inputBamsIndex: {description: "The indexes of the input BAM files.", category: "required"}
outputBamPath: {description: "The path where the merged BAM file will be written.", caregory: "required"}
createMd5File: {decription: "Whether to create an md5 file of the output BAM.", category: "advanced"}
compressionLevel: {description: "The compression level of the output BAM.", category: "advanced"}
compressionLevel: {description: "The compression level at which the BAM files are written.", category: "advanced"}
useJdkInflater: {description: "True, uses the java inflater. False, uses the optimized intel inflater.", category: "advanced"}
useJdkDeflater: {description: "True, uses the java deflator to compress the BAM files. False uses the optimized intel deflater.", category: "advanced"}
javaXmxMb: {description: "The maximum memory available to the program in megabytes. Should be lower than `memoryMb` to accommodate JVM overhead.", category: "advanced"}
memoryMb: {description: "The amount of memory this job will use in megabytes.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
...
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@@ -555,10 +561,14 @@ task GatherVcfs {
Array[File]+ inputVcfIndexes
String outputVcfPath = "out.vcf.gz"
Int compressionLevel = 1
Boolean useJdkInflater = false
Boolean useJdkDeflater = true # Achieves much better compression rates than the intel deflater
String javaXmx = "4G"
String memory = "5G"
Int timeMinutes = 1 + ceil(size(inputVcfs, "G") * 2)
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
compressionLevel: {description: "The compression level at which the BAM files are written.", category: "advanced"}
useJdkInflater: {description: "True, uses the java inflater. False, uses the optimized intel inflater.", category: "advanced"}
useJdkDeflater: {description: "True, uses the java deflator to compress the BAM files. False uses the optimized intel deflater.", category: "advanced"}
# outputs
outputVcf: {description: "Multiple VCF files gathered into one file."}
}
...
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@@ -601,14 +619,11 @@ task MarkDuplicates {
Array[File]+ inputBams
String outputBamPath
String metricsPath
Int compressionLevel = 1
Boolean createMd5File = false
Boolean useJdkInflater = true # Slightly faster than the intel one.
# Better results for compression level 1 (much smaller).
# Higher compression levels similar to intel deflater.
# NOTE: this might change in the future when the intel
# deflater is updated!
Boolean useJdkDeflater = true
Int compressionLevel = 1
Boolean useJdkInflater = false
Boolean useJdkDeflater = true # Achieves much better compression rates than the intel deflater
# The program default for READ_NAME_REGEX is appropriate in nearly every case.
# Sometimes we wish to supply "null" in order to turn off optical duplicate detection.
...
...
@@ -622,7 +637,7 @@ task MarkDuplicates {
String memoryMb = javaXmxMb + 512
Int timeMinutes = 1 + ceil(size(inputBams, "G") * 8)
outputBamPath: {description: "The location where the ouptut BAM file should be written.", category: "required"}
metricsPath: {description: "The location where the output metrics file should be written.", category: "required"}
compressionLevel: {description: "The compression level at which the BAM files are written.", category: "advanced"}
createMd5File: {description: "Whether to create a md5 file for the created BAM file.", category: "advanced"}
useJdkInflater: {description: "True, uses the java inflater. False, uses the optimized intel inflater.", category: "advanced"}
useJdkDeflater: {description: "True, uses the java deflator to compress the BAM files. False uses the optimized intel deflater.", category: "advanced"}
createMd5File: {description: "Whether to create a md5 file for the created BAM file.", category: "advanced"}
read_name_regex: {description: "Equivalent to the `READ_NAME_REGEX` option of MarkDuplicates.", category: "advanced"}
javaXmxMb: {description: "The maximum memory available to the program in megabytes. Should be lower than `memoryMb` to accommodate JVM overhead.", category: "advanced"}
memoryMb: {description: "The amount of memory this job will use in megabytes.", category: "advanced"}
...
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@@ -692,16 +709,20 @@ task MergeVCFs {
Array[File]+ inputVCFsIndexes
String outputVcfPath
Int compressionLevel = 1
Boolean useJdkInflater = true # Slightly faster than the intel one.
Boolean useJdkInflater = false
# Better results for compression level 1 (much smaller).
# Higher compression levels similar to intel deflater.
# NOTE: this might change in the future when the intel deflater is updated!
Boolean useJdkDeflater = true
# Second NOTE: No it did not change. Only the fastest algorithm with
# worse compression is wrapped in the intel GKL. Instead of using
# one of the slightly slower but better compressing alternatives from ISA-L.
# (Which are also faster than zlib.)
Boolean useJdkDeflater = true # Achieves much better compression rates than the intel deflater
String javaXmx = "4G"
String memory = "5G"
Int timeMinutes = 1 + ceil(size(inputVCFs, "G")) * 2
sortByName: {description: "Sort the output file by name, default is position.", category: "advanced"}
createMd5File: {description: "Whether to create an MD5 digest for any BAM or FASTQ files created.", category: "advanced"}
maxRecordsInRam: {description: "This will specify the number of records stored in RAM before spilling to disk.", category: "advanced"}
compressionLevel: {description: "Compression level for all compressed files created.", category: "advanced"}
compressionLevel: {description: "The compression level at which the BAM files are written.", category: "advanced"}
useJdkInflater: {description: "True, uses the java inflater. False, uses the optimized intel inflater.", category: "advanced"}
useJdkDeflater: {description: "True, uses the java deflator to compress the BAM files. False uses the optimized intel deflater.", category: "advanced"}
XmxGb: {description: "The maximum memory available to picard SortSam. Should be lower than `memory` to accommodate JVM overhead and BWA mem's memory usage.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
...
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@@ -917,7 +944,7 @@ task SortVcf {
String javaXmx = "8G"
String memory = "9G"
Int timeMinutes = 1 + ceil(size(vcfFiles, "G") * 5)
compressionLevel: {description: "The compression level at which the BAM files are written.", category: "advanced"}
useJdkInflater: {description: "True, uses the java inflater. False, uses the optimized intel inflater.", category: "advanced"}
useJdkDeflater: {description: "True, uses the java deflator to compress the BAM files. False uses the optimized intel deflater.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
