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wf_usher.wdl
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wf_usher.wdl
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version 1.0
import "../../tasks/phylogenetic_inference/task_usher.wdl" as usher_task
import "../../tasks/task_versioning.wdl" as versioning
workflow usher_workflow {
meta {
description: "Place samples onto global tree"
}
input {
Array[File] assembly_fasta
String tree_name
String organism # currently available: "sars-cov-2", "mpox", "RSV-A", "RSV-B"
}
call usher_task.usher {
input:
assembly_fasta = assembly_fasta,
tree_name = tree_name,
organism = organism
}
call versioning.version_capture {
}
output {
File usher_uncondensed_tree = usher.usher_uncondensed_tree
File usher_clades = usher.usher_clades
Array[File] usher_subtrees = usher.usher_subtrees
Array[File] usher_subtree_mutations = usher.usher_subtree_mutations
String usher_version = usher.usher_version
String usher_protobuf_version = usher.usher_protobuf_version
String usher_phb_version = version_capture.phb_version
String usher_phb_analysis_date = version_capture.date
}
}