augur_export_only - WDL Atlas

WORKFLOW augur_export_only

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

Imports

Namespace	Path
`nextstrain`	`../tasks/tasks_nextstrain.wdl`

Workflow: augur_export_only

Convert a newick formatted phylogenetic tree with other config settings and node values into a json suitable for auspice visualization. See https://nextstrain-augur.readthedocs.io/en/stable/usage/cli/export.html

Author: Broad Viral Genomics

viral-ngs@broadinstitute.org

Inputs

Name	Type	Description	Default
`auspice_config`	`File`	-	-
`sample_metadata`	`File?`	-	-
`tree`	`File`	-	-
`node_data_jsons`	`Array[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?`	-	-
5 optional inputs with default values
`include_root_sequence`	`Boolean`	-	true
`out_basename`	`String`	-	basename(basename(tree,".nwk"),"_timetree")
`machine_mem_gb`	`Int`	-	64
`docker`	`String`	-	"docker.io/nextstrain/base:build-20240318T173028Z"
`disk_size`	`Int`	-	300

Outputs

Name	Type	Expression
`auspice_json`	`File`	`export_auspice_json.virus_json`
`root_sequence_json`	`File`	`export_auspice_json.root_sequence_json`

Calls

This workflow calls the following tasks or subworkflows:

CALL TASKS `export_auspice_json` ↗

No explicit input mappings

Images

Container images used by tasks in this workflow:

🐳 Parameterized Image

⚙️ Parameterized

Configured via input:
docker

Used by 1 task:

export_auspice_json

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flowchart TD
    Start([augur_export_only])
    N1["export_auspice_json"]
    Start --> N1
    N1 --> End([End])
    classDef taskNode fill:#a371f7,stroke:#8b5cf6,stroke-width:2px,color:#fff
    classDef workflowNode fill:#58a6ff,stroke:#1f6feb,stroke-width:2px,color:#fff

version 1.0

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

workflow augur_export_only {
    meta {
        description: "Convert a newick formatted phylogenetic tree with other config settings and node values into a json suitable for auspice visualization. See https://nextstrain-augur.readthedocs.io/en/stable/usage/cli/export.html"
        author: "Broad Viral Genomics"
        email:  "viral-ngs@broadinstitute.org"
    }

    call nextstrain.export_auspice_json
    output {
        File auspice_json       = export_auspice_json.virus_json
        File root_sequence_json = export_auspice_json.root_sequence_json
    }
}