ace

ace, workflow for absolute copy number estimation from low-coverage whole-genome sequencing data

Overview

Dependencies

ace 1.20.0

Usage

Cromwell

java -jar cromwell.jar run ace.wdl --inputs inputs.json

Inputs

Required workflow parameters:

Parameter	Value	Description
`inputBamFile`	File	Input BAM file with aligned RNAseq reads.
`outputFileNamePrefix`	String	Output prefix, customizable. Default is the input file's basename.
`reference`	String	Name and version of reference genome

Optional workflow parameters:

Parameter	Value	Default	Description

Optional task parameters:

Parameter	Value	Default	Description
`runAce.binsizes`	String	"c(100, 500, 1000)"	The vector of disired bin sizes for bam files
`runAce.ploidies`	String	"c(2,3,4)"	Specifies for which ploidies fits will be made
`runAce.imagetype`	String	"pdf"	The image file type to create
`runAce.method`	String	"RMSE"	A standard method for error calculation, default is the root mean squared error (RMSE)
`runAce.penalty`	String	0.1	Penalty for the error calculated at lower cellularity
`runAce.trncname`	String	"FALSE"	Whether truncate name, which truncates the name to everything before the first instance of _
`runAce.printsummaries`	String	"TRUE"	super big summary files may crash the program, so you can set this argument to FALSE
`runAce.timeout`	Int	8	Timeout in hours, needed to override imposed limits
`runAce.jobMemory`	Int	24	Memory in Gb for this job

Outputs

Output	Type	Description
`resultZip`	File	Zipped folder for all outputs

Commands

This section lists command(s) run by ace workflow

Running ace

R --no-save<<CODE
library(ACE)
library(Biobase)
library(QDNAseq)
library(QDNAseq.hg38)
library(QDNAseq.hg19)
library(ggplot2)

file.symlink("~{bamFile}", "./")


runACE(inputdir = "./", outputdir = "./result", filetype='bam', genome = "~{genome}", binsizes = ~{binsizes}, ploidies = ~{ploidies}, imagetype= "~{imagetype}", method = "~{method}", penalty = ~{penalty}, trncname = ~{trncname}, printsummaries = ~{printsummaries}) 


files2zip <- dir('./result', full.names = TRUE)
zip(zipfile = paste('~{outputFileNamePrefix}','resultZip', sep='_'), files = files2zip)

CODE

Support

For support, please file an issue on the Github project or send an email to gsi@oicr.on.ca .

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