#

Module developed by Mike Sioda and Anthony Fodor
BioLockJ v1.4.2