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library.wdl
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library.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 "readgroup.wdl" as readgroupWorkflow
import "tasks/biopet/biopet.wdl" as biopet
import "tasks/common.wdl" as common
import "structs.wdl" as structs
workflow Library {
input {
Sample sample
Library library
String libraryDir
GamsInputs gamsInputs
}
scatter (rg in library.readgroups) {
call readgroupWorkflow.Readgroup as readgroup {
input:
readgroupDir = libraryDir + "/rg_" + rg.id,
readgroup = rg,
library = library,
sample = sample,
gamsInputs = gamsInputs
}
}
output {
Array[File] libExtendedFrags = select_all(readgroup.extendedFrags)
Array[FastqPair] libNotCombined = select_all(readgroup.notCombined)
Array[FastqPair]+ libCleanReads = readgroup.cleanReads
}
}