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Clarify and set default for interval_list input [VS-1391] #8853

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May 31, 2024
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Clarify and set default for interval_list input [VS-1391] #8853

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cd088c8
tweaks to interval_list input
rsasch May 31, 2024
0f1f742
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rsasch May 31, 2024
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4 changes: 2 additions & 2 deletions scripts/variantstore/wdl/GvsCalculatePrecisionAndSensitivity.wdl
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Expand Up @@ -9,7 +9,7 @@ workflow GvsCalculatePrecisionAndSensitivity {
String call_set_identifier
String dataset_name
String filter_set_name
File interval_list
File interval_list = "gs://gcp-public-data--broad-references/hg38/v0/wgs_calling_regions.hg38.noCentromeres.noTelomeres.interval_list"
File? vcf_eval_bed_file
Array[String] chromosomes = ["chr20"]
String project_id
Expand Down Expand Up @@ -37,7 +37,7 @@ workflow GvsCalculatePrecisionAndSensitivity {
chromosomes: "The chromosome(s) on which to analyze precision and sensitivity. The default value for this is `['chr20']`."
dataset_name: "The GVS BigQuery dataset name."
filter_set_name: "The filter_set_name used to generate the callset."
interval_list: "The intervals over which to calculate precision and sensitivity."
interval_list: "The intervals over which to extract VCFs for calculating precision and sensitivity."
project_id: "The Google Project ID where the GVS lives."
sample_names: "A list of the sample names that are controls and that will be used for the analysis. For every element on the list of sample names there must be a corresponding element on the list of `truth_vcfs`, `truth_vcf_indices`, and `truth_beds`."
truth_vcfs: "A list of the VCFs that contain the truth data used for analyzing the samples in `sample_names`."
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