Merge pull request #1354 from broadinstitute/develop

dev --> staging
broadinstitute · Aug 7, 2024 · c49bcc9 · c49bcc9
2 parents f972529 + 9b5e498
commit c49bcc9
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diff --git a/pipeline_versions.txt b/pipeline_versions.txt
@@ -1,42 +1,42 @@
 Pipeline Name	Version	Date of Last Commit
-CEMBA	 1.1.6	2023-12-18 
-BuildCembaReferences	 1.0.0	2020-11-15 
-Multiome	 5.3.1	2024-07-18 
-PairedTag	 1.3.1	2024-07-18 
-snm3C	 4.0.2	2024-07-09 
-BuildIndices	 3.0.0	2023-12-06 
+Optimus	 7.6.0	2024-08-06 
+Multiome	 5.5.0	2024-08-06 
+PairedTag	 1.5.0	2024-08-06 
+atac	 2.2.3	2024-08-02 
+SlideSeq	 3.4.0	2024-08-06 
+snm3C	 4.0.3	2024-08-05 
+MultiSampleSmartSeq2SingleNucleus	 1.4.2	2024-08-25-02 
 scATAC	 1.3.2	2023-08-03 
-Optimus	 7.4.0	2024-07-11 
-SlideSeq	 3.2.0	2024-07-11 
-atac	 2.2.0	2024-07-11 
-MultiSampleSmartSeq2	 2.2.21	2023-04-19 
 SmartSeq2SingleSample	 5.1.20	2023-04-19 
-MultiSampleSmartSeq2SingleNucleus	 1.4.0	2024-07-11 
-AnnotationFiltration	 1.2.5	2023-12-18 
-RNAWithUMIsPipeline	 1.0.16	2023-12-18 
-IlluminaGenotypingArray	 1.12.20	2024-06-12 
-GDCWholeGenomeSomaticSingleSample	 1.3.1	2024-01-19 
-UltimaGenomicsWholeGenomeCramOnly	 1.0.19	2024-06-12 
+BuildIndices	 3.0.0	2023-12-06 
+MultiSampleSmartSeq2	 2.2.21	2023-04-19 
+CEMBA	 1.1.6	2023-12-18 
+BuildCembaReferences	 1.0.0	2020-11-15 
+UltimaGenomicsWholeGenomeCramOnly	 1.0.20	2024-08-02 
+GDCWholeGenomeSomaticSingleSample	 1.3.2	2024-08-02  
+ExomeGermlineSingleSample	 3.1.22	2024-06-12 
+UltimaGenomicsWholeGenomeGermline	 1.0.20	2024-08-02 
+WholeGenomeGermlineSingleSample	 3.2.1	2024-06-12 
 VariantCalling	 2.2.1	2024-06-12 
-JointGenotypingByChromosomePartOne	 1.4.12	2023-12-18 
-JointGenotypingByChromosomePartTwo	 1.4.11	2023-12-18 
 UltimaGenomicsJointGenotyping	 1.1.7	2023-12-18 
 JointGenotyping	 1.6.10	2023-12-18 
 ReblockGVCF	 2.2.1	2024-06-12 
-WholeGenomeGermlineSingleSample	 3.2.1	2024-06-12 
-ExomeGermlineSingleSample	 3.1.22	2024-06-12 
-UltimaGenomicsWholeGenomeGermline	 1.0.19	2024-06-12 
-ExternalWholeGenomeReprocessing	 2.2.1	2024-06-12 
-ExternalExomeReprocessing	 3.2.1	2024-06-12 
-WholeGenomeReprocessing	 3.2.1	2024-06-12 
-ExomeReprocessing	 3.2.1	2024-06-12 
-CramToUnmappedBams	 1.1.2	2022-04-14 
-BroadInternalRNAWithUMIs	 1.0.32	2024-06-12 
-BroadInternalUltimaGenomics	 1.0.20	2024-06-12 
-BroadInternalImputation	 1.1.11	2024-05-21 
-BroadInternalArrays	 1.1.10	2024-06-12 
-CheckFingerprint	 1.0.19	2024-06-12 
-MultiSampleArrays	 1.6.1	2022-04-14 
-ValidateChip	 1.16.4	2023-12-18 
+JointGenotypingByChromosomePartTwo	 1.4.11	2023-12-18 
+JointGenotypingByChromosomePartOne	 1.4.12	2023-12-18 
+ExternalExomeReprocessing	 3.2.2	2024-08-02 
+ExternalWholeGenomeReprocessing	 2.2.2	2024-08-02 
+ExomeReprocessing	 3.2.2	2024-08-02 
+CramToUnmappedBams	 1.1.3	2024-08-02 
+WholeGenomeReprocessing	 3.2.2	2024-08-02 
+IlluminaGenotypingArray	 1.12.21	2024-08-02 
+Arrays	 2.6.27	2024-08-02 
+MultiSampleArrays	 1.6.2	2024-08-02 
+ValidateChip	 1.16.5	2024-08-02 
 Imputation	 1.1.13	2024-05-21 
-Arrays	 2.6.26	2024-06-12 
+RNAWithUMIsPipeline	 1.0.16	2023-12-18 
+BroadInternalUltimaGenomics	 1.0.21	2024-08-02 
+BroadInternalArrays	 1.1.11	2024-08-02 
+BroadInternalImputation	 1.1.12	2024-08-02 
+BroadInternalRNAWithUMIs	 1.0.33	2024-08-02 
+CheckFingerprint	 1.0.20	2024-08-02 
+AnnotationFiltration	 1.2.5	2023-12-18 
diff --git a/pipelines/broad/arrays/multi_sample/MultiSampleArrays.changelog.md b/pipelines/broad/arrays/multi_sample/MultiSampleArrays.changelog.md
@@ -1,3 +1,8 @@
+# 1.6.2
+2024-08-02 (Date of Last Commit)
+
+* The ubuntu_16_0_4 docker image version was pinned instead of using the latest tag; this does not affect the outputs of the pipeline
+
 # 1.6.1
 2022-04-14 (Date of Last Commit)
 

diff --git a/pipelines/broad/arrays/multi_sample/MultiSampleArrays.wdl b/pipelines/broad/arrays/multi_sample/MultiSampleArrays.wdl
@@ -18,7 +18,7 @@ version 1.0
 
 workflow MultiSampleArrays {
 
-  String pipeline_version = "1.6.1"
+  String pipeline_version = "1.6.2"
 
   input {
     File samples_fofn
@@ -83,7 +83,7 @@ task SplitFoFnToListFoFn {
   >>>
 
   runtime {
-    docker: "gcr.io/gcp-runtimes/ubuntu_16_0_4:latest"
+    docker: "gcr.io/gcp-runtimes/ubuntu_16_0_4@sha256:025124e2f1cf4d29149958f17270596bffe13fc6acca6252977c572dd5ba01bf"
     memory: "1 GiB"
   }
 

diff --git a/pipelines/broad/arrays/single_sample/Arrays.changelog.md b/pipelines/broad/arrays/single_sample/Arrays.changelog.md
@@ -1,3 +1,8 @@
+# 2.6.27
+2024-08-02 (Date of Last Commit)
+
+* The ubuntu_16_0_4 docker image version was pinned instead of using the latest tag; this does not affect the outputs of the pipeline
+
 # 2.6.26
 2024-06-12 (Date of Last Commit)
 

diff --git a/pipelines/broad/arrays/single_sample/Arrays.wdl b/pipelines/broad/arrays/single_sample/Arrays.wdl
@@ -23,7 +23,7 @@ import "../../../../tasks/broad/Utilities.wdl" as utils
 
 workflow Arrays {
 
-  String pipeline_version = "2.6.26"
+  String pipeline_version = "2.6.27"
 
   input {
     String chip_well_barcode

diff --git a/pipelines/broad/arrays/validate_chip/ValidateChip.changelog.md b/pipelines/broad/arrays/validate_chip/ValidateChip.changelog.md
@@ -1,3 +1,8 @@
+# 1.16.5
+2024-08-02 (Date of Last Commit)
+
+* The ubuntu_16_0_4 docker image version was pinned instead of using the latest tag; this does not affect the outputs of the pipeline
+
 # 1.16.4
 2023-12-18 (Date of Last Commit)
 

diff --git a/pipelines/broad/arrays/validate_chip/ValidateChip.wdl b/pipelines/broad/arrays/validate_chip/ValidateChip.wdl
@@ -21,7 +21,7 @@ import "../../../../tasks/broad/InternalArraysTasks.wdl" as InternalTasks
 
 workflow ValidateChip {
 
-  String pipeline_version = "1.16.4"
+  String pipeline_version = "1.16.5"
 
   input {
     String sample_alias

diff --git a/...seq/germline/single_sample/ugwgs/UltimaGenomicsWholeGenomeGermline.changelog.md b/...seq/germline/single_sample/ugwgs/UltimaGenomicsWholeGenomeGermline.changelog.md
@@ -1,3 +1,8 @@
+# 1.0.20
+2024-08-02 (Date of Last Commit)
+
+* The ubuntu_16_0_4 docker image version was pinned instead of using the latest tag; this does not affect the outputs of the pipeline
+
 # 1.0.19
 2024-06-12 (Date of Last Commit)
 

diff --git a/pipelines/broad/dna_seq/germline/single_sample/ugwgs/UltimaGenomicsWholeGenomeGermline.wdl b/pipelines/broad/dna_seq/germline/single_sample/ugwgs/UltimaGenomicsWholeGenomeGermline.wdl
@@ -50,7 +50,7 @@ workflow UltimaGenomicsWholeGenomeGermline {
     filtering_model_no_gt_name: "String describing the optional filtering model; default set to rf_model_ignore_gt_incl_hpol_runs"
   }
 
-  String pipeline_version = "1.0.19"
+  String pipeline_version = "1.0.20"
 
 
   References references = alignment_references.references

diff --git a/..._seq/somatic/single_sample/ugwgs/UltimaGenomicsWholeGenomeCramOnly.changelog.md b/..._seq/somatic/single_sample/ugwgs/UltimaGenomicsWholeGenomeCramOnly.changelog.md
@@ -1,3 +1,8 @@
+# 1.0.20
+2024-08-02 (Date of Last Commit)
+
+* The ubuntu_16_0_4 docker image version was pinned instead of using the latest tag; this does not affect the outputs of the pipeline
+
 # 1.0.19
 2024-06-12 (Date of Last Commit)
 

diff --git a/pipelines/broad/dna_seq/somatic/single_sample/ugwgs/UltimaGenomicsWholeGenomeCramOnly.wdl b/pipelines/broad/dna_seq/somatic/single_sample/ugwgs/UltimaGenomicsWholeGenomeCramOnly.wdl
@@ -43,7 +43,7 @@ workflow UltimaGenomicsWholeGenomeCramOnly {
     save_bam_file: "If true, then save intermeidate ouputs used by germline pipeline (such as the output BAM) otherwise they won't be kept as outputs."
   }
 
-  String pipeline_version = "1.0.19"
+  String pipeline_version = "1.0.20"
 
   References references = alignment_references.references
 

diff --git a/...tic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.changelog.md b/...tic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.changelog.md
@@ -1,3 +1,8 @@
+# 1.3.2
+2024-08-02  (Date of Last Commit)
+* 
+* The ubuntu_16_0_4 docker image version was pinned instead of using the latest tag; this does not affect the outputs of the pipeline
+
 # 1.3.1
 2024-01-19 (Date of Last Commit)
 

diff --git a/.../broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl b/.../broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl
@@ -623,7 +623,7 @@ task collect_insert_size_metrics {
 
 workflow GDCWholeGenomeSomaticSingleSample {
 
-    String pipeline_version = "1.3.1"
+    String pipeline_version = "1.3.2"
 
     input {
         File? input_cram

diff --git a/pipelines/broad/genotyping/illumina/IlluminaGenotypingArray.changelog.md b/pipelines/broad/genotyping/illumina/IlluminaGenotypingArray.changelog.md
@@ -1,3 +1,8 @@
+# 1.12.21
+2024-08-02 (Date of Last Commit)
+
+* The ubuntu_16_0_4 docker image version was pinned instead of using the latest tag; this does not affect the outputs of the pipeline  
+
 # 1.12.20
 2024-06-12 (Date of Last Commit)
 

diff --git a/pipelines/broad/genotyping/illumina/IlluminaGenotypingArray.wdl b/pipelines/broad/genotyping/illumina/IlluminaGenotypingArray.wdl
@@ -21,7 +21,7 @@ import "../../../../tasks/broad/Qc.wdl" as Qc
 
 workflow IlluminaGenotypingArray {
 
-  String pipeline_version = "1.12.20"
+  String pipeline_version = "1.12.21"
 
   input {
     String sample_alias

diff --git a/pipelines/broad/internal/arrays/imputation/BroadInternalImputation.changelog.md b/pipelines/broad/internal/arrays/imputation/BroadInternalImputation.changelog.md
@@ -1,3 +1,8 @@
+# 1.1.12
+2024-08-02 (Date of Last Commit)
+
+* The ubuntu_16_0_4 docker image version was pinned instead of using the latest tag; this does not affect the outputs of the pipeline
+
 # 1.1.11
 2024-05-21 (Date of Last Commit)
 

diff --git a/pipelines/broad/internal/arrays/imputation/BroadInternalImputation.wdl b/pipelines/broad/internal/arrays/imputation/BroadInternalImputation.wdl
@@ -9,7 +9,7 @@ workflow BroadInternalImputation {
         description: "Push outputs of Imputation.wdl to TDR dataset table ImputationOutputsTable and split out Imputation arrays into ImputationWideOutputsTable."
         allowNestedInputs: true
     }
-    String pipeline_version = "1.1.11"
+    String pipeline_version = "1.1.12"
 
     input {
         # inputs to wrapper task 

diff --git a/pipelines/broad/internal/arrays/single_sample/BroadInternalArrays.changelog.md b/pipelines/broad/internal/arrays/single_sample/BroadInternalArrays.changelog.md
@@ -1,3 +1,8 @@
+# 1.1.11
+2024-08-02 (Date of Last Commit)
+
+* The ubuntu_16_0_4 docker image version was pinned instead of using the latest tag; this does not affect the outputs of the pipeline
+
 # 1.1.10
 2024-06-12 (Date of Last Commit)
 

diff --git a/pipelines/broad/internal/arrays/single_sample/BroadInternalArrays.wdl b/pipelines/broad/internal/arrays/single_sample/BroadInternalArrays.wdl
@@ -9,7 +9,7 @@ workflow BroadInternalArrays {
         description: "Push outputs of Arrays.wdl to TDR dataset table ArraysOutputsTable."
     }
 
-    String pipeline_version = "1.1.10"
+    String pipeline_version = "1.1.11"
 
     input {
         # inputs to wrapper task

diff --git a/.../germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.changelog.md b/.../germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.changelog.md
@@ -1,3 +1,8 @@
+# 1.0.21
+2024-08-02 (Date of Last Commit)
+
+* The ubuntu_16_0_4 docker image version was pinned instead of using the latest tag; this does not affect the outputs of the pipeline
+
 # 1.0.20
 2024-06-12 (Date of Last Commit)
 

diff --git a/...ad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl b/...ad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl
@@ -6,7 +6,7 @@ import "../../../../../../../pipelines/broad/qc/CheckFingerprint.wdl" as FP
 
 workflow BroadInternalUltimaGenomics {
 
-  String pipeline_version = "1.0.20"
+  String pipeline_version = "1.0.21"
 
   input {
 

diff --git a/pipelines/broad/internal/rna_seq/BroadInternalRNAWithUMIs.changelog.md b/pipelines/broad/internal/rna_seq/BroadInternalRNAWithUMIs.changelog.md
@@ -1,3 +1,8 @@
+# 1.0.33
+2024-08-02 (Date of Last Commit)
+
+* The ubuntu_16_0_4 docker image version was pinned instead of using the latest tag; this does not affect the outputs of the pipeline
+
 # 1.0.32
 2024-06-12 (Date of Last Commit)
 

diff --git a/pipelines/broad/internal/rna_seq/BroadInternalRNAWithUMIs.wdl b/pipelines/broad/internal/rna_seq/BroadInternalRNAWithUMIs.wdl
@@ -7,7 +7,7 @@ import "../../../../tasks/broad/Utilities.wdl" as utils
 
 workflow BroadInternalRNAWithUMIs {
 
-  String pipeline_version = "1.0.32"
+  String pipeline_version = "1.0.33"
 
   input {
     # input needs to be either "hg19" or "hg38"

diff --git a/pipelines/broad/qc/CheckFingerprint.changelog.md b/pipelines/broad/qc/CheckFingerprint.changelog.md
@@ -1,3 +1,8 @@
+# 1.0.20
+2024-08-02 (Date of Last Commit)
+
+* The ubuntu_16_0_4 docker image version was pinned instead of using the latest tag; this does not affect the outputs of the pipeline
+
 # 1.0.19
 2024-06-12 (Date of Last Commit)
 

diff --git a/pipelines/broad/qc/CheckFingerprint.wdl b/pipelines/broad/qc/CheckFingerprint.wdl
@@ -24,7 +24,7 @@ import "../../../tasks/broad/Qc.wdl" as Qc
 
 workflow CheckFingerprint {
 
-  String pipeline_version = "1.0.19"
+  String pipeline_version = "1.0.20"
 
   input {
     File? input_vcf

diff --git a/pipelines/broad/reprocessing/cram_to_unmapped_bams/CramToUnmappedBams.changelog.md b/pipelines/broad/reprocessing/cram_to_unmapped_bams/CramToUnmappedBams.changelog.md
@@ -1,3 +1,8 @@
+# 1.1.3
+2024-08-02 (Date of Last Commit)
+
+* The ubuntu_16_0_4 docker image version was pinned instead of using the latest tag; this does not affect the outputs of the pipeline
+
 # 1.1.2
 2022-04-14 (Date of Last Commit)
 

diff --git a/pipelines/broad/reprocessing/cram_to_unmapped_bams/CramToUnmappedBams.wdl b/pipelines/broad/reprocessing/cram_to_unmapped_bams/CramToUnmappedBams.wdl
@@ -9,7 +9,7 @@ version 1.0
 # If the file is not provided, the output names of the unmapped bams will be the read_group_id<unmapped_bam_suffix>
 workflow CramToUnmappedBams {
 
-  String pipeline_version = "1.1.2"
+  String pipeline_version = "1.1.3"
 
   input {
     File? input_cram
@@ -222,7 +222,7 @@ task SplitUpOutputMapFile {
   >>>
 
   runtime {
-    docker: "gcr.io/gcp-runtimes/ubuntu_16_0_4:latest"
+    docker: "gcr.io/gcp-runtimes/ubuntu_16_0_4@sha256:025124e2f1cf4d29149958f17270596bffe13fc6acca6252977c572dd5ba01bf"
     disks: "local-disk " + disk_size + " HDD"
     memory: "~{memory_in_MiB} MiB"
   }

diff --git a/pipelines/broad/reprocessing/exome/ExomeReprocessing.changelog.md b/pipelines/broad/reprocessing/exome/ExomeReprocessing.changelog.md
@@ -1,3 +1,8 @@
+# 3.2.2
+2024-08-02 (Date of Last Commit)
+
+* The ubuntu_16_0_4 docker image version was pinned instead of using the latest tag; this does not affect the outputs of the pipeline
+
 # 3.2.1
 2024-06-12 (Date of Last Commit)
 

diff --git a/pipelines/broad/reprocessing/exome/ExomeReprocessing.wdl b/pipelines/broad/reprocessing/exome/ExomeReprocessing.wdl
@@ -7,7 +7,7 @@ import "../../../../structs/dna_seq/DNASeqStructs.wdl"
 workflow ExomeReprocessing {
 
 
-  String pipeline_version = "3.2.1"
+  String pipeline_version = "3.2.2"
 
   input {
     File? input_cram

diff --git a/pipelines/broad/reprocessing/external/exome/ExternalExomeReprocessing.changelog.md b/pipelines/broad/reprocessing/external/exome/ExternalExomeReprocessing.changelog.md
@@ -1,3 +1,8 @@
+# 3.2.2
+2024-08-02 (Date of Last Commit)
+
+* The ubuntu_16_0_4 docker image version was pinned instead of using the latest tag; this does not affect the outputs of the pipeline
+
 # 3.2.1
 2024-06-12 (Date of Last Commit)
 

diff --git a/pipelines/broad/reprocessing/external/exome/ExternalExomeReprocessing.wdl b/pipelines/broad/reprocessing/external/exome/ExternalExomeReprocessing.wdl
@@ -5,7 +5,7 @@ import "../../../../../tasks/broad/CopyFilesFromCloudToCloud.wdl" as Copy
 
 workflow ExternalExomeReprocessing {
 
-  String pipeline_version = "3.2.1"
+  String pipeline_version = "3.2.2"
 
 
   input {

diff --git a/...es/broad/reprocessing/external/wgs/ExternalWholeGenomeReprocessing.changelog.md b/...es/broad/reprocessing/external/wgs/ExternalWholeGenomeReprocessing.changelog.md
@@ -1,3 +1,8 @@
+# 2.2.2
+2024-08-02 (Date of Last Commit)
+
+* The ubuntu_16_0_4 docker image version was pinned instead of using the latest tag; this does not affect the outputs of the pipeline
+
 # 2.2.1
 2024-06-12 (Date of Last Commit)
 

diff --git a/pipelines/broad/reprocessing/external/wgs/ExternalWholeGenomeReprocessing.wdl b/pipelines/broad/reprocessing/external/wgs/ExternalWholeGenomeReprocessing.wdl
@@ -6,7 +6,7 @@ import "../../../../../tasks/broad/CopyFilesFromCloudToCloud.wdl" as Copy
 workflow ExternalWholeGenomeReprocessing {
 
 
-  String pipeline_version = "2.2.1"
+  String pipeline_version = "2.2.2"
 
   input {
     File? input_cram

diff --git a/pipelines/broad/reprocessing/wgs/WholeGenomeReprocessing.changelog.md b/pipelines/broad/reprocessing/wgs/WholeGenomeReprocessing.changelog.md
@@ -1,3 +1,8 @@
+# 3.2.2
+2024-08-02 (Date of Last Commit)
+
+* The ubuntu_16_0_4 docker image version was pinned instead of using the latest tag; this does not affect the outputs of the pipeline
+
 # 3.2.1
 2024-06-12 (Date of Last Commit)
-Original file line number
+Diff line change
@@ Expand Up @@
     workflow BroadInternalUltimaGenomics {
-      String pipeline_version = "1.0.20"
+      String pipeline_version = "1.0.21"
       input {
@@ Expand Down @@