GenomeAssembly#

Add to module run order:
#BioModule biolockj.module.assembly.GenomeAssembly

Description#

Assemble WGS sequences with MetaSPAdes, bin contigs with Metabat2 and check quality with checkM.

Properties#

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

GenomeAssembly 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
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/genome_assembly:v1.2.0

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

Citation#

checkM database
https://data.ace.uq.edu.au/public/CheckM_databases/checkm_data_2015_01_16.tar.gz
HMMER
http://eddylab.org/software/hmmer/hmmer.tar.gz
MASH
https://github.com/marbl/Mash/releases/download/v2.2/mash-Linux64-v2.2.tar
Metabat2
https://bitbucket.org/berkeleylab/metabat/downloads/metabat-static-binary-linux-x64_v2.12.1.tar.gz
MetaSPAdes
https://github.com/ablab/spades/releases/download/v3.13.0/SPAdes-3.13.0-Linux.tar.gz
PPLACER
https://github.com/matsen/pplacer/releases/download/v1.1.alpha19/pplacer-linux-v1.1.alpha19.zip
PRODIGAL
https://github.com/hyattpd/Prodigal/releases/download/v2.6.3/prodigal.linux

Module developed by Shan Sun
BioLockJ v1.4.2