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CellRangerVdj.wdl
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CellRangerVdj.wdl
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version 1.0
import "modules/Vdj.wdl" as Vdj
workflow CellRangerVdj {
input {
String sampleName
String fastqNames
Array[File] inputFastq
String referenceGenome
String chain = "auto"
# docker-related
String dockerRegistry
}
call Vdj.Vdj {
input:
sampleName = sampleName,
fastqNames = fastqNames,
inputFastq = inputFastq,
referenceGenome = referenceGenome,
chain = chain,
dockerRegistry = dockerRegistry
}
output {
Array[File] annotationFiles = Vdj.annotationFiles
Array[File] fastaFiles = Vdj.fastaFiles
Array[File] fastqFiles = Vdj.fastqFiles
Array[File] bamFiles = Vdj.bamFiles
File cellBarcodes = Vdj.cellBarcodes
File vloupe = Vdj.vloupe
File webSummary = Vdj.webSummary
File metricsSummary = Vdj.metricsSummary
File clonotypes = Vdj.clonotypes
File airr = Vdj.airr
File allContigProtoBuf = Vdj.allContigProtoBuf
File vdjReference = Vdj.vdjReference
File pipestanceMeta = Vdj.pipestanceMeta
}
}