RarefySeqs#

Add to module run order:
#BioModule biolockj.module.seq.RarefySeqs

Description#

Randomly sub-sample sequences to reduce all samples to the configured maximum.

Properties#

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

RarefySeqs properties:#

Property	Description
rarefySeqs.max	numeric Randomly select this number of sequences to keep in each sample default: null
rarefySeqs.min	numeric Discard samples with less than minimum number of sequences default: 1

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
pipeline.defaultSeqMerger	string Java class name for default module used combined paired read files default: biolockj.module.seq.PearMergeReads
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 Randomly sub-sample sequences to reduce all samples to the configured maximum rarefySeqs.max. Samples with less than the minimum number of reads rarefySeqs.min are discarded.
This module will add biolockj.module.implicit.RegisterNumReads if there is not already a module to count starting reads per sample.
If the input data are paired reads, this module will add a sequence merger, based on property pipeline.defaultSeqMerger (currently: biolockj.module.seq.PearMergeReads).

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:
RarefySeqs.imageOwner
RarefySeqs.imageName
RarefySeqs.imageTag

Citation#

Module developed by Mike Sioda
BioLockJ v1.4.2