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pipeline.wdl
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pipeline.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 "sample.wdl" as sampleWorkflow
import "tasks/biopet/sampleconfig.wdl" as sampleconfig
import "structs.wdl" as structs
workflow pipeline {
input {
Array[File] sampleConfigFiles
String outputDir
VirusAssemblyInputs virusAssemblyInputs
}
call sampleconfig.SampleConfigCromwellArrays as configFile {
input:
inputFiles = sampleConfigFiles,
outputPath = "samples.json"
}
Root config = read_json(configFile.outputFile)
# Running sample subworkflow
scatter (sm in config.samples) {
call sampleWorkflow.Sample as sample {
input:
sampleDir = outputDir + "/samples/" + sm.id,
sample = sm,
virusAssemblyInputs = virusAssemblyInputs
}
}
# Put the jobs that need to be done over the result of all samples
# below this line.
output {
}
}