sarscov2_lineages
pipes/WDL/workflows/sarscov2_lineages.wdl

WORKFLOW sarscov2_lineages

File Path pipes/WDL/workflows/sarscov2_lineages.wdl
WDL Version 1.0
Type workflow

Imports

Namespace Path
nextstrain ../tasks/tasks_nextstrain.wdl
sarscov2 ../tasks/tasks_sarscov2.wdl

Workflow: sarscov2_lineages

Call Nextclade and Pangolin lineages on a single SARS-CoV-2 genome

Subworkflow Usage

This workflow is called as a subworkflow by 1 other workflow:

Inputs

Name Type Description Default
genome_fasta File - -
root_sequence File? - -
auspice_reference_tree_json File? - -
pathogen_json File? - -
gene_annotations_json File? - -
min_length Int? - -
max_ambig Float? - -
analysis_mode String? - -
4 optional inputs with default values

Outputs

Name Type Expression
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_version String nextclade_one_sample.nextclade_version
pango_lineage String pangolin_one_sample.pango_lineage
pangolin_conflicts String pangolin_one_sample.pangolin_conflicts
pangolin_notes String pangolin_one_sample.pangolin_notes
scorpio_call String pangolin_one_sample.scorpio_call
scorpio_notes String pangolin_one_sample.scorpio_notes
pango_lineage_report File pangolin_one_sample.pango_lineage_report
pangolin_docker String pangolin_one_sample.pangolin_docker
pangolin_versions String pangolin_one_sample.pangolin_versions

Calls

This workflow calls the following tasks or subworkflows:

CALL TASKS nextclade_one_sample ↗

Input Mappings (2)
Input Value
genome_fasta genome_fasta
dataset_name "sars-cov-2"

CALL TASKS pangolin_one_sample ↗

Input Mappings (1)
Input Value
genome_fasta genome_fasta

Images

Container images used by tasks in this workflow:

🐳 Parameterized Image
⚙️ Parameterized

Configured via input:
docker

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

Configured via input:
docker

Used by 1 task:
  • pangolin_one_sample
← Back to Index

sarscov2_lineages - Workflow Graph

🖱️ Scroll to zoom • Drag to pan • Double-click to reset • ESC to close

sarscov2_lineages - WDL Source Code

version 1.0

import "../tasks/tasks_nextstrain.wdl" as nextstrain
import "../tasks/tasks_sarscov2.wdl" as sarscov2

workflow sarscov2_lineages {
    meta {
        description: "Call Nextclade and Pangolin lineages on a single SARS-CoV-2 genome"
    }

    input {
        File genome_fasta
    }

    call nextstrain.nextclade_one_sample {
        input:
            genome_fasta = genome_fasta,
            dataset_name  = "sars-cov-2"
    }

    call sarscov2.pangolin_one_sample {
        input:
            genome_fasta = genome_fasta
    }

    output {
        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_version  = nextclade_one_sample.nextclade_version
        String pango_lineage      = pangolin_one_sample.pango_lineage
        String pangolin_conflicts = pangolin_one_sample.pangolin_conflicts
        String pangolin_notes     = pangolin_one_sample.pangolin_notes
        String scorpio_call       = pangolin_one_sample.scorpio_call
        String scorpio_notes      = pangolin_one_sample.scorpio_notes
        File   pango_lineage_report = pangolin_one_sample.pango_lineage_report
        String pangolin_docker    = pangolin_one_sample.pangolin_docker
        String pangolin_versions  = pangolin_one_sample.pangolin_versions
    }
}