augur_from_beast_mcc
pipes/WDL/workflows/augur_from_beast_mcc.wdl

WORKFLOW augur_from_beast_mcc

File Path pipes/WDL/workflows/augur_from_beast_mcc.wdl
WDL Version 1.0
Type workflow

Imports

Namespace Path
nextstrain ../tasks/tasks_nextstrain.wdl

Workflow: augur_from_beast_mcc

Visualize BEAST output with Nextstrain. This workflow converts a BEAST MCC tree (.tree file) into an Auspice v2 json file. See https://nextstrain-augur.readthedocs.io/en/stable/faq/import-beast.html for details.

Author: Broad Viral Genomics
viral-ngs@broadinstitute.org

Inputs

Name Type Description Default
beast_mcc_tree File A maximum clade credibility (MCC) tree (.tree file) that is output from a BEAST run. -
auspice_config File A file specifying options to customize the auspice export; see: https://nextstrain.github.io/auspice/customise-client/introduction -
most_recent_tip_date Float? - -
tip_date_regex String? - -
tip_date_format String? - -
tip_date_delimiter String? - -
sample_metadata File? - -
lat_longs_tsv File? - -
colors_tsv File? - -
geo_resolutions Array[String]? - -
color_by_metadata Array[String]? - -
description_md File? - -
maintainers Array[String]? - -
title String? - -
7 optional inputs with default values

Outputs

Name Type Expression
beast_mcc_tree_newick File augur_import_beast.tree_newick
auspice_input_json File export_auspice_json.virus_json

Calls

This workflow calls the following tasks or subworkflows:

CALL TASKS augur_import_beast ↗

Input Mappings (1)
Input Value
beast_mcc_tree beast_mcc_tree

CALL TASKS export_auspice_json ↗

Input Mappings (4)
Input Value
tree augur_import_beast.tree_newick
node_data_jsons [augur_import_beast.node_data_json]
auspice_config auspice_config
include_root_sequence false

Images

Container images used by tasks in this workflow:

🐳 Parameterized Image
⚙️ Parameterized

Configured via input:
docker

Used by 2 tasks:
  • augur_import_beast
  • export_auspice_json
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augur_from_beast_mcc - Workflow Graph

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augur_from_beast_mcc - WDL Source Code

version 1.0

import "../tasks/tasks_nextstrain.wdl" as nextstrain

workflow augur_from_beast_mcc {
    meta {
        description: "Visualize BEAST output with Nextstrain. This workflow converts a BEAST MCC tree (.tree file) into an Auspice v2 json file. See https://nextstrain-augur.readthedocs.io/en/stable/faq/import-beast.html for details."
        author: "Broad Viral Genomics"
        email:  "viral-ngs@broadinstitute.org"
    }

    input {
        File beast_mcc_tree
        File auspice_config
    }

    parameter_meta {
        beast_mcc_tree: {
          description: "A maximum clade credibility (MCC) tree (.tree file) that is output from a BEAST run.",
          patterns: ["*.tree"]
        }
        auspice_config: {
          description: "A file specifying options to customize the auspice export; see: https://nextstrain.github.io/auspice/customise-client/introduction",
          patterns: ["*.json", "*.txt"]
        }
    }

    call nextstrain.augur_import_beast {
        input:
            beast_mcc_tree = beast_mcc_tree
    }
    call nextstrain.export_auspice_json {
        input:
            tree                  = augur_import_beast.tree_newick,
            node_data_jsons       = [augur_import_beast.node_data_json],
            auspice_config        = auspice_config,
            include_root_sequence = false
    }

    output {
        File beast_mcc_tree_newick = augur_import_beast.tree_newick
        File auspice_input_json    = export_auspice_json.virus_json
    }
}