fixed dimensionality for alignment pipelines, updated submodules

dbmi-bgm · Dec 4, 2023 · 9c2a48f · 9c2a48f
1 parent 29cefce
commit 9c2a48f
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Showing 8 changed files with 16 additions and 13 deletions.
diff --git a/VERSION b/VERSION
@@ -1 +1 @@
-v1.1.0
+v1.1.1
diff --git a/cgap-pipeline-somatic-sentieon b/cgap-pipeline-somatic-sentieon
diff --git a/cgap-pipeline-upstream-GATK b/cgap-pipeline-upstream-GATK
diff --git a/docs/news-main.rst b/docs/news-main.rst
@@ -1,6 +1,9 @@
 ================
 News and Updates
 ================
+  **v1.1.1**
+
+  * Fixed dimensionality for upstream pipelines
 
   **v1.1.0**
 

diff --git a/portal-pipeline-utils b/portal-pipeline-utils
diff --git a/portal_objects/metaworkflows/WES_upstream_sentieon_proband.yaml b/portal_objects/metaworkflows/WES_upstream_sentieon_proband.yaml
@@ -15,11 +15,11 @@ input:
   # File argument
   fastqs_R1:
     argument_type: file.fastq
-    dimensionality: 1
+    dimensionality: 2
 
   fastqs_R2:
     argument_type: file.fastq
-    dimensionality: 1
+    dimensionality: 2
 
   reference_bwa:
     argument_type: file.bwt
@@ -71,12 +71,12 @@ workflows:
       fastq_R1:
         argument_type: file.fastq
         source_argument_name: fastqs_R1
-        scatter: 1
+        scatter: 2
 
       fastq_R2:
         argument_type: file.fastq
         source_argument_name: fastqs_R2
-        scatter: 1
+        scatter: 2
 
       reference_fa:
         argument_type: file.fa

diff --git a/portal_objects/metaworkflows/WGS_upstream_sentieon_proband.yaml b/portal_objects/metaworkflows/WGS_upstream_sentieon_proband.yaml
@@ -15,11 +15,11 @@ input:
   # File argument
   fastqs_R1:
     argument_type: file.fastq
-    dimensionality: 1
+    dimensionality: 2
 
   fastqs_R2:
     argument_type: file.fastq
-    dimensionality: 1
+    dimensionality: 2
 
   reference_bwa:
     argument_type: file.bwt
@@ -67,12 +67,12 @@ workflows:
       fastq_R1:
         argument_type: file.fastq
         source_argument_name: fastqs_R1
-        scatter: 1
+        scatter: 2
 
       fastq_R2:
         argument_type: file.fastq
         source_argument_name: fastqs_R2
-        scatter: 1
+        scatter: 2
 
       reference_fa:
         argument_type: file.fa

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "cgap-pipeline-main"
-version = "1.1.0"
+version = "1.1.1"
 description = "Main repository for deploying pipelines that impelement the CGAP-pipeline specification."
 authors = ["CGAP Team"]