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gatk docker update 4.6.1.0 #1403

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gatk docker update 4.6.1.0 #1403

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b3a4a9a
gatk docker update
nikellepetrillo Oct 28, 2024
4de6e1d
gatk docker update
nikellepetrillo Oct 28, 2024
56f8447
adding CompareVcfsVerbosely to Ultima tests
meganshand Oct 30, 2024
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2 changes: 1 addition & 1 deletion pipelines/broad/annotation_filtration/AnnotationFiltration.wdl
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Expand Up @@ -15,7 +15,7 @@ workflow AnnotationFiltration {
File ref_dict
File? funcotator_interval_list

String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
File? custom_data_source_tar_gz
}

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2 changes: 1 addition & 1 deletion pipelines/broad/annotation_filtration/test_inputs/Plumbing/hg38.json
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Expand Up @@ -10,6 +10,6 @@
"AnnotationFiltration.ref_fasta_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
"AnnotationFiltration.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",

"AnnotationFiltration.gatk_docker": "us.gcr.io/broad-gatk/gatk:4.5.0.0",
"AnnotationFiltration.gatk_docker": "us.gcr.io/broad-gatk/gatk:4.6.1.0",
"AnnotationFiltration.custom_data_source_tar_gz": "gs://broad-public-datasets/funcotator/funcotator_dataSources.v1.6.20190124g.tar.gz"
}
2 changes: 1 addition & 1 deletion pipelines/broad/annotation_filtration/test_inputs/Scientific/hg38.json
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Expand Up @@ -8,6 +8,6 @@
"AnnotationFiltration.ref_fasta_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
"AnnotationFiltration.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",

"AnnotationFiltration.gatk_docker": "us.gcr.io/broad-gatk/gatk:4.5.0.0",
"AnnotationFiltration.gatk_docker": "us.gcr.io/broad-gatk/gatk:4.6.1.0",
"AnnotationFiltration.custom_data_source_tar_gz": "gs://broad-public-datasets/funcotator/funcotator_dataSources.v1.6.20190124g.tar.gz"
}
2 changes: 1 addition & 1 deletion pipelines/broad/arrays/validate_chip/ValidateChip.wdl
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Expand Up @@ -324,7 +324,7 @@ task GenotypeConcordance {
>>>

runtime {
docker: "us.gcr.io/broad-gatk/gatk:4.2.6.1"
docker: "us.gcr.io/broad-gatk/gatk:4.6.1.0"
disks: "local-disk " + disk_size + " HDD"
memory: "7000 MiB"
preemptible: preemptible_tries
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2 changes: 1 addition & 1 deletion pipelines/broad/dna_seq/germline/joint_genotyping/JointGenotyping.wdl
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Expand Up @@ -214,7 +214,7 @@ workflow JointGenotyping {
extract_extra_args = extract_extra_args,
resource_args = resource_args,
output_prefix = callset_name,
gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
}
}
if (!run_vets) {
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4 changes: 2 additions & 2 deletions .../broad/dna_seq/germline/joint_genotyping/UltimaGenomics/UltimaGenomicsJointGenotyping.wdl
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Expand Up @@ -168,7 +168,7 @@ workflow UltimaGenomicsJointGenotyping {
extract_extra_args = "--mode SNP",
train_extra_args = "--mode SNP",
score_extra_args = "--mode SNP",
gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
}

call Filtering.JointVcfFiltering as TrainAndApplyFilteringModelINDELs {
Expand All @@ -184,7 +184,7 @@ workflow UltimaGenomicsJointGenotyping {
extract_extra_args = "--mode INDEL",
train_extra_args = "--mode INDEL",
score_extra_args = "--mode INDEL",
gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
}

call FilteringThreshold.ExtractOptimizeSingleSample as FindFilteringThresholdAndFilter {
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4 changes: 2 additions & 2 deletions pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/ReblockGVCF.wdl
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Expand Up @@ -26,8 +26,8 @@ workflow ReblockGVCF {

String gvcf_basename = basename(gvcf, gvcf_file_extension)
# docker images
String gatk_docker_gcp = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
String gatk_docker_azure = "terrapublic.azurecr.io/gatk:4.6.0.0"
String gatk_docker_gcp = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
String gatk_docker_azure = "terrapublic.azurecr.io/gatk:4.6.1.0"
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Has this version of gatk been uploaded to azurecr.io? I believe Kevin did this for 4.6.0.0, and I'm not sure if we added this to the gatk release process yet or not. I think this was a todo still for the GATK team at the time of the 4.6.0.0 release.

String gatk_docker = if cloud_provider == "gcp" then gatk_docker_gcp else gatk_docker_azure

# make sure either gcp or azr is supplied as cloud_provider input
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4 changes: 2 additions & 2 deletions pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl
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Expand Up @@ -68,8 +68,8 @@ workflow ExomeGermlineSingleSample {
}

# docker images
String gatk_docker_gcp = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
String gatk_docker_azure = "terrapublic.azurecr.io/gatk:4.6.0.0"
String gatk_docker_gcp = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
String gatk_docker_azure = "terrapublic.azurecr.io/gatk:4.6.1.0"
String gatk_docker = if cloud_provider == "gcp" then gatk_docker_gcp else gatk_docker_azure

# make sure either gcp or azr is supplied as cloud_provider input
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4 changes: 2 additions & 2 deletions pipelines/broad/dna_seq/germline/variant_calling/VariantCalling.wdl
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Expand Up @@ -40,8 +40,8 @@ workflow VariantCalling {
}

# docker images
String gatk_docker_gcp = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
String gatk_docker_azure = "terrapublic.azurecr.io/gatk:4.6.0.0"
String gatk_docker_gcp = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
String gatk_docker_azure = "terrapublic.azurecr.io/gatk:4.6.1.0"
String gatk_docker = if cloud_provider == "gcp" then gatk_docker_gcp else gatk_docker_azure

String gatk_1_3_docker_gcp = "us.gcr.io/broad-gotc-prod/gatk:1.3.0-4.2.6.1-1649964384"
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4 changes: 2 additions & 2 deletions .../broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl
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Expand Up @@ -533,7 +533,7 @@ task gatk_baserecalibrator {
}

runtime {
docker: "us.gcr.io/broad-gatk/gatk:4.6.0.0"
docker: "us.gcr.io/broad-gatk/gatk:4.6.1.0"
memory: mem + " MiB"
disks: "local-disk " + disk_space + " HDD"
preemptible: preemptible
Expand Down Expand Up @@ -580,7 +580,7 @@ task gatk_applybqsr {
}

runtime {
docker: "us.gcr.io/broad-gatk/gatk:4.6.0.0"
docker: "us.gcr.io/broad-gatk/gatk:4.6.1.0"
memory: mem + " MiB"
disks: "local-disk " + disk_space + " HDD"
preemptible: preemptible
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10 changes: 5 additions & 5 deletions scripts/BuildAFComparisonTable.wdl
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Expand Up @@ -117,7 +117,7 @@ task AnnotateWithAF_t {
>>>

runtime {
docker: "us.gcr.io/broad-gatk/gatk:4.6.0.0"
docker: "us.gcr.io/broad-gatk/gatk:4.6.1.0"
disks: "local-disk " + disk_size + " HDD"
memory: mem + " GB" # some of the gnomad vcfs are like 38 gigs so maybe need more ?
}
Expand Down Expand Up @@ -145,7 +145,7 @@ task GatherVCFsCloud {
>>>

runtime {
docker: "us.gcr.io/broad-gatk/gatk:4.6.0.0"
docker: "us.gcr.io/broad-gatk/gatk:4.6.1.0"
disks: "local-disk " + disk_size + " HDD"
memory: "16 GB"
}
Expand All @@ -169,7 +169,7 @@ task MakeSitesOnlyVcf {
>>>

runtime {
docker: "us.gcr.io/broad-gatk/gatk:4.6.0.0"
docker: "us.gcr.io/broad-gatk/gatk:4.6.1.0"
disks: "local-disk " + disk_size + " HDD"
memory: "16 GB"
}
Expand Down Expand Up @@ -224,7 +224,7 @@ task VariantsToTable {
>>>

runtime {
docker: "us.gcr.io/broad-gatk/gatk:4.6.0.0"
docker: "us.gcr.io/broad-gatk/gatk:4.6.1.0"
disks: "local-disk " + disk_size + " HDD"
memory: "16 GB"
}
Expand Down Expand Up @@ -280,7 +280,7 @@ task RemoveSymbolicAlleles {
File output_vcf_index = "~{output_basename}.vcf.gz.tbi"
}
runtime {
docker: "us.gcr.io/broad-gatk/gatk:4.6.0.0"
docker: "us.gcr.io/broad-gatk/gatk:4.6.1.0"
disks: "local-disk " + disk_size + " HDD"
memory: "4 GB"
}
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4 changes: 2 additions & 2 deletions scripts/RemoveBadSitesByID.wdl
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Expand Up @@ -129,7 +129,7 @@ task SplitX {
>>>

runtime {
docker: "us.gcr.io/broad-gatk/gatk:4.6.0.0"
docker: "us.gcr.io/broad-gatk/gatk:4.6.1.0"
disks: "local-disk " + disk_size + " HDD"
memory: "16 GB"
}
Expand Down Expand Up @@ -215,7 +215,7 @@ task RemoveBadSitesFromVcf {
>>>

runtime {
docker: "us.gcr.io/broad-gatk/gatk:4.6.0.0"
docker: "us.gcr.io/broad-gatk/gatk:4.6.1.0"
disks: "local-disk 100 HDD"
memory: "16 GB"
}
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6 changes: 3 additions & 3 deletions tasks/broad/BamProcessing.wdl
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Expand Up @@ -136,7 +136,7 @@ task BaseRecalibrator {
File ref_fasta_index
Int bqsr_scatter
Int preemptible_tries
String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.3.0.0"
String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
}

Float ref_size = size(ref_fasta, "GiB") + size(ref_fasta_index, "GiB") + size(ref_dict, "GiB")
Expand Down Expand Up @@ -188,7 +188,7 @@ task ApplyBQSR {
Int compression_level
Int bqsr_scatter
Int preemptible_tries
String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.3.0.0"
String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
Int memory_multiplier = 1
Int additional_disk = 20
Boolean bin_base_qualities = true
Expand Down Expand Up @@ -247,7 +247,7 @@ task GatherBqsrReports {
Array[File] input_bqsr_reports
String output_report_filename
Int preemptible_tries
String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.3.0.0"
String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
}

command {
Expand Down
2 changes: 1 addition & 1 deletion tasks/broad/CheckContaminationSomatic.wdl
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Expand Up @@ -14,7 +14,7 @@ task CalculateSomaticContamination {
File contamination_vcf_index

# runtime
String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.2.4.1"
String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
File? gatk_override
Int? additional_disk
Int memory_mb = 3000
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2 changes: 1 addition & 1 deletion tasks/broad/DragenTasks.wdl
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Expand Up @@ -25,7 +25,7 @@ task CalibrateDragstrModel {
File alignment ## can handle cram or bam.
File alignment_index
#Setting default docker value for workflows that haven't yet been azurized.
String docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
String docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
Int preemptible_tries = 3
Int threads = 4
Int? memory_mb
Expand Down
8 changes: 4 additions & 4 deletions tasks/broad/GermlineVariantDiscovery.wdl
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Expand Up @@ -99,7 +99,7 @@ task HaplotypeCaller_GATK4_VCF {
Boolean use_spanning_event_genotyping = true
File? dragstr_model
#Setting default docker value for workflows that haven't yet been azurized.
String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
Int memory_multiplier = 1
}

Expand Down Expand Up @@ -261,7 +261,7 @@ task HardFilterVcf {
String vcf_basename
File interval_list
Int preemptible_tries
String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
}

Int disk_size = ceil(2 * size(input_vcf, "GiB")) + 20
Expand Down Expand Up @@ -337,7 +337,7 @@ task CNNScoreVariants {
File ref_fasta_index
File ref_dict
Int preemptible_tries
String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
}

Int disk_size = ceil(size(bamout, "GiB") + size(ref_fasta, "GiB") + (size(input_vcf, "GiB") * 2))
Expand Down Expand Up @@ -394,7 +394,7 @@ task FilterVariantTranches {
File dbsnp_resource_vcf_index
String info_key
Int preemptible_tries
String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
}

Int disk_size = ceil(size(hapmap_resource_vcf, "GiB") +
Expand Down
8 changes: 4 additions & 4 deletions tasks/broad/IlluminaGenotypingArrayTasks.wdl
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Expand Up @@ -404,7 +404,7 @@ task SelectVariants {
>>>

runtime {
docker: "us.gcr.io/broad-gatk/gatk:4.6.0.0"
docker: "us.gcr.io/broad-gatk/gatk:4.6.1.0"
bootDiskSizeGb: 15
disks: "local-disk " + disk_size + " HDD"
memory: "3500 MiB"
Expand Down Expand Up @@ -441,7 +441,7 @@ task SelectIndels {
>>>

runtime {
docker: "us.gcr.io/broad-gatk/gatk:4.6.0.0"
docker: "us.gcr.io/broad-gatk/gatk:4.6.1.0"
bootDiskSizeGb: 15
disks: "local-disk " + disk_size + " HDD"
memory: "3500 MiB"
Expand Down Expand Up @@ -577,7 +577,7 @@ task SubsetArrayVCF {
}

runtime {
docker: "us.gcr.io/broad-gatk/gatk:4.6.0.0"
docker: "us.gcr.io/broad-gatk/gatk:4.6.1.0"
bootDiskSizeGb: 15
disks: "local-disk " + disk_size + " HDD"
memory: "3500 MiB"
Expand Down Expand Up @@ -676,7 +676,7 @@ task ValidateVariants {
>>>

runtime {
docker: "us.gcr.io/broad-gatk/gatk:4.6.0.0"
docker: "us.gcr.io/broad-gatk/gatk:4.6.1.0"
bootDiskSizeGb: 15
disks: "local-disk " + disk_size + " HDD"
memory: "3500 MiB"
Expand Down
16 changes: 8 additions & 8 deletions tasks/broad/ImputationTasks.wdl
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Expand Up @@ -65,7 +65,7 @@ task GenerateChunk {
Int disk_size_gb = ceil(2*size(vcf, "GiB")) + 50 # not sure how big the disk size needs to be since we aren't downloading the entire VCF here
Int cpu = 1
Int memory_mb = 8000
String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
}
Int command_mem = memory_mb - 1000
Int max_heap = memory_mb - 500
Expand Down Expand Up @@ -112,7 +112,7 @@ task CountVariantsInChunks {
File panel_vcf
File panel_vcf_index

String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
Int cpu = 1
Int memory_mb = 4000
Int disk_size_gb = 2 * ceil(size([vcf, vcf_index, panel_vcf, panel_vcf_index], "GiB")) + 20
Expand Down Expand Up @@ -266,7 +266,7 @@ task GatherVcfs {
Array[File] input_vcfs
String output_vcf_basename

String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
Int cpu = 1
Int memory_mb = 16000
Int disk_size_gb = ceil(3*size(input_vcfs, "GiB"))
Expand Down Expand Up @@ -336,7 +336,7 @@ task UpdateHeader {
String basename

Int disk_size_gb = ceil(4*(size(vcf, "GiB") + size(vcf_index, "GiB"))) + 20
String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
Int cpu = 1
Int memory_mb = 8000
}
Expand Down Expand Up @@ -372,7 +372,7 @@ task RemoveSymbolicAlleles {
String output_basename

Int disk_size_gb = ceil(3*(size(original_vcf, "GiB") + size(original_vcf_index, "GiB")))
String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
Int cpu = 1
Int memory_mb = 4000
}
Expand Down Expand Up @@ -659,7 +659,7 @@ task SubsetVcfToRegion {
Int disk_size_gb = ceil(2*size(vcf, "GiB")) + 50 # not sure how big the disk size needs to be since we aren't downloading the entire VCF here
Int cpu = 1
Int memory_mb = 8000
String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
}
Int command_mem = memory_mb - 1000
Int max_heap = memory_mb - 500
Expand Down Expand Up @@ -754,7 +754,7 @@ task SelectVariantsByIds {
File ids
String basename

String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
Int cpu = 1
Int memory_mb = 16000
Int disk_size_gb = ceil(1.2*size(vcf, "GiB")) + 100
Expand Down Expand Up @@ -820,7 +820,7 @@ task InterleaveVariants {
Array[File] vcfs
String basename

String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0"
Int cpu = 1
Int memory_mb = 16000
Int disk_size_gb = ceil(3.2*size(vcfs, "GiB")) + 100
Expand Down
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