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