Merged updates between HMIS and genepi 2.0.0

files/minimac4.yaml

@@ -27,6 +27,7 @@ workflow:
 #if( $population != "mixed")
 
     - name: Quality Control (Report)
+      type: rmd_docker
       rmd: qc-report.Rmd
       params: $mafFile
       output: ${qcreport}.html

mkdocs.yml

@@ -1,4 +1,4 @@
-site_name: Michigan Imputation Server
+site_name: Munich Imputation Server
 theme: readthedocs
 
 nav:
@@ -23,27 +23,16 @@ nav:
   - API: api.md
   - Docker: docker.md
   - Create Reference Panels: create-reference-panels.md
-- ASHG2023:
-  - Overview: workshops/ASHG2023.md
-  - "Session 1: Imputation and the Server": workshops/ASHG2023/Session1.md
-  - "Session 2: Run a job, Data Preparation and Data Download": workshops/ASHG2023/Session2.md
-  - "Session 3: Performing GWAS using imputed data": workshops/ASHG2023/Session3.md
-  - "Session 4: nf-gwas, Imputation Bot and PGS Server": workshops/ASHG2023/Session4.md
-  - "Session 5: HLA Imputation": workshops/ASHG2023/Session5.md
-  - "Session 6: TOPMed Imputation Server": workshops/ASHG2023/Session6.md
 - Contact: contact.md
 
-
-repo_name: genepi/imputationserver
-repo_url: https://github.com/genepi/imputationserver
+repo_name: hmgu-itg/imputationserver
+repo_url: https://github.com/hmgu-itg/imputationserver
 edit_uri: edit/master/docs
 
 extra:
   social:
     - type: github-alt
-      link: https://github.com/genepi/imputationserver
-    - type: twitter
-      link: https://twitter.com/umimpute
+      link: https://github.com/hmgu-itg/imputationserver
 
 markdown_extensions:
     - toc:

pom.xml

@@ -211,6 +211,11 @@
 			<artifactId>yamlbeans</artifactId>
 			<version>1.15</version>
 		</dependency>
+		<dependency>
+			<groupId>org.apache.commons</groupId>
+			<artifactId>commons-collections4</artifactId>
+			<version>4.4</version>
+		</dependency>
 
 		<dependency>
 			<groupId>genepi</groupId>