ace, workflow for absolute copy number estimation from low-coverage whole-genome sequencing data
java -jar cromwell.jar run ace.wdl --inputs inputs.json
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 |
Parameter | Value | Default | Description |
---|
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 |
Output | Type | Description |
---|---|---|
resultZip |
File | Zipped folder for all outputs |
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
For support, please file an issue on the Github project or send an email to gsi@oicr.on.ca .
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