Merge pull request #386 from broadinstitute/staging

jessicaway · web-flow · commit e65a36708ee6 · 2021-08-04T15:06:04.000-04:00
Staging -&gt; Master
diff --git a/.dockstore.yml b/.dockstore.yml
@@ -1,37 +1,54 @@
 version: 1.2
 workflows:
+
   - name: Optimus
     subclass: WDL
     primaryDescriptorPath: /pipelines/skylab/optimus/Optimus.wdl
+
   - name: Smartseq2_Multisample
     subclass: WDL
     primaryDescriptorPath: /pipelines/skylab/smartseq2_multisample/MultiSampleSmartSeq2.wdl
+
   - name: Smartseq2_Single_Sample
     subclass: WDL
+    primaryDescriptorPath: /pipelines/skylab/smartseq2_single_sample/SmartSeq2SingleSample.wdl
+
   - name: Smartseq2_Single_Nucleus_Multisample
     subclass: WDL
     primaryDescriptorPath: /pipelines/skylab/smartseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.wdl
+
   - name: Smartseq2_Single_Nucleus
     subclass: WDL
     primaryDescriptorPath: /pipelines/skylab/smartseq2_single_nucleus/SmartSeq2SingleNucleus.wdl
+
   - name: IlluminaGenotypingArray
     subclass: WDL
     primaryDescriptorPath: /pipelines/broad/genotyping/illumina/IlluminaGenotypingArray.wdl
+
   - name: scATAC
     subclass: WDL
     primaryDescriptorPath: /pipelines/skylab/scATAC/scATAC.wdl
+
   - name: JointGenotyping
     subclass: WDL
     primaryDescriptorPath: /pipelines/broad/dna_seq/germline/joint_genotyping/JointGenotyping.wdl
+
   - name: ExomeGermlineSingleSample
     subclass: WDL
     primaryDescriptorPath: /pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl
+
   - name: WholeGenomeGermlineSingleSample
     subclass: WDL
     primaryDescriptorPath: /pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl
+
   - name: OptimusPostProcessing
     subclass: WDL
     primaryDescriptorPath: /projects/hca_mvp/OptimusPostProcessing.wdl
+
   - name: CEMBA
     subclass: WDL
-    primaryDescriptorPath: /pipelines/cemba/cemba_methylcseq/CEMBA.wdl
+    primaryDescriptorPath: /pipelines/cemba/cemba_methylcseq/CEMBA.wdl
+
+  - name: OptimusTestHcaAdapter
+    subclass: WDL
+    primaryDescriptorPath: /tests/skylab/hca_adapter/pr/optimus_test_hca_adapter_PR.wdl
diff --git a/pipelines/broad/arrays/single_sample/Arrays.changelog.md b/pipelines/broad/arrays/single_sample/Arrays.changelog.md
@@ -1,3 +1,9 @@
+
+# 2.3.6
+2021-08-02
+
+* Increased the version number to make new release tag for Dockstore 
+
 # 2.3.5
 2021-07-29
 
diff --git a/pipelines/broad/arrays/single_sample/Arrays.wdl b/pipelines/broad/arrays/single_sample/Arrays.wdl
@@ -21,7 +21,7 @@ import "../../../../tasks/broad/InternalArraysTasks.wdl" as InternalTasks
 
 workflow Arrays {
 
-  String pipeline_version = "2.3.5"
+  String pipeline_version = "2.3.6"
 
   input {
 
diff --git a/pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.changelog.md b/pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.changelog.md
@@ -1,3 +1,8 @@
+# 2.4.6
+2021-08-02
+
+* Increased the version number to make new release tag for Dockstore 
+
 # 2.4.5
 2021-06-22
 
diff --git a/pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl b/pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl
@@ -40,7 +40,7 @@ import "../../../../../../structs/dna_seq/DNASeqStructs.wdl"
 workflow ExomeGermlineSingleSample {
 
 
-  String pipeline_version = "2.4.5"
+  String pipeline_version = "2.4.6"
 
   input {
     PapiSettings papi_settings
diff --git a/pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.changelog.md b/pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.changelog.md
@@ -1,3 +1,9 @@
+
+# 2.3.6
+2021-08-02
+
+* Increased the version number to make new release tag for Dockstore 
+
 # 2.3.5
 2021-06-22
 
diff --git a/pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl b/pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl
@@ -38,7 +38,7 @@ import "../../../../../../structs/dna_seq/DNASeqStructs.wdl"
 # WORKFLOW DEFINITION
 workflow WholeGenomeGermlineSingleSample {
 
-  String pipeline_version = "2.3.5"
+  String pipeline_version = "2.3.6"
 
   input {
     SampleAndUnmappedBams sample_and_unmapped_bams
diff --git a/pipelines/broad/genotyping/illumina/IlluminaGenotypingArray.changelog.md b/pipelines/broad/genotyping/illumina/IlluminaGenotypingArray.changelog.md
@@ -1,7 +1,12 @@
+# 1.11.3
+2021-08-02
+
+* Increased the version number to make new release tag for Dockstore 
+
 # 1.11.2
 2021-07-13
 
-* Make chip_well_barcode and analysis_version_number available as outputs of the WDL.
+* Make chip_well_barcode and analysis_version_number available as outputs of the WDL
 
 # 1.11.1
 2021-05-19
@@ -11,7 +16,7 @@
 # 1.11.0
 2020-10-01
 
-* Added use of BafRegress to the pipeline.  BafRegress detects and estimates sample contamination using B allele frequency data from Illumina genotyping arrays using a regression model.
+* Added use of BafRegress to the pipeline.  BafRegress detects and estimates sample contamination using B allele frequency data from Illumina genotyping arrays using a regression model
 
 # 1.10.0
 2020-08-18
@@ -21,8 +26,7 @@
 # 1.9
 2020-07-31
 
-* Fixed a bug in CollectArraysVariantCallingMetrics and GenotypeConcordance where the metrics file is 
-  being parsed incorrectly if there is a space in the sample name value 
+* Fixed a bug in CollectArraysVariantCallingMetrics and GenotypeConcordance where the metrics file is being parsed incorrectly if there is a space in the sample name value 
   
 # 1.8.1
 2020-07-31
diff --git a/pipelines/broad/genotyping/illumina/IlluminaGenotypingArray.wdl b/pipelines/broad/genotyping/illumina/IlluminaGenotypingArray.wdl
@@ -20,7 +20,7 @@ import "../../../../tasks/broad/IlluminaGenotypingArrayTasks.wdl" as GenotypingT
 
 workflow IlluminaGenotypingArray {
 
-  String pipeline_version = "1.11.2"
+  String pipeline_version = "1.11.3"
 
   input {
 
diff --git a/pipelines/broad/reprocessing/exome/ExomeReprocessing.changelog.md b/pipelines/broad/reprocessing/exome/ExomeReprocessing.changelog.md
@@ -1,3 +1,10 @@
+
+# 2.4.8
+2021-08-02
+
+* Increased the version number to make new release tag for Dockstore 
+
+
 # 2.4.7
 2021-06-22
 
diff --git a/pipelines/broad/reprocessing/exome/ExomeReprocessing.wdl b/pipelines/broad/reprocessing/exome/ExomeReprocessing.wdl
@@ -6,7 +6,7 @@ import "../../../../structs/dna_seq/DNASeqStructs.wdl"
 
 workflow ExomeReprocessing {
 
-  String pipeline_version = "2.4.7"
+  String pipeline_version = "2.4.8"
 
   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 +1,9 @@
+
+# 2.4.8
+2021-08-02
+
+* Increased the version number to make new release tag for Dockstore 
+
 # 2.4.7
 2021-06-22
 
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 = "2.4.7"
+  String pipeline_version = "2.4.8"
 
   input {
     File? input_cram
diff --git a/pipelines/broad/reprocessing/external/wgs/ExternalWholeGenomeReprocessing.changelog.md b/pipelines/broad/reprocessing/external/wgs/ExternalWholeGenomeReprocessing.changelog.md
@@ -1,3 +1,9 @@
+# 1.3.8
+2021-08-02
+
+* Increased the version number to make new release tag for Dockstore 
+
+
 # 1.3.7
 2021-06-22
 
diff --git a/pipelines/broad/reprocessing/external/wgs/ExternalWholeGenomeReprocessing.wdl b/pipelines/broad/reprocessing/external/wgs/ExternalWholeGenomeReprocessing.wdl
@@ -5,7 +5,7 @@ import "../../../../../tasks/broad/CopyFilesFromCloudToCloud.wdl" as Copy
 
 workflow ExternalWholeGenomeReprocessing {
 
-  String pipeline_version = "1.3.7"
+  String pipeline_version = "1.3.8"
 
   input {
     File? input_cram
diff --git a/pipelines/broad/reprocessing/wgs/WholeGenomeReprocessing.changelog.md b/pipelines/broad/reprocessing/wgs/WholeGenomeReprocessing.changelog.md
@@ -1,3 +1,9 @@
+
+# 2.3.8
+2021-08-02
+
+* Increased the version number to make new release tag for Dockstore
+
 # 2.3.7
 2021-06-22
 
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 = "2.3.7"
+  String pipeline_version = "2.3.8"
 
   input {
     File? input_cram
diff --git a/pipelines/skylab/optimus/Optimus.changelog.md b/pipelines/skylab/optimus/Optimus.changelog.md
@@ -1,3 +1,9 @@
+
+# 4.2.7
+2021-08-02 (Date of Last Commit)
+
+* Increased the version number to make new release tag for Dockstore 
+
 # 4.2.6
 2021-07-19 (Date of Last Commit)
 
diff --git a/pipelines/skylab/optimus/Optimus.wdl b/pipelines/skylab/optimus/Optimus.wdl
@@ -59,7 +59,7 @@ workflow Optimus {
 
   # version of this pipeline
 
-  String pipeline_version = "4.2.6"
+  String pipeline_version = "4.2.7"
 
   # this is used to scatter matched [r1_fastq, r2_fastq, i1_fastq] arrays
   Array[Int] indices = range(length(r1_fastq))
diff --git a/pipelines/skylab/smartseq2_multisample/MultiSampleSmartSeq2.changelog.md b/pipelines/skylab/smartseq2_multisample/MultiSampleSmartSeq2.changelog.md
@@ -1,3 +1,9 @@
+
+# 2.2.4
+2021-08-02 (Date of Last Commit)
+
+* Increased the version number to make new release tag for Dockstore 
+
 # 2.2.3
 2021-07-19 (Date of Last Commit)
 
diff --git a/pipelines/skylab/smartseq2_multisample/MultiSampleSmartSeq2.wdl b/pipelines/skylab/smartseq2_multisample/MultiSampleSmartSeq2.wdl
@@ -40,7 +40,7 @@ workflow MultiSampleSmartSeq2 {
       Boolean paired_end
   }
   # Version of this pipeline
-  String pipeline_version = "2.2.3"
+  String pipeline_version = "2.2.4"
 
   if (false) {
      String? none = "None"
diff --git a/pipelines/skylab/smartseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.changelog.md b/pipelines/skylab/smartseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.changelog.md
@@ -1,3 +1,8 @@
+# 1.0.2
+2021-08-02 (Date of Last Commit)
+
+* Increased the version number to make new release tag for Dockstore 
+
 # 1.0.1
 2021-07-19 (Date of Last Commit)
 
diff --git a/pipelines/skylab/smartseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.wdl b/pipelines/skylab/smartseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.wdl
@@ -37,7 +37,7 @@ workflow MultiSampleSmartSeq2SingleNucleus {
       String? input_id_metadata_field
   }
   # Version of this pipeline
-  String pipeline_version = "1.0.1"
+  String pipeline_version = "1.0.2"
 
   if (false) {
      String? none = "None"
diff --git a/projects/hca_mvp/OptimusPostProcessing.wdl b/projects/hca_mvp/OptimusPostProcessing.wdl
@@ -12,36 +12,36 @@ workflow OptimusPostProcessing {
     Array[File] library_looms
     Array[File] analysis_file_jsons
     Array[File] links_jsons
-    Array[String] library
+    Array[String] post_processing_library
     Array[String] species
     Array[String] organ
     String project_id
     String project_name
     String output_basename
-    String staging_area = "gs://broad-dsp-monster-hca-prod-lantern/"
+    String post_processing_staging_area = "gs://broad-dsp-monster-hca-prod-lantern/"
     String version_timestamp = "2021-05-24T12:00:00.000000Z"
   }
 
 
   # version of this pipeline
   String pipeline_version = "1.0.0"
 
-  String project_stratum_string = "project=" + project_id + ";library=" + library[0] + ";species=" + species[0] + ";organ=" + organ[0]
+  String project_stratum_string = "project=" + project_id + ";library=" + post_processing_library[0] + ";species=" + species[0] + ";organ=" + organ[0]
 
   # Build staging bucket
-  String staging_bucket = staging_area + project_id + "/staging/"
+  String staging_bucket = post_processing_staging_area + project_id + "/staging/"
 
   call PostProcessing.CheckMetadata {
       input:
-        library = library,
+        library = post_processing_library,
         species = species,
         organ = organ
   }
 
   call PostProcessing.MergeLooms {
     input:
       library_looms = library_looms,
-      library = library[0],
+      library = post_processing_library[0],
       species = species[0],
       organ = organ[0],
       project_id = project_id,
diff --git a/projects/hca_mvp/getTerraMetadata.wdl b/projects/hca_mvp/getTerraMetadata.wdl
diff --git a/tests/skylab/hca_adapter/pr/ValidateHcaAdapter.wdl b/tests/skylab/hca_adapter/pr/ValidateHcaAdapter.wdl
diff --git a/tests/skylab/hca_adapter/pr/optimus_test_hca_adapter_PR.wdl b/tests/skylab/hca_adapter/pr/optimus_test_hca_adapter_PR.wdl

-Original file line number
+Diff line change
@@ @@ -1,3 +1,9 @@ @@
++
 +# 2.3.6
 +2021-08-02
++
 +* Increased the version number to make new release tag for Dockstore
++
 # 2.3.5
 -07-29