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Fixing duplicate inputs bug #514

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merged 4 commits into from
Feb 15, 2024
Merged

Fixing duplicate inputs bug #514

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4ab9dea
Fixing duplicate inputs on Terra error
jpramosbarroso Feb 15, 2024
c73b177
Merge branch 'master' into jprb_visualization
jpramosbarroso Feb 15, 2024
17a234c
Fixing .pdf ending in output
jpramosbarroso Feb 15, 2024
86aeb02
Adapting to nested inputs
jpramosbarroso Feb 15, 2024
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50 changes: 17 additions & 33 deletions pipes/WDL/workflows/create_enterics_qc_viz.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -6,35 +6,6 @@ workflow CreateEntericsQCViz {
allowNestedInputs: true
}

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"}
custom_est_coverage_thresholds: {description: "json string with custom estimated coverage threshlds"}
custom_contig_thresholds: {description: "json string with custom number contig thresholds"}
custom_assembly_thresholds: {description: "json string with custom assembly length thresholds"}
custom_mean_q_thresholds: {description: "json string with custom mean q thresholds"}
}

input {

Array[String] sample_ids
String input_table_name
String workspace_name
String workspace_project

String? grouping_column_name
String? output_filename

String? custom_est_coverage_thresholds
String? custom_contig_thresholds
String? custom_assembly_thresholds
String? custom_mean_q_thresholds
}

call create_viz

output {
Expand All @@ -49,15 +20,28 @@ task create_viz {
String workspace_project
String input_table_name

String grouping_column_name = "gambit_predicted_taxon"
String output_filename = "QC_visualizations.pdf"
String grouping_column_name = "gambit_predicted_taxon"
String output_filename = "QC_visualizations.html"

String? custom_est_coverage_thresholds
String? custom_contig_thresholds
String? custom_assembly_thresholds
String? custom_mean_q_thresholds

String docker = "us-central1-docker.pkg.dev/pgs-automation/enterics-visualizations/create_visualization_html:v1"
String docker = "us-central1-docker.pkg.dev/pgs-automation/enterics-visualizations/create_visualization_html:v1"
}

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"}
custom_est_coverage_thresholds: {description: "json string with custom estimated coverage threshlds"}
custom_contig_thresholds: {description: "json string with custom number contig thresholds"}
custom_assembly_thresholds: {description: "json string with custom assembly length thresholds"}
custom_mean_q_thresholds: {description: "json string with custom mean q thresholds"}
}

command {
Expand All @@ -78,6 +62,6 @@ task create_viz {
}

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