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modelWorkflow.wdl
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modelWorkflow.wdl
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version 1.0
task run_Model {
input {
File setup_os_script
File clone_repository_script
File copy_cromwell_logs_script
File copy_model_output_script
String model_git_repository
File install_model_script
String name_of_this_model_run
File model_configuration_yml
String model_executable
File run_model_script
String model_input_folder
String model_output_folder
String model_output_file_types
String model_runtime_docker
}
String model_output_file_listing = "model_output_files.txt"
command {
${setup_os_script}
${clone_repository_script} "${model_git_repository}"
${install_model_script} "${model_input_folder}"
${run_model_script} "${model_executable}" "${model_configuration_yml}"
python3 ${copy_model_output_script} "${model_output_folder}" "${model_output_file_types}" "${model_output_file_listing}" "${name_of_this_model_run}"
${copy_cromwell_logs_script} "${model_output_folder}" "${name_of_this_model_run}"
}
runtime {
docker: "${model_runtime_docker}"
}
output {
Array[File] output_files = read_lines(model_output_file_listing)
}
}
workflow modelWorkflow {
input {
File setup_os_script
File clone_repository_script
File copy_cromwell_logs_script
File copy_model_output_script
}
call run_Model {
input:
setup_os_script = setup_os_script,
clone_repository_script = clone_repository_script,
copy_cromwell_logs_script = copy_cromwell_logs_script,
copy_model_output_script = copy_model_output_script
}
}