CreateEntericsQCVizGeneral
pipes/WDL/workflows/create_enterics_qc_viz_general.wdl

WORKFLOW CreateEntericsQCVizGeneral

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

📋Tasks in this document

Workflow: CreateEntericsQCVizGeneral

Inputs

Name Type Description Default
sample_ids Array[String] selected rows of data from data table which will be used for plotting -
input_table_name String name of the Terra data table - root entity type - from where input data is selected -
workspace_name String name of Terra workspace where data lives -
workspace_project String name of Terra project associated with Terra workspace -
grouping_column_name String? name of column to be used for grouping/coloring - ex. gambit_predicted_taxon (organism) -
output_filename String? name of output file containing visualizations -
1 optional input with default value

Outputs

Name Type Expression
viz_pdf File create_viz.vizualizations

Calls

This workflow calls the following tasks or subworkflows:

CALL TASKS create_viz

Input Mappings (6)
Input Value
sample_ids sample_ids
workspace_name workspace_name
workspace_project workspace_project
input_table_name input_table_name
grouping_column_name grouping_column_name
output_filename output_filename

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] - -
workspace_name String - -
workspace_project String - -
input_table_name String - -
3 optional inputs with default values

Command

python3 /scripts/general_create_visualizations.py -s ~{sep=" " sample_ids} \
                                          -t ~{input_table_name} \
                                          -w ~{workspace_name} \
                                          -p ~{workspace_project} \
                                          ~{"-g" + grouping_column_name} \
                                          ~{"-o" + output_filename}

Outputs

Name Type Expression
vizualizations File "~{output_filename}"

Runtime

Key Value
docker docker
← Back to Index

CreateEntericsQCVizGeneral - Workflow Graph

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

CreateEntericsQCVizGeneral - WDL Source Code

version 1.0

workflow CreateEntericsQCVizGeneral {

    parameter_meta {
        sample_ids: {description: "selected rows of data from data table which will be used for plotting"}
        input_table_name: {description: "name of the Terra data table - root entity type - from where input data is selected"}
        workspace_name: {description: "name of Terra workspace where data lives"}
        workspace_project: {description: "name of Terra project associated with Terra workspace"}
        grouping_column_name: {description: "name of column to be used for grouping/coloring - ex. gambit_predicted_taxon (organism)"}
        output_filename: {description: "name of output file containing visualizations"}
    }

    input {

        Array[String]   sample_ids
        String          input_table_name
        String          workspace_name
        String          workspace_project

        String?         grouping_column_name
        String?         output_filename
    }

    call create_viz {
        input:
            sample_ids              =   sample_ids,
            workspace_name          =   workspace_name,
            workspace_project       =   workspace_project,
            input_table_name        =   input_table_name,
            grouping_column_name    =   grouping_column_name,
            output_filename         =   output_filename
    }

    output {
        File    viz_pdf     =   create_viz.vizualizations
    }
}

task create_viz {
    input {
        Array[String]   sample_ids
        String          workspace_name
        String          workspace_project
        String          input_table_name

        String          grouping_column_name    = "gambit_predicted_taxon"
        String          output_filename         = "QC_vizualizations.pdf"

        String  docker                          =   "broadinstitute/horsefish:pgs_visualizations"        
    }

    command {
        python3 /scripts/general_create_visualizations.py -s ~{sep=' ' sample_ids} \
                                                  -t ~{input_table_name} \
                                                  -w ~{workspace_name} \
                                                  -p ~{workspace_project} \
                                                  ~{"-g" + grouping_column_name} \
                                                  ~{"-o" + output_filename}
    }

    runtime {
        docker: docker
    }

    output {
        File vizualizations = "~{output_filename}"
    }
}