CreateEntericsQCViz
pipes/WDL/workflows/create_enterics_qc_viz.wdl

WORKFLOW CreateEntericsQCViz

File Path pipes/WDL/workflows/create_enterics_qc_viz.wdl
WDL Version 1.0
Type mixed

📋Tasks in this document

Workflow: CreateEntericsQCViz

Inputs

Name Type Description Default
sample_ids Array[String] - -
gambit_predicted_taxon Array[String] - -
est_coverage_clean Array[String] - -
number_contigs Array[String] - -
assembly_length Array[String] - -
thresholds_file File? - -
2 optional inputs with default values

Outputs

Name Type Expression
visualization_html File create_viz.html

Calls

This workflow calls the following tasks or subworkflows:

CALL TASKS create_viz

No explicit input mappings

Images

Container images used by tasks in this workflow:

🐳 Parameterized Image
⚙️ Parameterized

Configured via input:
docker

Used by 1 task:
  • create_viz

Tasks

TASKS create_viz

Inputs

Name Type Description Default
sample_ids Array[String] selected samples of data -
gambit_predicted_taxon Array[String] predicted gambits for selected samples -
est_coverage_clean Array[String] estimated coverage metrics for selected samples -
number_contigs Array[String] number contigs metrics for selected samples -
assembly_length Array[String] assembly length metrics for selected samples -
thresholds_file File? JSON file containing custom thresholds -
2 optional inputs with default values

Command

python3 /scripts/create_enterics_visualizations_html.py -s "~{sep="" "" sample_ids}" \
                                                        -g "~{sep="" "" gambit_predicted_taxon}" \
                                                        -ecc ~{sep=" " est_coverage_clean} \
                                                        -nc ~{sep=" " number_contigs} \
                                                        -al ~{sep=" " assembly_length} \
                                                        ~{'-o "' + output_filename + '"'} \
                                                        ~{'-t "' + thresholds_file + '"'}

Outputs

Name Type Expression
html File output_filename

Runtime

Key Value
docker docker
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CreateEntericsQCViz - WDL Source Code

version 1.0

workflow CreateEntericsQCViz {

    meta {
        allowNestedInputs: true
    }

    call create_viz {
    }

    output {
        File    visualization_html     =   create_viz.html
    }
}

task create_viz {

    input {
        Array[String]   sample_ids
        Array[String]   gambit_predicted_taxon
        Array[String]   est_coverage_clean
        Array[String]   number_contigs
        Array[String]   assembly_length

        File?           thresholds_file

        String          output_filename                  =   "QC_visualizations.html"

        String          docker                           =   "us-central1-docker.pkg.dev/pgs-automation/enterics-visualizations/create_visualization_html:v6"       
    }

    parameter_meta {
        sample_ids: {description: "selected samples of data"}
        gambit_predicted_taxon: {description: "predicted gambits for selected samples"}
        est_coverage_clean: {description: "estimated coverage metrics for selected samples"}
        number_contigs: {description: "number contigs metrics for selected samples"}
        assembly_length: {description: "assembly length metrics for selected samples"}
        output_filename: {description: "name of output file containing visualizations"}
        thresholds_file: {description: "JSON file containing custom thresholds"}
    }

    command {
        python3 /scripts/create_enterics_visualizations_html.py -s "~{sep='" "' sample_ids}" \
                                                                -g "~{sep='" "' gambit_predicted_taxon}" \
                                                                -ecc ~{sep=' ' est_coverage_clean} \
                                                                -nc ~{sep=' ' number_contigs} \
                                                                -al ~{sep=' ' assembly_length} \
                                                                ~{'-o "' + output_filename + '"'} \
                                                                ~{'-t "' + thresholds_file + '"'}
    }

    runtime {
        docker: docker
    }

    output {
        File html = output_filename
    }
}