update_data_tables

WORKFLOW update_data_tables

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

Imports

Namespace	Path
`terra`	`../tasks/tasks_terra.wdl`

Workflow: update_data_tables

Create data tables in Terra workspace from provided tsv load file.

Author: Broad Viral Genomics

viral-ngs@broadinstitute.org

Inputs

Name	Type	Description	Default
`workspace_name`	`String`	-	-
`terra_project`	`String`	-	-
`tsv_file`	`File`	-	-
`cleaned_reads_unaligned_bams_string`	`Array[String]`	-	-
`meta_by_filename_json`	`File`	-	-
1 optional input with default value
`docker`	`String`	-	"schaluvadi/pathogen-genomic-surveillance:api-wdl"

Outputs

Name	Type	Expression
`tables`	`Array[String]`	`upload_reads_assemblies_entities_tsv.tables`

Calls

This workflow calls the following tasks or subworkflows:

CALL TASKS `upload_reads_assemblies_entities_tsv` ↗

No explicit input mappings

Images

Container images used by tasks in this workflow:

🐳 Parameterized Image

⚙️ Parameterized

Configured via input:
docker

Used by 1 task:

upload_reads_assemblies_entities_tsv

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flowchart TD
    Start([update_data_tables])
    N1["upload_reads_assemblies_entities_tsv"]
    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

#DX_SKIP_WORKFLOW

import "../tasks/tasks_terra.wdl" as terra

workflow update_data_tables {
    meta {
        description: "Create data tables in Terra workspace from provided tsv load file."
        author: "Broad Viral Genomics"
        email:  "viral-ngs@broadinstitute.org"
    }

    call terra.upload_reads_assemblies_entities_tsv

    output {
        Array[String] tables = upload_reads_assemblies_entities_tsv.tables
    }
}