Merge pull request #1536 from HumanCellAtlas/staging

Release from staging to master 2023-11-07
HumanCellAtlas · Nov 7, 2023 · 6e48562 · 6e48562
2 parents 84dc722 + 944ebbb
commit 6e48562
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Showing 4 changed files with 24 additions and 2 deletions.
diff --git a/changelog.md b/changelog.md
@@ -6,8 +6,13 @@ Starting after v5.0.0 release, updates will be declared for schemas independentl
 and (starting with v4.0.0) this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html). Unreleased changes may be indicated under the `Unreleased` heading.
 
 ## [Unreleased](https://github.com/HumanCellAtlas/metadata-schema/tree/staging)
+
 ## [Released](https://github.com/HumanCellAtlas/metadata-schema/)
 
+### [type/protocol/analysis/analysis_protocol.json - v10.1.0] - 2023-11-07
+### Added
+Added alignment_software & alignment_software_version field in analysis_protocol Fixes#1533
+
 ### [core/biomaterial/biomaterial_core.json - v8.4.0] - 2023-08-22
 ### Added
 Added timecourse module. Fixes #1511

diff --git a/docs/jsonBrowser/type.md b/docs/jsonBrowser/type.md
@@ -145,6 +145,8 @@ protocol_core | Core protocol-level information. | object | yes | [See core  pro
 type | The type of protocol. | object | yes | [See module  process_type_ontology](module.md#process-type-ontology) | Protocol type |  | 
 computational_method | A URI to a versioned workflow and versioned execution environment in a GA4GH-compliant repository. | string | no |  | Computational method |  | SmartSeq2SingleCell; 10x
 matrix | Information related to protocols that output a matrix. | object | no | [See module  matrix](module.md#matrix) | Matrix |  | 
+alignment_software | Name of alignment software used to map FASTQ files to reference genome. | string | no |  | Alignment software |  | Cellranger; kallisto bustools; GSNAP; STAR
+alignment_software_version | Version of alignment software used to map FASTQ files to reference genome. | string | no |  | Alignment software version |  | v2.0.1; 2.4.2a; v0.45.2
 
 ## Aggregate generation protocol
 _Information about how cultured cells are developed into cell aggregates._

diff --git a/json_schema/type/protocol/analysis/analysis_protocol.json b/json_schema/type/protocol/analysis/analysis_protocol.json
@@ -8,6 +8,9 @@
         "protocol_core",
         "type"
     ],
+    "dependencies": {
+        "alignment_software_version": ["alignment_software"]
+    },
     "title": "Analysis protocol",
     "name": "analysis_protocol",
     "type": "object",
@@ -58,6 +61,18 @@
             "type": "object",
             "$ref": "module/protocol/matrix.json",
             "user_friendly": "Matrix"
+        },
+        "alignment_software": {
+            "description": "Name of alignment software used to map FASTQ files to reference genome.",
+            "type": "string",
+            "user_friendly": "Alignment software",
+            "example": "Cellranger; kallisto bustools; GSNAP; STAR"
+        }, 
+        "alignment_software_version": {
+            "description": "Version of alignment software used to map FASTQ files to reference genome.",
+            "type": "string",
+            "user_friendly": "Alignment software version",
+            "example": "v2.0.1; 2.4.2a; v0.45.2"
         }
     }
 }
diff --git a/json_schema/versions.json b/json_schema/versions.json
@@ -1,5 +1,5 @@
 {
-    "last_update_date": "2023-08-22T11:35:16Z",
+    "last_update_date": "2023-11-07T15:13:34Z",
     "version_numbers": {
         "core": {
             "biomaterial": {
@@ -114,7 +114,7 @@
             },
             "protocol": {
                 "analysis": {
-                    "analysis_protocol": "10.0.0"
+                    "analysis_protocol": "10.1.0"
                 },
                 "biomaterial_collection": {
                     "aggregate_generation_protocol": "2.1.0",