nextclade_single
pipes/WDL/workflows/nextclade_single.wdl

WORKFLOW nextclade_single

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

Imports

Namespace Path
nextstrain ../tasks/tasks_nextstrain.wdl

Workflow: nextclade_single

Run Nextclade on a single genome

Inputs

Name Type Description Default
taxid Int - -
taxdump_tgz File - -
nextclade_by_taxid_tsv File - -
genome_fasta File - -
root_sequence File? - -
auspice_reference_tree_json File? - -
pathogen_json File? - -
gene_annotations_json File? - -
3 optional inputs with default values

Outputs

Name Type Expression
nextclade_dataset String? dataset
nextclade_clade String? nextclade_one_sample.nextclade_clade
nextclade_tsv File? nextclade_one_sample.nextclade_tsv
nextclade_json File? nextclade_one_sample.nextclade_json
nextclade_aa_subs String? nextclade_one_sample.aa_subs_csv
nextclade_aa_dels String? nextclade_one_sample.aa_dels_csv
nextclade_shortclade String? nextclade_one_sample.nextclade_shortclade
nextclade_subclade String? nextclade_one_sample.nextclade_subclade
nextclade_pango String? nextclade_one_sample.nextclade_pango
nextclade_version String? nextclade_one_sample.nextclade_version

Calls

This workflow calls the following tasks or subworkflows:

CALL TASKS taxid_to_nextclade_dataset_name ↗

No explicit input mappings

CALL TASKS nextclade_one_sample ↗

Input Mappings (1)
Input Value
dataset_name dataset

Images

Container images used by tasks in this workflow:

🐳 Parameterized Image
⚙️ Parameterized

Configured via input:
docker

Used by 1 task:
  • taxid_to_nextclade_dataset_name
🐳 Parameterized Image
⚙️ Parameterized

Configured via input:
docker

Used by 1 task:
  • nextclade_one_sample
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nextclade_single - Workflow Graph

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nextclade_single - WDL Source Code

version 1.0

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

workflow nextclade_single {
    meta {
        description: "Run Nextclade on a single genome"
    }

    call nextstrain.taxid_to_nextclade_dataset_name

    if (defined(taxid_to_nextclade_dataset_name.nextclade_dataset_name) 
        && taxid_to_nextclade_dataset_name.nextclade_dataset_name != "") {

        String dataset = taxid_to_nextclade_dataset_name.nextclade_dataset_name

        call nextstrain.nextclade_one_sample {
            input:
                dataset_name = dataset
        }
    }

    output {
        String? nextclade_dataset  = dataset
        String? nextclade_clade    = nextclade_one_sample.nextclade_clade
        File?   nextclade_tsv      = nextclade_one_sample.nextclade_tsv
        File?   nextclade_json     = nextclade_one_sample.nextclade_json
        String? nextclade_aa_subs  = nextclade_one_sample.aa_subs_csv
        String? nextclade_aa_dels  = nextclade_one_sample.aa_dels_csv
        String? nextclade_shortclade = nextclade_one_sample.nextclade_shortclade
        String? nextclade_subclade = nextclade_one_sample.nextclade_subclade
        String? nextclade_pango    = nextclade_one_sample.nextclade_pango
        String? nextclade_version  = nextclade_one_sample.nextclade_version
    }
}