sarscov2_nextclade_multi

WORKFLOW sarscov2_nextclade_multi

File Path	`pipes/WDL/workflows/sarscov2_nextclade_multi.wdl`
WDL Version	1.0
Type	workflow

Imports

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

Workflow: sarscov2_nextclade_multi

Create Nextclade visualizations on many SARS-CoV-2 genomes

Inputs

Name	Type	Description	Default
`genome_fastas`	`Array[File]+`	-	-
`root_sequence`	`File?`	-	-
`auspice_reference_tree_json`	`File?`	-	-
`pathogen_json`	`File?`	-	-
`gene_annotations_json`	`File?`	-	-
`basename`	`String`	-	-
`genome_ids_setdefault_blank`	`File?`	-	-
2 optional inputs with default values
`disk_size`	`Int`	-	150
`docker`	`String`	-	"nextstrain/nextclade:3.18.0"

Outputs

Name	Type	Expression
`nextclade_tsv`	`File`	`nextclade_many_samples.nextclade_tsv`
`nextclade_json`	`File`	`nextclade_many_samples.nextclade_json`
`auspice_json`	`File`	`nextclade_many_samples.auspice_json`

Calls

This workflow calls the following tasks or subworkflows:

CALL TASKS `nextclade_many_samples` ↗

Input Mappings (2)

Input	Value
`genome_fastas`	`genome_fastas`
`dataset_name`	`"sars-cov-2"`

Images

Container images used by tasks in this workflow:

🐳 Parameterized Image

⚙️ Parameterized

Configured via input:
docker

Used by 1 task:

nextclade_many_samples

← Back to Index

flowchart TD
    Start([sarscov2_nextclade_multi])
    N1["nextclade_many_samples"]
    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 sarscov2_nextclade_multi {
    meta {
        description: "Create Nextclade visualizations on many SARS-CoV-2 genomes"
    }

    input {
        Array[File]+ genome_fastas
    }

    call nextstrain.nextclade_many_samples {
        input:
            genome_fastas = genome_fastas,
            dataset_name  = "sars-cov-2"
    }

    output {
        File nextclade_tsv  = nextclade_many_samples.nextclade_tsv
        File nextclade_json = nextclade_many_samples.nextclade_json
        File auspice_json   = nextclade_many_samples.auspice_json
    }
}