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TSPS-789 lower allowable nubmer of variants qc check to 3 #1762

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Merged
jsotobroad merged 4 commits into from
Feb 5, 2026
Merged

TSPS-789 lower allowable nubmer of variants qc check to 3 #1762

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ca95b69
lower allowable nubmer of variants qc check to 3 milliion from 10 mil…
Feb 4, 2026
a64b603
Updated pipeline_versions.txt with all pipeline version information
actions-user Feb 4, 2026
17a08a8
update comment to kick off pr tests again
Feb 4, 2026
0fe42cd
fix changelog message
Feb 4, 2026
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4 changes: 2 additions & 2 deletions pipeline_versions.txt
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Original file line number Diff line number Diff line change
@@ -1,12 +1,12 @@
ArrayImputationQC 1.2.5 2025-12-23
ArrayImputationQC 1.3.0 2026-02-04
ArrayImputationQuotaConsumed 1.1.0 2025-09-29
BuildIndices 5.0.3 2025-12-16
CramToUnmappedBams 1.1.3 2024-08-02
ExomeGermlineSingleSample 3.2.7 2026-01-21
ExomeReprocessing 3.3.7 2026-01-21
IlluminaGenotypingArray 1.12.27 2026-01-21
Imputation 1.1.23 2025-10-03
ImputationBeagle 2.5.0 2026-01-27
ImputationBeagle 2.5.1 2026-2-04
JointGenotyping 1.7.3 2025-08-11
MultiSampleSmartSeq2SingleNucleus 2.2.4 2026-01-21
Multiome 6.1.4 2026-01-22
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5 changes: 5 additions & 0 deletions pipelines/wdl/arrays/imputation_beagle/ImputationBeagle.changelog.md
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@@ -1,3 +1,8 @@
# 2.5.1
2026-2-04 (Date of Last Commit)

* Update input_qc_version to 1.3.0 to match the latest changes in InputQC wdl.

# 2.5.0
2026-01-27 (Date of Last Commit)

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4 changes: 2 additions & 2 deletions pipelines/wdl/arrays/imputation_beagle/ImputationBeagle.wdl
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Expand Up @@ -5,8 +5,8 @@ import "../../../../tasks/wdl/ImputationTasks.wdl" as tasks
import "../../../../tasks/wdl/ImputationBeagleTasks.wdl" as beagleTasks

workflow ImputationBeagle {
String pipeline_version = "2.5.0"
String input_qc_version = "1.2.5"
String pipeline_version = "2.5.1"
String input_qc_version = "1.3.0"
String quota_consumed_version = "1.1.0"

input {
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5 changes: 5 additions & 0 deletions pipelines/wdl/arrays/imputation_beagle/input_qc/ArrayImputationQC.changelog.md
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@@ -1,3 +1,8 @@
# 1.3.0
2026-02-04 (Date of Last Commit)

* Lower variant number check to 3 million from 10 million to further prevent whole genome inputs from being submitted

# 1.2.5
2025-12-23 (Date of Last Commit)

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2 changes: 1 addition & 1 deletion pipelines/wdl/arrays/imputation_beagle/input_qc/ArrayImputationQC.wdl
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Expand Up @@ -4,7 +4,7 @@ import "../../../../../tasks/wdl/ImputationBeagleQcTasks.wdl" as tasks

workflow InputQC {
# if this changes, update the input_qc_version value in ImputationBeagle.wdl
String pipeline_version = "1.2.5"
String pipeline_version = "1.3.0"


input {
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2 changes: 1 addition & 1 deletion ...ion_beagle/input_qc/test_inputs/Plumbing/NA12878_wgs_chr20_qc_fails_too_many_records.json
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{
"ArrayImputationQC.multi_sample_vcf": "gs://broad-gotc-test-storage/imputation_beagle/input_qc/scientific/vcfs/NA12878.annotated.chr20.g.vcf.gz",
"ArrayImputationQC.multi_sample_vcf": "gs://broad-gotc-test-storage/imputation_beagle/input_qc/scientific/vcfs/NA12878.annotated.chr20_over_three_million_sites.g.vcf.gz",
"ArrayImputationQC.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
"ArrayImputationQC.reference_panel_path_prefix": "gs://broad-gotc-test-storage/imputation_beagle/scientific/1000G_HGDP_no_singletons_reference_panel/hgdp.tgp.gwaspy.AN_added.bcf.ac2",
"ArrayImputationQC.contigs": ["this_contig_is_not_in_inputs_1", "this_contig_is_not_in_inputs_2", "this_contig_is_not_in_inputs_3"],
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8 changes: 4 additions & 4 deletions tasks/wdl/ImputationBeagleQcTasks.wdl
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Expand Up @@ -18,14 +18,14 @@ task QcChecks {
# create empty qc messages file
touch qc_messages.txt

# check for a large number of variants in input vcf and exit if greater than 10 million
# check for a large number of variants in input vcf and exit if greater than 3 million
line_count=$(bcftools stats ~{vcf_input} | grep "number of records:" | awk '{print $6}')
if [ "$line_count" -gt 10000000 ]; then
echo "Greater than 10 million variants found in the input VCF." >> qc_messages.txt
if [ "$line_count" -gt 3000000 ]; then
echo "Greater than 3 million variants found in the input VCF." >> qc_messages.txt
echo "false" > passes_qc.txt
exit 0
else
echo "Less than or equal to 10 million variants found in input VCF."
echo "$line_count variants found in input VCF."
fi

# grab header from vcf
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