Merge pull request #1317 from broadinstitute/develop

Dev -> Staging
broadinstitute · Jul 2, 2024 · ddc7397 · ddc7397
2 parents 9efa59e + 55c6b12
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diff --git a/.github/workflows/update_versions_file.yml b/.github/workflows/update_versions_file.yml
@@ -0,0 +1,54 @@
+# This is a github action that will update a file named “pipeline_versions.txt” (or create if it doesn’t exist) with the following content: 
+# tab-delimited with columns  “pipeline name”, “version”, “date of last commit”. 
+
+name: Update Pipeline Versions
+on:
+  pull_request:
+    # This workflow will run on PR to master and staging branches
+    branches:
+      - master
+      - staging
+  workflow_dispatch:
+
+jobs:
+  update_versions:
+    runs-on: ubuntu-latest
+
+    steps:
+      # This step checks out the code - explicitly fetch the history and checkout the branch to enable us to push files back to the repo
+      - name: Checkout repository
+        uses: actions/checkout@v3
+        with:
+          ref: ${{ github.head_ref }} # This fetches the branch name that triggered the workflow
+          fetch-depth: 0 # This fetches all history for all branches and tags
+
+      # This step sets up Python environment
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.x
+
+      # This step updates a a file called "pipeline_versions.txt" with the names, versions, and last commit dates of all the pipelines found in the 
+      # "warp/pipelines" directory by parsing the contents of the "*.changelog.md" files.
+      - name: Update Pipeline Versions
+        run: |
+          echo "Current directory: "
+          pwd
+          ls -lht
+          echo -e "Pipeline Name\tVersion\tDate of Last Commit" > pipeline_versions.txt
+          find pipelines -name "*.changelog.md" -type f | while read -r file; do
+            pipeline_name=$(basename "$file" .changelog.md)
+            version=$(head -n 1 "$file" | sed 's/#//')
+            last_commit_date=$(sed -n '2p' "$file" | sed 's/([^)]*)//g')
+            echo -e "$pipeline_name\t$version\t$last_commit_date" >> pipeline_versions.txt
+          done
+        
+      # This step commits and pushes the changes to the repository
+      - name: Commit and push changes
+        run: |
+          git config --local user.email "[email protected]"
+          git config --local user.name "GitHub Action"
+          git add pipeline_versions.txt
+          git commit -m "Update pipeline versions"
+          git push
+        
diff --git a/pipeline_versions.txt b/pipeline_versions.txt
@@ -0,0 +1,42 @@
+Pipeline Name	Version	Date of Last Commit
+MultiSampleSmartSeq2	 2.2.21	2023-04-19 
+SmartSeq2SingleSample	 5.1.20	2023-04-19 
+snm3C	 4.0.0	2024-03-15 
+Optimus	 7.1.0	2024-05-20 
+scATAC	 1.3.2	2023-08-03 
+MultiSampleSmartSeq2SingleNucleus	 1.3.4	2024-04-12 
+SlideSeq	 3.1.6	2024-05-20 
+BuildIndices	 3.0.0	2023-12-06 
+PairedTag	 0.7.0	2024-05-20
+atac	 2.0.0	2024-05-20 
+Multiome	 5.0.0	2024-05-20 
+CEMBA	 1.1.6	2023-12-18 
+BuildCembaReferences	 1.0.0	2020-11-15 
+IlluminaGenotypingArray	 1.12.17	2024-03-26 
+ExomeReprocessing	 3.1.19	2024-03-26 
+WholeGenomeReprocessing	 3.1.20	2024-03-26 
+ExternalExomeReprocessing	 3.1.21	2024-03-26 
+ExternalWholeGenomeReprocessing	 2.1.21	2024-03-26 
+CramToUnmappedBams	 1.1.2	2022-04-14 
+AnnotationFiltration	 1.2.5	2023-12-18 
+BroadInternalUltimaGenomics	 1.0.17	2024-03-26 
+BroadInternalRNAWithUMIs	 1.0.29	2024-03-26 
+BroadInternalImputation	 1.1.10	2023-12-18 
+BroadInternalArrays	 1.1.7	2024-03-26 
+UltimaGenomicsWholeGenomeCramOnly	 1.0.16	2024-03-26 
+GDCWholeGenomeSomaticSingleSample	 1.3.1	2024-01-19 
+VariantCalling	 2.1.18	2024-03-26 
+JointGenotyping	 1.6.10	2023-12-18 
+JointGenotypingByChromosomePartOne	 1.4.12	2023-12-18 
+JointGenotypingByChromosomePartTwo	 1.4.11	2023-12-18 
+UltimaGenomicsJointGenotyping	 1.1.7	2023-12-18 
+ReblockGVCF	 2.1.12	2024-03-26 
+ExomeGermlineSingleSample	 3.1.19	2024-03-26 
+UltimaGenomicsWholeGenomeGermline	 1.0.16	2024-03-26 
+WholeGenomeGermlineSingleSample	 3.1.20	2024-03-26 
+RNAWithUMIsPipeline	 1.0.16	2023-12-18 
+CheckFingerprint	 1.0.16	2024-03-26 
+ValidateChip	 1.16.4	2023-12-18 
+Imputation	 1.1.12	2023-12-18 
+MultiSampleArrays	 1.6.1	2022-04-14 
+Arrays	 2.6.23	2024-03-26 
diff --git a/pipelines/broad/arrays/single_sample/Arrays.changelog.md b/pipelines/broad/arrays/single_sample/Arrays.changelog.md
@@ -1,3 +1,8 @@
+# 2.6.24
+2024-07-01 (Date of Last Commit)
+
+* CalculateReadGroupChecksum requires more memory and disk; this does not affect this pipeline
+
 # 2.6.23
 2024-03-26 (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 = "2.6.23"
+  String pipeline_version = "2.6.24"
 
   input {
     String chip_well_barcode

diff --git a/...nes/broad/dna_seq/germline/joint_genotyping/reblocking/ReblockGVCF.changelog.md b/...nes/broad/dna_seq/germline/joint_genotyping/reblocking/ReblockGVCF.changelog.md
@@ -1,3 +1,8 @@
+# 2.1.13
+2024-07-01 (Date of Last Commit)
+
+* CalculateReadGroupChecksum requires more memory and disk; this does not affect this pipeline
+
 # 2.1.12
 2024-03-26 (Date of Last Commit)
 

diff --git a/pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/ReblockGVCF.wdl b/pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/ReblockGVCF.wdl
@@ -5,7 +5,7 @@ import "../../../../../../tasks/broad/Qc.wdl" as QC
 
 workflow ReblockGVCF {
 
-  String pipeline_version = "2.1.12"
+  String pipeline_version = "2.1.13"
 
 
   input {

diff --git a/...oad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.changelog.md b/...oad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.changelog.md
@@ -1,3 +1,8 @@
+# 3.1.20
+2024-07-01 (Date of Last Commit)
+
+* CalculateReadGroupChecksum requires more memory and disk; this does not affect this pipeline
+
 # 3.1.19
 2024-03-26 (Date of Last Commit)
 

diff --git a/pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl b/pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl
@@ -44,7 +44,7 @@ import "../../../../../../structs/dna_seq/DNASeqStructs.wdl"
 # WORKFLOW DEFINITION
 workflow ExomeGermlineSingleSample {
 
-  String pipeline_version = "3.1.19"
+  String pipeline_version = "3.1.20"
 
 
   input {

diff --git a/...seq/germline/single_sample/ugwgs/UltimaGenomicsWholeGenomeGermline.changelog.md b/...seq/germline/single_sample/ugwgs/UltimaGenomicsWholeGenomeGermline.changelog.md
@@ -1,3 +1,8 @@
+# 1.0.17
+2024-07-01 (Date of Last Commit)
+
+* CalculateReadGroupChecksum requires more memory and disk; this does not affect this pipeline
+
 # 1.0.16
 2024-03-26 (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 = "1.0.16"
+  String pipeline_version = "1.0.17"
 
 
   References references = alignment_references.references

diff --git a/...dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.changelog.md b/...dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.changelog.md
@@ -1,3 +1,8 @@
+# 3.1.21
+2024-07-01 (Date of Last Commit)
+
+* CalculateReadGroupChecksum requires more memory and disk
+
 # 3.1.20
 2024-03-26 (Date of Last Commit)
 

diff --git a/pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl b/pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl
@@ -40,7 +40,7 @@ import "../../../../../../structs/dna_seq/DNASeqStructs.wdl"
 workflow WholeGenomeGermlineSingleSample {
 
 
-  String pipeline_version = "3.1.20"
+  String pipeline_version = "3.1.21"
 
 
   input {

diff --git a/pipelines/broad/dna_seq/germline/variant_calling/VariantCalling.changelog.md b/pipelines/broad/dna_seq/germline/variant_calling/VariantCalling.changelog.md
@@ -1,3 +1,8 @@
+# 2.1.19
+2024-07-01 (Date of Last Commit)
+
+* CalculateReadGroupChecksum requires more memory and disk; this does not affect this pipeline
+
 # 2.1.18
 2024-03-26 (Date of Last Commit)
 

diff --git a/pipelines/broad/dna_seq/germline/variant_calling/VariantCalling.wdl b/pipelines/broad/dna_seq/germline/variant_calling/VariantCalling.wdl
@@ -9,7 +9,7 @@ import "../../../../../tasks/broad/DragenTasks.wdl" as DragenTasks
 workflow VariantCalling {
 
 
-  String pipeline_version = "2.1.18"
+  String pipeline_version = "2.1.19"
 
 
   input {

diff --git a/..._seq/somatic/single_sample/ugwgs/UltimaGenomicsWholeGenomeCramOnly.changelog.md b/..._seq/somatic/single_sample/ugwgs/UltimaGenomicsWholeGenomeCramOnly.changelog.md
@@ -1,3 +1,8 @@
+# 1.0.17
+2024-07-01 (Date of Last Commit)
+
+* CalculateReadGroupChecksum requires more memory and disk; this does not affect this pipeline
+
 # 1.0.16
 2024-03-26 (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 = "1.0.16"
+  String pipeline_version = "1.0.17"
 
   References references = alignment_references.references
 

diff --git a/pipelines/broad/genotyping/illumina/IlluminaGenotypingArray.changelog.md b/pipelines/broad/genotyping/illumina/IlluminaGenotypingArray.changelog.md
@@ -1,3 +1,8 @@
+# 1.12.18
+2024-07-01 (Date of Last Commit)
+
+* CalculateReadGroupChecksum requires more memory and disk; this does not affect this pipeline
+
 # 1.12.17
 2024-03-26 (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 = "1.12.17"
+  String pipeline_version = "1.12.18"
 
   input {
     String sample_alias

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 @@
+# 1.1.8
+2024-07-01 (Date of Last Commit)
+
+* CalculateReadGroupChecksum requires more memory and disk; this does not affect this pipeline
+
 # 1.1.7
 2024-03-26 (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 = "1.1.7"
+    String pipeline_version = "1.1.8"
 
     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 @@
+# 1.0.18
+2024-07-01 (Date of Last Commit)
+
+* CalculateReadGroupChecksum requires more memory and disk; this does not affect this pipeline
+
 # 1.0.17
 2024-03-26 (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 = "1.0.17"
+  String pipeline_version = "1.0.18"
 
   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 @@
+# 1.0.30
+2024-07-01 (Date of Last Commit)
+
+* CalculateReadGroupChecksum requires more memory and disk; this does not affect this pipeline
+
 # 1.0.29
 2024-03-26 (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 = "1.0.29"
+  String pipeline_version = "1.0.30"
 
   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 @@
+# 1.0.17
+2024-07-01 (Date of Last Commit)
+
+* CalculateReadGroupChecksum requires more memory and disk; this does not affect this pipeline
+
 # 1.0.16
 2024-03-26 (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 = "1.0.16"
+  String pipeline_version = "1.0.17"
 
   input {
     File? input_vcf

diff --git a/pipelines/broad/reprocessing/exome/ExomeReprocessing.changelog.md b/pipelines/broad/reprocessing/exome/ExomeReprocessing.changelog.md
@@ -1,3 +1,8 @@
+# 3.1.20
+2024-07-01 (Date of Last Commit)
+
+* CalculateReadGroupChecksum requires more memory and disk; this does not affect this pipeline
+
 # 3.1.19
 2024-03-26 (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 = "3.1.19"
+  String pipeline_version = "3.1.20"
 
   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 @@
+# 3.1.22
+2024-07-01 (Date of Last Commit)
+
+* CalculateReadGroupChecksum requires more memory and disk; this does not affect this pipeline
+
 # 3.1.21
 2024-03-26 (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 = "3.1.21"
+  String pipeline_version = "3.1.22"
 
 
   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 @@
+# 2.1.22
+2024-07-01 (Date of Last Commit)
+
+* CalculateReadGroupChecksum requires more memory and disk
+
 # 2.1.21
 2024-03-26 (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 = "2.1.21"
+  String pipeline_version = "2.1.22"
 
   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 @@
+# 3.1.21
+2024-07-01 (Date of Last Commit)
+
+* CalculateReadGroupChecksum requires more memory and disk
+
 # 3.1.20
 2024-03-26 (Date of Last Commit)
 

diff --git a/pipelines/broad/reprocessing/wgs/WholeGenomeReprocessing.wdl b/pipelines/broad/reprocessing/wgs/WholeGenomeReprocessing.wdl
@@ -6,7 +6,7 @@ import "../../../../structs/dna_seq/DNASeqStructs.wdl"
 
 workflow WholeGenomeReprocessing {
 
-  String pipeline_version = "3.1.20"
+  String pipeline_version = "3.1.21"
 
   input {
     File? input_cram

diff --git a/pipelines/skylab/multiome/Multiome.changelog.md b/pipelines/skylab/multiome/Multiome.changelog.md
@@ -1,3 +1,9 @@
+# 5.1.0
+2024-06-28 (Date of Last Commit)
+
+* Updated the STARsolo parameters for estimating cells to Emptydrops_CR
+* Added an optional input for expected cells which is used for metric calculation
+
 # 5.0.0
 2024-05-20 (Date of Last Commit)