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nextflow.config
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nextflow.config
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params {
//---------------------------------------------------------------------------------------------------------------------
//------------------ Executables ------------------------------------
//---------------------------------------------------------------------------------------------------------------------
//Directory to nextflow executable.
nextflowDir = ""
//Path to cortex directory
cortexDir = ""
//Path to cortex bin directory.
cortexBinDir = cortexDir + "/bin"
//Path to cortex scripts directory
cortexScriptDir = cortexDir + "/scripts"
//---------------------------------------------------------------------------------------------------------------------
//------------------ Sample, Result, and Config Directory ------------------------------------
//---------------------------------------------------------------------------------------------------------------------
//Where samples are located, the fastq file pairs.
sampleDir = ""
//Where the output will be dumped.
resultsDir = ""
//Where logs ware stored, default is in the resultsDir
logDir = resultsDir + "/logs"
//Where this GenomicsCortexVarNextflow folder is located (path/to/GenomicsCortexVarNextflow)
cloneDir = ""
//---------------------------------------------------------------------------------------------------------------------
//------------------ Sample Management ------------------------------------
//---------------------------------------------------------------------------------------------------------------------
//Please write the sample names according to its read files
//Example: if there are 2 samples, Sample_Magellan and Sample_Maverick, it should be written as ["Sample_Magellan", "Sample_Maverick"]
//This means in the sample directory given, there are files with Sample_Magellan.read1.fq and Sample_Magellan.read2.fq, and Sample_Maverick.read1.fq and Sample_Maverick.read2.fq.
sampleList =
//This variable should be filled with how the samples are named. It is the string after the sample name, but before the read number.
//Example: for Sample_Magellan.read2.fq, sampleReadPattern should be ".read" because it is .read2.
//Another Example: Sample_Magellan_read2.fq, sampleReadPattern should be "_read" because it is _read2.
sampleReadPattern = ""
//This variable should be filled with the string after the read number, cortex supports both raw .fq and gzipped .fq.gz
//Example: for Sample_Magellan.read2.fq, the read number is "2", so the sampleReadExtension is ".fq".
sampleReadExtension = ""
//Please provide a path to a text file containing paths of reference reads (such as .fna files) for each chromosome.
//on each separate lines, this is required for making reference graph and to do path divergence variant calling.
//Path Divergence requires one fasta per chromosome, which explains the need of this parameter
pathToReferenceList = ""
//Sorts the sample list given
sampleList.sort()
//---------------------------------------------------------------------------------------------------------------------
//------------------ Executor ------------------------------------
//---------------------------------------------------------------------------------------------------------------------
//Type of executor (Refer to https://www.nextflow.io/docs/latest/executor.html)
executor = ""
//---------------------------------------------------------------------------------------------------------------------
//------------------ Cortex_var Process Parameters ------------------------------------
//---------------------------------------------------------------------------------------------------------------------
//kmer size for the de Bruijn graph
kmerSize = ""
//------------------------------------------
// Make sample de Bruijn graph parameters
//------------------------------------------
//Run make sample de Bruijn Graph? ("y"/"n")
runMakeSampleGraph = ""
//Quality score threshold for making sample de Bruijn Graph
quality_score_threshold =
//Executable (must be compiled/made first, refer to chapter 4 in user manual)
cortexBinMakeGraph = cortexBinDir + "/cortex_var_" + kmerSize + "_c1"
//Cortex Config
makeGraphCortexConfig = "--kmer_size " + kmerSize + " --mem_height --mem_width "
//Queue name in the cluster (if current node, put empty string '', refer to 'https://www.nextflow.io/docs/latest/executor.html')
makeGraphQueue = ""
//Maximum number of nodes to be used in parallel, refer to 'https://www.nextflow.io/docs/latest/process.html?highlight=maxforks#maxforks'
makeGraphMaxNodes =
//Walltime (https://www.nextflow.io/docs/latest/process.html#process-time)
makeGraphWalltime = ""
//Cpus needed (number of cores) (https://www.nextflow.io/docs/latest/process.html#cpus)
makeGraphCpusNeeded = ""
//Error Strategy (https://www.nextflow.io/docs/latest/process.html#errorstrategy)
makeGraphErrorStrategy = ""
//----------------------------------------------
// Make cleaned pooled graph parameters
//----------------------------------------------
//Run make cleaned pooled graph? ("y"/"n")
//Not recommended to run this step if coverage is high, refer to chapter 9.2 in cortex_var user manual
runMakePoolAndCleanError = ""
//Executable (must be compiled/made first, refer to chapter 4 in user manual)
cortexBinPoolAndCleanError = cortexBinDir + "/cortex_var_" + kmerSize + "_c1"
//Cortex Config
poolAndCleanCortexConfig = "--kmer_size " + kmerSize + " --mem_height --mem_width "
//Queue name in the cluster (if current node, put empty string '', refer to 'https://www.nextflow.io/docs/latest/executor.html')
poolAndCleanErrorQueue = ""
//Maximum number of nodes to be used in parallel, refer to 'https://www.nextflow.io/docs/latest/process.html?highlight=maxforks#maxforks'
poolAndCleanErrorMaxNodes =
//Walltime (https://www.nextflow.io/docs/latest/process.html#process-time)
poolAndCleanErrorWalltime = ""
//Cpus needed (number of cores) (https://www.nextflow.io/docs/latest/process.html#cpus)
poolAndCleanErrorCpusNeeded = ""
//Error Strategy (https://www.nextflow.io/docs/latest/process.html#errorstrategy)
poolAndCleanErrorErrorStrategy = ""
//----------------------------------------------
// Clean sample graphs parameters
//----------------------------------------------
//Run clean sample graph? ("y"/"n")
runCleanSampleGraph = ""
//Executable (must be compiled/made first, refer to chapter 4 in user manual)
cortexBinCleanGraphPerSampleHighCoverage = cortexBinDir + "/cortex_var_" + kmerSize + "_c1"
cortexBinCleanGraphPerSampleLowCoverage = cortexBinDir + "/cortex_var_" + kmerSize + "_c2"
//Cortex Config
cleanGraphPerSampleCortexConfig = "--kmer_size " + kmerSize + " --mem_height --mem_width "
//Queue name in the cluster (if current node, put empty string '', refer to 'https://www.nextflow.io/docs/latest/executor.html')
cleanGraphPerSampleQueue = ""
//Maximum number of nodes to be used in parallel, refer to 'https://www.nextflow.io/docs/latest/process.html?highlight=maxforks#maxforks'
cleanGraphPerSampleMaxNodes =
//Walltime (https://www.nextflow.io/docs/latest/process.html#process-time)
cleanGraphPerSampleWalltime = ""
//Cpus needed (number of cores) (https://www.nextflow.io/docs/latest/process.html#cpus)
cleanGraphPerSampleCpusNeeded = ""
//Error Strategy (https://www.nextflow.io/docs/latest/process.html#errorstrategy)
cleanGraphPerSampleErrorStrategy = ""
//----------------------------------------------
// Make reference graph
//----------------------------------------------
//Run make reference graph? ("y"/"n")
runMakeReferenceGraph = ""
//Executable (must be compiled/made first, refer to chapter 4 in user manual)
cortexDirMakeReferenceGraph = cortexBinDir + "/cortex_var_" + kmerSize + "_c1"
//Cortex Config
makeReferenceGraphCortexConfig = "--kmer_size " + kmerSize + " --mem_height --mem_width "
//Queue name in the cluster (if current node, put empty string '', refer to 'https://www.nextflow.io/docs/latest/executor.html')
makeReferenceGraphQueue = ""
//Walltime (https://www.nextflow.io/docs/latest/process.html#process-time)
makeReferenceGraphWalltime = ""
//Cpus needed (number of cores) (https://www.nextflow.io/docs/latest/process.html#cpus)
makeReferenceGraphCpusNeeded = ""
//Error Strategy (https://www.nextflow.io/docs/latest/process.html#errorstrategy)
makeReferenceGraphErrorStrategy = ""
//----------------------------------------------
// Make combination graph
//----------------------------------------------
//Run make combination graph? ("y"/"n")
runMakeCombinationGraph = ""
//Path to reference graph ctx file (default is path to where it would be made by makeReferencegraph)
pathToRefCtx = resultsDir + "/makeReferenceGraphOutput/ref.ctx"
//Please provide the largest number of colors of graph to run when making combination graph here
//This determines the number of color for cortex, being finalCombinationGraphMaxColor + 1
//Example:
//finalCombinationGraphMaxColor = 3 would require the cortex executable to be cortexBinDir + "/cortex_var_" + kmerSize + "c3"
finalCombinationGraphMaxColor =
//Executable (must be compiled/made first, refer to chapter 4 in user manual)
cortexDirMakeCombinationGraph = cortexBinDir + "/cortex_var_" + kmerSize + "_c" + finalCombinationGraphMaxColor
//Cortex Config
makeCombinationGraphCortexConfig = "--kmer_size " + kmerSize + " --mem_height --mem_width "
//Queue name in the cluster (if current node, put empty string '', refer to 'https://www.nextflow.io/docs/latest/executor.html')
makeCombinationGraphQueue = ""
//Maximum number of nodes to be used at once, refer to 'https://www.nextflow.io/docs/latest/process.html?highlight=maxforks#maxforks'
makeCombinationGraphMaxNodes =
//Walltimes (https://www.nextflow.io/docs/latest/process.html#process-time)
makeCombinationGraphWalltime = ""
//Cpus needed (number of cores) (https://www.nextflow.io/docs/latest/process.html#cpus)
makeCombinationGraphCpusNeeded = ""
//Error Strategy (https://www.nextflow.io/docs/latest/process.html#errorstrategy)
makeCombinationGraphErrorStrategy = ""
//----------------------------------------------
// Variant Calling
//----------------------------------------------
//Run Variant Calling? ("y"/"n")
runVariantCalling = ""
//Run Path Divergence? ("y"/"n")
PD = ""
//Path Divergence Only ("y"/"n")
populationPD = ""
individualPD = ""
//Max var length to look for (page 18 in cortex manual
maxVarLength =
//Executable (must be compiled/made first, refer to chapter 4 in user manual)
cortexDirVariantCalling = cortexBinDir + "/cortex_var_" + kmerSize + "_c" + finalCombinationGraphMaxColor
//Cortex Config
variantCallingCortexConfig = "--kmer_size " + kmerSize + " --mem_height --mem_width "
//Queue name in the cluster (if current node, put empty string '', refer to 'https://www.nextflow.io/docs/latest/executor.html')
variantCallingQueue = ""
//Maximum number of nodes to be used at once, refer to 'https://www.nextflow.io/docs/latest/process.html?highlight=maxforks#maxforks'
variantCallingMaxNodes =
//Walltimes (https://www.nextflow.io/docs/latest/process.html#process-time)
variantCallingWalltime = ""
//Cpus needed (number of cores) (https://www.nextflow.io/docs/latest/process.html#cpus)
variantCallingCpusNeeded = ""
//Error Strategy (https://www.nextflow.io/docs/latest/process.html#errorstrategy)
variantCallingErrorStrategy = ""
//----------------------------------------------
// Conversion to VCF
//----------------------------------------------
//Run Conversion to VCF? ("y"/"n")
runConversionToVCF = ""
//Stampy Variables, refer to page 15 of cortex_var manual
stampyBin = ""
stampyHashProducts = ""
//VCFTools Directory
VCFToolsDir = ""
//Sample ploidy
samplePloidy =
//Reference fasta file
referenceFasta = ""
//Queue name in the cluster (if current node, put empty string '', refer to 'https://www.nextflow.io/docs/latest/executor.html'
runConversionToVCFQueue = ""
//Maximum number of nodes to be used at once, refer to 'https://www.nextflow.io/docs/latest/process.html?highlight=maxforks#maxforks'
runConversionToVCFMaxNodes =
//Walltimes (https://www.nextflow.io/docs/latest/process.html#process-time)
runConversionToVCFWalltime = ""
//Cpus needed (number of cores) (https://www.nextflow.io/docs/latest/process.html#cpus)
runConversionToVCFCpusNeeded = ""
}