pipeline.wdl

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
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# SOFTWARE.

import "tasks/common.wdl" as common
import "sample.wdl" as sampleWorkflow
import "structs.wdl" as structs

workflow pipeline {
    input {
        File sampleConfigFile
        Array[Sample] samples = []
        String outputDir = "."

        File dockerImagesFile
    }

    call common.YamlToJson {
        input:
            yaml = sampleConfigFile
    }
    SampleConfig sampleConfig = read_json(YamlToJson.json)

    # Do the jobs that should be executed per sample.
    # Modify sample.wdl to change what is happening per sample
    scatter (sample in sampleConfig.samples) {
        call sampleWorkflow.sample as sampleWorkflow {
            input:
                sample = sample,
                outputDir = outputDir + "/samples/" + sample.id
        }
    }

    # Put the jobs that need to be done over the result of all samples
    # below this line.

    output {
        # REPLACE THESE WITH REAL OUTPUTS
        Array[File] out = flatten(sampleWorkflow.out)
    }
}