Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

VS-942. Fix an error where NO variants were found #8388

Merged
merged 7 commits into from
Jun 28, 2023
Merged

VS-942. Fix an error where NO variants were found #8388

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
7 commits
Select commit Hold shift + click to select a range
541a9f5
Fix a bug where there were NO variants in a range.
gbggrant Jun 21, 2023
ca73262
Merge remote-tracking branch 'origin/ah_var_store' into gg_FixExomes
gbggrant Jun 22, 2023
1d6ddf6
Add the branch to the .dockstore.yml
gbggrant Jun 22, 2023
35a023a
Update docker in order to test the fix.
gbggrant Jun 22, 2023
a778e4c
Merge remote-tracking branch 'origin/ah_var_store' into gg_FixExomes
gbggrant Jun 27, 2023
c92dbdd
Don't forget the override jar in GvsJointVariantCalling.wdl
gbggrant Jun 28, 2023
e3308ca
Point to 'official' docker (retagged)
gbggrant Jun 28, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 0 additions & 1 deletion .dockstore.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -111,7 +111,6 @@ workflows:
branches:
- master
- ah_var_store
- gg_VS-987_OutOfDateDocker
- name: GvsImportGenomes
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsImportGenomes.wdl
Expand Down
8 changes: 4 additions & 4 deletions scripts/variantstore/wdl/GvsCreateFilterSet.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -315,7 +315,7 @@ task ExtractFilterTask {
>>>

runtime {
docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:varstore_2023_06_21"
docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:varstore_2023_06_22"
memory: "7 GB"
disks: "local-disk 10 HDD"
bootDiskSizeGb: 15
Expand Down Expand Up @@ -397,7 +397,7 @@ task PopulateFilterSetInfo {
>>>

runtime {
docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:varstore_2023_06_21"
docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:varstore_2023_06_22"
memory: "3500 MB"
disks: "local-disk 250 HDD"
bootDiskSizeGb: 15
Expand Down Expand Up @@ -457,7 +457,7 @@ task PopulateFilterSetSites {
>>>

runtime {
docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:varstore_2023_06_21"
docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:varstore_2023_06_22"
memory: "3500 MB"
disks: "local-disk 200 HDD"
bootDiskSizeGb: 15
Expand Down Expand Up @@ -509,7 +509,7 @@ task PopulateFilterSetTranches {
>>>

runtime {
docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:varstore_2023_06_21"
docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:varstore_2023_06_22"
memory: "3500 MB"
disks: "local-disk 200 HDD"
bootDiskSizeGb: 15
Expand Down
2 changes: 1 addition & 1 deletion scripts/variantstore/wdl/GvsExtractCallset.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -354,7 +354,7 @@ task ExtractTask {
echo ~{interval_index},${OUTPUT_FILE_DEST},${OUTPUT_FILE_BYTES},${OUTPUT_FILE_INDEX_DEST},${OUTPUT_FILE_INDEX_BYTES} >> manifest.txt
>>>
runtime {
docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:varstore_2023_06_21"
docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:varstore_2023_06_22"
memory: "12 GB"
disks: "local-disk 150 HDD"
bootDiskSizeGb: 15
Expand Down
2 changes: 1 addition & 1 deletion scripts/variantstore/wdl/GvsImportGenomes.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -323,7 +323,7 @@ task LoadData {
>>>

runtime {
docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:varstore_2023_06_21"
docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:varstore_2023_06_22"
maxRetries: load_data_maxretries
memory: "3.75 GB"
disks: "local-disk 50 HDD"
Expand Down
2 changes: 1 addition & 1 deletion scripts/variantstore/wdl/GvsJointVariantCalling.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,7 @@ workflow GvsJointVariantCalling {
Int SNP_VQSR_CLASSIC_mem_gb_override = ""
}
# This is the most updated snapshot of the code as of June 22, 2023
File gatk_override = "gs://gvs_quickstart_storage/jars/gatk-package-4.2.0.0-726-g63a0bea-SNAPSHOT-local.jar"
File gatk_override = "gs://gvs_quickstart_storage/jars/gatk-package-4.2.0.0-721-ga778e4c-SNAPSHOT-local.jar"
File interval_list = "gs://gcp-public-data--broad-references/hg38/v0/wgs_calling_regions.hg38.noCentromeres.noTelomeres.interval_list"

File interval_weights_bed = "gs://broad-public-datasets/gvs/weights/gvs_vet_weights_1kb.bed"
Expand Down
4 changes: 2 additions & 2 deletions scripts/variantstore/wdl/GvsUtils.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -41,7 +41,7 @@ task MergeVCFs {
}

runtime {
docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:varstore_2023_06_21"
docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:varstore_2023_06_22"
preemptible: select_first([preemptible_tries, 3])
memory: "3 GiB"
disks: "local-disk ~{disk_size} HDD"
Expand Down Expand Up @@ -127,7 +127,7 @@ task SplitIntervals {
>>>

runtime {
docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:varstore_2023_06_21"
docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:varstore_2023_06_22"
bootDiskSizeGb: 15
memory: "~{disk_memory} GB"
disks: "local-disk ~{disk_size} HDD"
Expand Down
2 changes: 1 addition & 1 deletion scripts/variantstore/wdl/GvsWarpTasks.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -138,7 +138,7 @@ task GatherTranches {
bootDiskSizeGb: 15
disks: "local-disk " + disk_size + " HDD"
preemptible: 1
docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:varstore_2023_06_21"
docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:varstore_2023_06_22"
}

output {
Expand Down
2 changes: 1 addition & 1 deletion src/main/java/org/broadinstitute/hellbender/tools/gvs/extract/ExtractCohortEngine.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1150,7 +1150,7 @@ void createVariantsFromSortedRanges(final SortedSet<Long> sampleIdsToExtract,
}

// finish writing out reference rows
if (lastSample != maxSampleId) {
if ((lastSample != null) && (lastSample != maxSampleId)) {
processReferenceData(currentPositionRecords, sortedReferenceRangeIterator, referenceCache, lastPosition, lastSample + 1, maxSampleId, sampleIdsToExtract);
}

Expand Down
Loading