PearMergeReads#

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

Description#

Run pear, the Paired-End reAd mergeR

Properties#

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

PearMergeReads properties:#

Property	Description
exe.pear	executable Path for the "pear" executable; if not supplied, any script that needs the pear command will assume it is on the PATH. default: null
pearMergeReads.pearParams	string optionally pass additional parameters to pear. default: null

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: 0.0.0 none

Adds modules#

pre-requisite modules
none found
post-requisite modules
none found

Docker#

If running in docker, this module will run in a docker container from this image:

biolockjdevteam/pear:v1.2.9

This can be modified using the following properties:
PearMergeReads.imageOwner
PearMergeReads.imageName
PearMergeReads.imageTag

Citation#

Jiajie Zhang, Kassian Kobert, Tomáš Flouri, Alexandros Stamatakis, PEAR: a fast and accurate Illumina Paired-End reAd mergeR, Bioinformatics, Volume 30, Issue 5, 1 March 2014, Pages 614–620, https://doi.org/10.1093/bioinformatics/btt593
https://cme.h-its.org/exelixis/web/software/pear/doc.html
Module developed by Mike Sioda