diff --git a/pipes/WDL/workflows/create_enterics_qc_viz.wdl b/pipes/WDL/workflows/create_enterics_qc_viz.wdl index df9960af7..516ecf20b 100644 --- a/pipes/WDL/workflows/create_enterics_qc_viz.wdl +++ b/pipes/WDL/workflows/create_enterics_qc_viz.wdl @@ -1,18 +1,12 @@ version 1.0 -import "../tasks/tasks_terra.wdl" as terra - workflow CreateEntericsQCViz { meta { allowNestedInputs: true } - call terra.check_terra_env call create_viz { - input: - workspace_name = check_terra_env.workspace_name, - workspace_project = check_terra_env.workspace_namespace } output { @@ -21,36 +15,37 @@ workflow CreateEntericsQCViz { } 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_visualizations.html" + Array[String] gambit_predicted_taxon + Array[String] est_coverage_clean + Array[String] number_contigs + Array[String] assembly_length File? thresholds_file - String docker = "us-central1-docker.pkg.dev/pgs-automation/enterics-visualizations/create_visualization_html:v4" + String output_filename = "QC_visualizations.html" + + String docker = "us-central1-docker.pkg.dev/pgs-automation/enterics-visualizations/create_visualization_html:v5" } 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)"} + 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}" \ - -dt "~{input_table_name}" \ - -w "~{workspace_name}" \ - -bp "~{workspace_project}" \ - ~{'-g "' + grouping_column_name + '"'} \ + -g "~{sep='" "' gambit_predicted_taxon}" \ + -ecc ~{sep=' ' est_coverage_clean} \ + -nc ~{sep=' ' number_contigs} \ + -al ~{sep=' ' assembly_length} \ ~{'-o "' + output_filename + '"'} \ ~{'-t "' + thresholds_file + '"'} }