Merge pull request #828 from broadinstitute/emerge_gcr_images

BroadInternalArrays and BroadInternalImputation: change docker from dockerhub to gcr
broadinstitute · Sep 30, 2022 · 70317fc · 70317fc
2 parents c8f2a9c + bc3b8a3
commit 70317fc
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diff --git a/pipelines/broad/arrays/imputation/Imputation.changelog.md b/pipelines/broad/arrays/imputation/Imputation.changelog.md
@@ -1,7 +1,8 @@
 # 1.1.5
-2022-09-23 (Date of Last Commit)
+2022-09-30 (Date of Last Commit)
 
 * Updated BCFTools/VCFTools and Minimac4 Docker images to fix vulnerabilities.
+* Updated tasks FormatImputationOutputs, FormatImputationWideOutputs, and IngestOutputsToTDR with GCR images instead of Dockerhub.
 
 # 1.1.4
 2022-08-23 (Date of Last Commit)

diff --git a/pipelines/broad/arrays/single_sample/Arrays.changelog.md b/pipelines/broad/arrays/single_sample/Arrays.changelog.md
@@ -1,7 +1,8 @@
 # 2.6.15
-2022-09-23 (Date of Last Commit)
+2022-09-30 (Date of Last Commit)
 
 * Updated Picard-Python Docker image in Utilities.wdl to fix vulnerabilities.
+* Updated tasks FormatArraysOutputs and IngestOutputsToTDR with GCR images instead of Dockerhub.
 
 # 2.6.14
 2022-09-07 (Date of Last Commit)

diff --git a/pipelines/broad/arrays/validate_chip/ValidateChip.changelog.md b/pipelines/broad/arrays/validate_chip/ValidateChip.changelog.md
@@ -1,7 +1,8 @@
 # 1.16.0
-2022-09-07 (Date of Last Commit)
+2022-09-30 (Date of Last Commit)
 
 * Updated task IngestOutputsToTDR in InternalTasks.wdl with new docker tag to accommodate changes for BroadInternalArrays pipeline. Change has no effect on this pipeline.
+* Updated task IngestOutputsToTDR with GCR images instead of Dockerhub.
 
 # 1.15.9
 2022-06-15 (Date of Last Commit)

diff --git a/...seq/germline/single_sample/ugwgs/UltimaGenomicsWholeGenomeGermline.changelog.md b/...seq/germline/single_sample/ugwgs/UltimaGenomicsWholeGenomeGermline.changelog.md
@@ -1,7 +1,8 @@
 # 1.0.4
-2022-09-23 (Date of Last Commit)
+2022-09-30 (Date of Last Commit)
 
 * Updated Picard-Python Docker image in Utilities.wdl to fix vulnerabilities.
+* Updated task IngestOutputsToTDR with GCR images instead of Dockerhub.
 
 # 1.0.3
 2022-09-20 (Date of Last Commit)

diff --git a/..._seq/somatic/single_sample/ugwgs/UltimaGenomicsWholeGenomeCramOnly.changelog.md b/..._seq/somatic/single_sample/ugwgs/UltimaGenomicsWholeGenomeCramOnly.changelog.md
@@ -1,7 +1,8 @@
 # 1.0.4
-2022-09-23 (Date of Last Commit)
+2022-09-30 (Date of Last Commit)
 
 * Updated Picard-Python Docker image in Utilities.wdl to fix vulnerabilities.
+* Updated task IngestOutputsToTDR with GCR images instead of Dockerhub.
 
 # 1.0.3
 2022-09-20 (Date of Last Commit)

diff --git a/pipelines/broad/internal/arrays/imputation/BroadInternalImputation.changelog.md b/pipelines/broad/internal/arrays/imputation/BroadInternalImputation.changelog.md
@@ -1,17 +1,19 @@
 # 1.1.1
-2022-09-23 (Date of Last Commit)
+2022-09-30 (Date of Last Commit)
 
 * Updated Picard-Python, BCFTools/VCFTools, and Minimac4 Docker images to fix vulnerabilities.
+* Updated tasks FormatImputationOutputs, FormatImputationWideOutputs, and IngestOutputsToTDR with GCR images instead of Dockerhub.
 
 # 1.1.0
-2022-09-06 (Date of Last Commit)
+2022-09-20 (Date of Last Commit)
 
 * Updated call to IngestOutputsToTDR to remove 'prefix_column'. Python script has been updated and not longer requires this input parameter.
 * Update task IngestOutputsToTDR to not require 'prefix_column'. Python script has been updated and not longer requires this input parameter.
 
 * Update task FormatImputationOutputs with new docker tag.
 * Update task FormatImputationWideOutputs with new docker tag.
 * Update task IngestOutputsToTDR with new docker tag.
+* Update tasks FormatImputationOutputs, FormatImputationWideOutputs, and IngestOutputsToTDR with GCR image instead of DockerHub image.
 
 # 1.0.9
 2022-08-29 (Date of Last Commit)

diff --git a/pipelines/broad/internal/arrays/single_sample/BroadInternalArrays.changelog.md b/pipelines/broad/internal/arrays/single_sample/BroadInternalArrays.changelog.md
@@ -1,17 +1,18 @@
 # 1.0.7
-2022-09-23 (Date of Last Commit)
+2022-09-30 (Date of Last Commit)
 
 * Updated Picard-Python Docker image in Utilities.wdl to fix vulnerabilities.
+* Updated tasks FormatArraysOutputs and IngestOutputsToTDR with GCR images instead of Dockerhub.
 
 # 1.0.6
-2022-09-02 (Date of Last Commit)
+2022-09-20 (Date of Last Commit)
 
 * Updated call to IngestOutputsToTDR to remove 'prefix_column'. Python script has been updated and not longer requires this input parameter.
 * Update task IngestOutputsToTDR to not require 'prefix_column'. Python script has been updated and not longer requires this input parameter.
 
 * Update task FormatArraysOutputs with new docker tag.
 * Update task IngestOutputsToTDR with new docker tag.
-
+* Update tasks FormatArraysOutputs and IngestOutputsToTDR with GCR image instead of DockerHub image.
 
 # 1.0.5
 2022-08-29 (Date of Last Commit)

diff --git a/.../germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.changelog.md b/.../germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.changelog.md
@@ -1,7 +1,8 @@
 # 1.0.5
-2022-09-23 (Date of Last Commit)
+2022-09-30 (Date of Last Commit)
 
 * Updated Picard-Python Docker image in Utilities.wdl to fix vulnerabilities.
+* Updated task IngestOutputsToTDR with GCR images instead of Dockerhub.
 
 # 1.0.4
 2022-09-20 (Date of Last Commit)

diff --git a/pipelines/broad/internal/rna_seq/BroadInternalRNAWithUMIs.changelog.md b/pipelines/broad/internal/rna_seq/BroadInternalRNAWithUMIs.changelog.md
@@ -1,7 +1,8 @@
 # 1.0.18
-2022-09-23 (Date of Last Commit)
+2022-09-30 (Date of Last Commit)
 
 * Updated Picard-Python Docker image in Utilities.wdl to fix vulnerabilities.
+* Updated task IngestOutputsToTDR with GCR images instead of Dockerhub.
 
 # 1.0.17
 2022-09-07 (Date of Last Commit)

diff --git a/pipelines/broad/qc/CheckFingerprint.changelog.md b/pipelines/broad/qc/CheckFingerprint.changelog.md
@@ -1,7 +1,8 @@
 # 1.0.9
-2022-09-23 (Date of Last Commit)
+2022-09-30 (Date of Last Commit)
 
 * Updated Picard-Python Docker image in Utilities.wdl to fix vulnerabilities.
+* Updated task IngestOutputsToTDR with GCR images instead of Dockerhub.
 
 # 1.0.8
 2022-09-07 (Date of Last Commit)

diff --git a/tasks/broad/InternalArraysTasks.wdl b/tasks/broad/InternalArraysTasks.wdl
@@ -541,7 +541,7 @@ task FormatArraysOutputs {
     >>>
 
     runtime {
-        docker: "broadinstitute/horsefish:eMerge_09022022"
+        docker: "gcr.io/emerge-production/emerge_wdls:emerge_09022022"
     }
 
     output {

diff --git a/tasks/broad/InternalImputationTasks.wdl b/tasks/broad/InternalImputationTasks.wdl
@@ -48,7 +48,7 @@ task FormatImputationOutputs {
     >>>
 
     runtime {
-        docker: "broadinstitute/horsefish:eMerge_09022022"
+        docker: "gcr.io/emerge-production/emerge_wdls:emerge_09022022"
     }
 
     output {
@@ -115,7 +115,7 @@ task FormatImputationWideOutputs{
     >>>
 
     runtime {
-        docker: "broadinstitute/horsefish:eMerge_09022022"
+        docker: "gcr.io/emerge-production/emerge_wdls:emerge_09022022"
     }
 
     output {

diff --git a/tasks/broad/InternalTasks.wdl b/tasks/broad/InternalTasks.wdl
@@ -193,7 +193,7 @@ task IngestOutputsToTDR {
     }
 
     runtime {
-        docker: "broadinstitute/horsefish:eMerge_09022022"
+        docker: "gcr.io/emerge-production/emerge_wdls:emerge_09022022"
     }
 
     output {