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VS 678 - adding optional interval list to the subcohort extract workflow #8601

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merged 3 commits into from
Dec 7, 2023
Merged

VS 678 - adding optional interval list to the subcohort extract workflow #8601

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d0ab861
adding an optional interval list argument to be passed through to Gvs…
koncheto-broad Nov 28, 2023
bbef228
dockstooooooooore
koncheto-broad Nov 28, 2023
a628b48
cleaning up dockstore before merge
koncheto-broad Dec 6, 2023
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5 changes: 5 additions & 0 deletions scripts/variantstore/wdl/GvsExtractCohortFromSampleNames.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -31,6 +31,7 @@ workflow GvsExtractCohortFromSampleNames {
# set to "NONE" if all the reference data was loaded into GVS in GvsImportGenomes
String drop_state = "NONE"

File? interval_list
Int? extract_preemptible_override
Int? extract_maxretries_override
Int? extract_scatter_count_override
Expand Down Expand Up @@ -91,6 +92,9 @@ workflow GvsExtractCohortFromSampleNames {

File cohort_sample_names_file = select_first([write_array_task.output_file, cohort_sample_names])

# allow an interval list to be passed in, but default it to our standard one if no args are here
File working_interval_list = select_first([interval_list, "gs://gcp-public-data--broad-references/hg38/v0/wgs_calling_regions.hg38.noCentromeres.noTelomeres.interval_list"])

call GvsPrepareCallset.GvsPrepareCallset {
input:
call_set_identifier = cohort_table_prefix,
Expand Down Expand Up @@ -130,6 +134,7 @@ workflow GvsExtractCohortFromSampleNames {
split_intervals_mem_override = split_intervals_mem_override,
memory_override = extract_memory_override,
disk_override = extract_disk_override,
interval_list = working_interval_list,

gatk_override = gatk_override,
write_cost_to_db = write_cost_to_db
Expand Down
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