fetch_annotations - WDL Atlas

WORKFLOW fetch_annotations

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

Imports

Namespace	Path
`ncbi`	`../tasks/tasks_ncbi.wdl`

Workflow: fetch_annotations

Inputs

Name	Type	Description	Default
`accessions`	`Array[String]+`	-	-
`emailAddress`	`String`	-	-
`combined_out_prefix`	`String`	-	-
1 optional input with default value
`docker`	`String`	-	"quay.io/broadinstitute/viral-phylo:2.5.1.0"

Outputs

Name	Type	Expression
`combined_fasta`	`File`	`download_annotations.combined_fasta`
`genomes_fasta`	`Array[File]`	`download_annotations.genomes_fasta`
`features_tbl`	`Array[File]`	`download_annotations.features_tbl`
`viral_phylo_version`	`String`	`download_annotations.viralngs_version`

Calls

This workflow calls the following tasks or subworkflows:

CALL TASKS `download_annotations` ↗

No explicit input mappings

Images

Container images used by tasks in this workflow:

🐳 Parameterized Image

⚙️ Parameterized

Configured via input:
docker

Used by 1 task:

download_annotations

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flowchart TD
    Start([fetch_annotations])
    N1["download_annotations"]
    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_ncbi.wdl" as ncbi

workflow fetch_annotations {
    call ncbi.download_annotations
    output {
        File        combined_fasta      = download_annotations.combined_fasta
        Array[File] genomes_fasta       = download_annotations.genomes_fasta
        Array[File] features_tbl        = download_annotations.features_tbl
        String      viral_phylo_version = download_annotations.viralngs_version
    }
}