Np revert both vbid dockers (#1136)

* add summary task * revert vbid dockers * changelogs * changelogs * changelogs * Update pipelines/broad/dna_seq/germline/single_sample/ugwgs/UltimaGenomicsWholeGenomeGermline.changelog.md * Update pipelines/broad/dna_seq/germline/single_sample/ugwgs/UltimaGenomicsWholeGenomeGermline.wdl * Update pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.changelog.md Co-authored-by: ekiernan <[email protected]> --------- Co-authored-by: ekiernan <[email protected]>
broadinstitute · Nov 30, 2023 · 41bb4b3 · 41bb4b3
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diff --git a/...oad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.changelog.md b/...oad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.changelog.md
@@ -1,7 +1,8 @@
 # 3.1.14
-2023-11-21 (Date of Last Commit)
+2023-11-29 (Date of Last Commit)
 
 * Fixed bug in ReblockGVCFs; this does not affect this pipeline.
+* Reverted the VerifyBamID docker image back to the 3.1.10 ExomeGermlineSingleSample pipeline version
 
 # 3.1.13
 2023-10-10 (Date of Last Commit)

diff --git a/...seq/germline/single_sample/ugwgs/UltimaGenomicsWholeGenomeGermline.changelog.md b/...seq/germline/single_sample/ugwgs/UltimaGenomicsWholeGenomeGermline.changelog.md
@@ -2,6 +2,7 @@
 2023-11-21 (Date of Last Commit)
 
 * Fixed bug in ReblockGVCFs; this does not affect this pipeline.
+* Reverted the VerifyBamID docker image back to the 1.0.9 UltimaGenomicsWholeGenomeGermline pipeline version
 
 # 1.0.10
 2023-09-18 (Date of Last Commit)

diff --git a/...dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.changelog.md b/...dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.changelog.md
@@ -1,7 +1,8 @@
 # 3.1.15
-2023-11-21 (Date of Last Commit)
+2023-11-29 (Date of Last Commit)
 
 * Fixed bug in ReblockGVCFs; this does not affect this pipeline.
+* Reverted the VerifyBamID docker image back to the 3.1.11 WholeGenomeGermlineSingleSample pipeline version
 
 # 3.1.14 
 2023-10-10 (Date of Last Commit)

diff --git a/pipelines/broad/dna_seq/germline/variant_calling/VariantCalling.changelog.md b/pipelines/broad/dna_seq/germline/variant_calling/VariantCalling.changelog.md
@@ -1,7 +1,8 @@
 # 2.1.13
-2023-11-21 (Date of Last Commit)
+2023-11-29 (Date of Last Commit)
 
 * Fixed bug in ReblockGVCFs; this does not affect this pipeline.
+* Reverted the VerifyBamID docker image back to the 2.1.10 VariantCalling pipeline version
 
 # 2.1.12
 2023-09-18 (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 @@
 # 1.0.11
-2023-11-21 (Date of Last Commit)
+2023-11-29 (Date of Last Commit)
 
 * Fixed bug in ReblockGVCFs; this does not affect this pipeline.
+* Reverted the VerifyBamID docker image back to the 1.0.8 UltimaGenomicsWholeGenomeCramOnly pipeline version
 
 # 1.0.10
 2023-09-18 (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 @@
 # 1.0.12
-2023-11-21 (Date of Last Commit)
+2023-11-29 (Date of Last Commit)
 
 * Fixed bug in ReblockGVCFs; this does not affect this pipeline.
+* Reverted the VerifyBamID docker image back to the 1.0.9 BroadInternalUltimaGenomics pipeline version
 
 # 1.0.11
 2023-09-18 (Date of Last Commit)

diff --git a/pipelines/broad/reprocessing/exome/ExomeReprocessing.changelog.md b/pipelines/broad/reprocessing/exome/ExomeReprocessing.changelog.md
@@ -1,7 +1,8 @@
 # 3.1.14
-2023-11-21 (Date of Last Commit)
+2023-11-29 (Date of Last Commit)
 
 * Fixed bug in ReblockGVCFs; this does not affect this pipeline.
+* Reverted the VerifyBamID docker image back to the 3.1.10 ExomeReprocessing pipeline version
 
 # 3.1.13
 2023-10-10 (Date of Last Commit)

diff --git a/pipelines/broad/reprocessing/external/exome/ExternalExomeReprocessing.changelog.md b/pipelines/broad/reprocessing/external/exome/ExternalExomeReprocessing.changelog.md
@@ -1,7 +1,8 @@
 # 3.1.16
-2023-11-21 (Date of Last Commit)
+2023-11-29 (Date of Last Commit)
 
 * Fixed bug in ReblockGVCFs; this does not affect this pipeline.
+* Reverted the VerifyBamID docker image back to the 3.1.12 ExternalExomeReprocessing pipeline version
 
 # 3.1.15
 2023-10-10 (Date of Last Commit)

diff --git a/...es/broad/reprocessing/external/wgs/ExternalWholeGenomeReprocessing.changelog.md b/...es/broad/reprocessing/external/wgs/ExternalWholeGenomeReprocessing.changelog.md
@@ -1,7 +1,8 @@
 # 2.1.16
-2023-11-21 (Date of Last Commit)
+2023-11-29 (Date of Last Commit)
 
 * Fixed bug in ReblockGVCFs; this does not affect this pipeline.
+* Reverted the VerifyBamID docker image back to the 2.1.12 ExternalWholeGenomeReprocessing pipeline version
 
 # 2.1.15
 2023-10-10 (Date of Last Commit)

diff --git a/pipelines/broad/reprocessing/wgs/WholeGenomeReprocessing.changelog.md b/pipelines/broad/reprocessing/wgs/WholeGenomeReprocessing.changelog.md
@@ -1,7 +1,8 @@
 # 3.1.15
-2023-11-21 (Date of Last Commit)
+2023-11-29 (Date of Last Commit)
 
 * Fixed bug in ReblockGVCFs; this does not affect this pipeline.
+* Reverted the VerifyBamID docker image back to the 3.1.11 WholeGenomeReprocessing pipeline version
 
 # 3.1.14
 2023-10-10 (Date of Last Commit)

diff --git a/tasks/broad/BamProcessing.wdl b/tasks/broad/BamProcessing.wdl
@@ -417,9 +417,7 @@ task CheckContamination {
     Float contamination_underestimation_factor
     Boolean disable_sanity_check = false
 
-    # this docker image was built using the commit hash c1cba76e979904eb69c31520a0d7f5be63c72253 (v1.0.6)from the VerifyBamID repo
-    # https://github.com/Griffan/VerifyBamID/commit/c1cba76e979904eb69c31520a0d7f5be63c72253
-    String docker = "us.gcr.io/broad-gotc-prod/verify-bam-id:1.0.1-c1cba76e979904eb69c31520a0d7f5be63c72253-1692099985"
+     String docker = "us.gcr.io/broad-gotc-prod/verify-bam-id:1.0.1-c1cba76e979904eb69c31520a0d7f5be63c72253-1639071840"
   }
 
   Int disk_size = ceil(size(input_bam, "GiB") + size(ref_fasta, "GiB")) + 30
@@ -468,8 +466,6 @@ task CheckContamination {
     preemptible: preemptible_tries
     memory: "7.5 GiB"
     disks: "local-disk " + disk_size + " HDD"
-    # this docker image was built using the commit hash c1cba76e979904eb69c31520a0d7f5be63c72253 from the VerifyBamID repo
-    # https://github.com/Griffan/VerifyBamID/commit/c1cba76e979904eb69c31520a0d7f5be63c72253
     docker: docker
     cpu: 2
   }

diff --git a/tasks/broad/UltimaGenomicsWholeGenomeGermlineTasks.wdl b/tasks/broad/UltimaGenomicsWholeGenomeGermlineTasks.wdl
@@ -390,9 +390,8 @@ task CheckContamination {
     References references
     String output_prefix
 
-    # this docker image was built using the commit hash f6cb51761861e57c43879aa262df5cf8e670cf7c (v2.0.1) from the VerifyBamID repo
-    # https://github.com/Griffan/VerifyBamID/commit/f6cb51761861e57c43879aa262df5cf8e670cf7c
-    String docker = "us.gcr.io/broad-gotc-prod/verify-bam-id:1.0.1-f6cb51761861e57c43879aa262df5cf8e670cf7c-1692216226"
+
+    String docker = "us.gcr.io/broad-gotc-prod/verify-bam-id:f6cb51761861e57c43879aa262df5cf8e670cf7c-1606775309"
     Int disk_size_gb = ceil(if ceil((size(input_bam, "GB")) +
                             (size(references.ref_fasta, "GB") +
                             size(references.ref_fasta_index, "GB") +