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readgroup.wdl
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readgroup.wdl
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version 1.0
# Copyright (c) 2018 Sequencing Analysis Support Core - Leiden University Medical Center
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
# The above copyright notice and this permission notice shall be included in all
# copies or substantial portions of the Software.
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
import "tasks/biopet/biopet.wdl" as biopet
import "QC/QC.wdl" as qcWorkflow
import "tasks/fastqc.wdl" as fastqc
import "tasks/flash.wdl" as flash
import "tasks/common.wdl" as common
import "structs.wdl" as structs
workflow Readgroup {
input {
Readgroup readgroup
Library library
Sample sample
String readgroupDir
GamsInputs gamsInputs
}
# FIXME: workaround for namepace issue in cromwell
String sampleId = sample.id
String libraryId = library.id
String readgroupId = readgroup.id
call qcWorkflow.QC as qc {
input:
outputDir = readgroupDir,
reads = readgroup.reads,
sample = sampleId,
library = libraryId,
readgroup = readgroupId
}
if (select_first([gamsInputs.combineReads, false])) {
call flash.Flash as flash {
input:
inputFastq = qc.readsAfterQC,
outdirPath = readgroupDir + "/flash"
}
}
output {
File? extendedFrags = flash.extendedFrags
FastqPair? notCombined = flash.notCombined
FastqPair cleanReads = qc.readsAfterQC
}
}