Merge branch 'master' into develop

# Conflicts:
#	files/imputationserver-beagle.yaml
#	files/imputationserver-hla.yaml
#	files/imputationserver-pgs.yaml
#	files/minimac4.yaml
#	pom.xml
#	src/main/java/genepi/imputationserver/steps/imputation/ImputationPipeline.java

.github/workflows/create-release.yml

@@ -17,7 +17,7 @@ jobs:
  java-version: '11'
  distribution: 'adopt'
  - name: Build MIS
- run: mvn -Dtest=AllTestsNoChrX test
+ run: mvn -Dtest=AllTestsNoChrX install
  - uses: ncipollo/release-action@v1
  with:
  allowUpdates: true

files/imputationserver-beagle.yaml

@@ -1,7 +1,7 @@
 id: imputationserver-beagle
 name: Genotype Imputation supporting Beagle (Minimac4)
 description: This is the new Michigan Imputation Server Pipeline using <a href="https://github.com/statgen/Minimac4">Minimac4</a>. Documentation can be found <a href="http://imputationserver.readthedocs.io/en/latest/">here</a>.<br><br>If your input data is <b>GRCh37/hg19</b> please ensure chromosomes are encoded without prefix (e.g. <b>20</b>).<br>If your input data is <b>GRCh38hg38</b> please ensure chromosomes are encoded with prefix 'chr' (e.g. <b>chr20</b>).
-version: 1.6.0
+version: 1.6.5
 website: https://imputationserver.readthedocs.io
 category:
 
@@ -120,6 +120,15 @@ workflow:
  false: no
  visible: true
 
+ - id: meta
+ description: Generate Meta-imputation file
+ type: checkbox
+ value: no
+ values:
+ true: yes
+ false: no
+ visible: true
+
  - id: myseparator
  type: separator
 

files/imputationserver-hla.yaml

@@ -1,7 +1,7 @@
 id: imputationserver-hla
 name: Genotype Imputation HLA (Minimac4)
 description: This is the new Michigan Imputation Server Pipeline using <a href="https://github.com/statgen/Minimac4">Minimac4</a>. Documentation can be found <a href="http://imputationserver.readthedocs.io/en/latest/">here</a>.<br><br>If your input data is <b>GRCh37/hg19</b> please ensure chromosomes are encoded without prefix (e.g. <b>20</b>).<br>If your input data is <b>GRCh38hg38</b> please ensure chromosomes are encoded with prefix 'chr' (e.g. <b>chr20</b>).
-version: 1.6.0
+version: 1.6.5
 website: https://imputationserver.readthedocs.io
 category:
 
@@ -120,6 +120,15 @@ workflow:
  false: no
  visible: true
 
+ - id: meta
+ description: Generate Meta-imputation file
+ type: checkbox
+ value: no
+ values:
+ true: yes
+ false: no
+ visible: true
+
  - id: myseparator
  type: separator
 

files/imputationserver-pgs.yaml

@@ -1,7 +1,7 @@
 id: imputationserver-pgs
 name: Genotype Imputation (PGS Calc Integration)
 description: This is the new Michigan Imputation Server Pipeline using <a href="https://github.com/statgen/Minimac4">Minimac4</a>. Documentation can be found <a href="http://imputationserver.readthedocs.io/en/latest/">here</a>.<br><br>If your input data is <b>GRCh37/hg19</b> please ensure chromosomes are encoded without prefix (e.g. <b>20</b>).<br>If your input data is <b>GRCh38hg38</b> please ensure chromosomes are encoded with prefix 'chr' (e.g. <b>chr20</b>).
-version: 1.6.0
+version: 1.6.5
 website: https://imputationserver.readthedocs.io
 category:
 
@@ -119,6 +119,15 @@ workflow:
  false: no
  visible: true
 
+ - id: meta
+ description: Generate Meta-imputation file
+ type: checkbox
+ value: no
+ values:
+ true: yes
+ false: no
+ visible: true
+
  - id: myseparator0
  type: separator
 

files/minimac4.yaml

@@ -1,7 +1,7 @@
 id: imputationserver
 name: Genotype Imputation (Minimac4)
 description: This is the new Michigan Imputation Server Pipeline using <a href="https://github.com/statgen/Minimac4">Minimac4</a>. Documentation can be found <a href="http://imputationserver.readthedocs.io/en/latest/">here</a>.<br><br>If your input data is <b>GRCh37/hg19</b> please ensure chromosomes are encoded without prefix (e.g. <b>20</b>).<br>If your input data is <b>GRCh38hg38</b> please ensure chromosomes are encoded with prefix 'chr' (e.g. <b>chr20</b>).
-version: 1.6.0
+version: 1.6.5
 website: https://imputationserver.readthedocs.io
 category:
 
@@ -10,7 +10,7 @@ installation:
  - import:
  source: ${app_local_folder}/bin
  target: ${app_hdfs_folder}/bin
- 
+
 workflow:
 
  setups:
@@ -31,14 +31,14 @@ workflow:
  params: $mafFile
  output: ${qcreport}.html
  generates: $qcreport
- 
-#end 
+
+#end
 
  onFailure:
  name: Send Notification on Failure
  jar: imputationserver.jar
  classname: genepi.imputationserver.steps.FailureNotification
- 
+
  steps:
 
 #if($mode == "imputation" || $mode == "phasing")
@@ -70,8 +70,8 @@ workflow:
  value: hg19
  values:
  hg19: GRCh37/hg19
- hg38: GRCh38/hg38 
- details: Please note that the final SNP coordinates always match the reference build. 
+ hg38: GRCh38/hg38
+ details: Please note that the final SNP coordinates always match the reference build.
 
  - id: r2Filter
  description: rsq Filter
@@ -91,21 +91,21 @@ workflow:
  values:
  eagle: Eagle v2.4 (phased output)
  no_phasing: No phasing
- 
+
  - id: population
  description: Population
  type: list
  values:
  bind: refpanel
  property: populations
  category: RefPanel
- 
+
  - id: mode
  description: Mode
  type: list
  value: imputation
  values:
- qconly: Quality Control Only 
+ qconly: Quality Control Only
  imputation: Quality Control & Imputation
  phasing: Quality Control & Phasing Only
 
@@ -118,15 +118,15 @@ workflow:
  true: yes
  false: no
  visible: true
- 
+
  - id: meta
  description: Generate Meta-imputation file
  type: checkbox
  value: no
  values:
  true: yes
  false: no
- visible: true 
+ visible: true
 
  - id: myseparator
  type: separator
@@ -140,12 +140,12 @@ workflow:
  - id: check1
  description: I will not attempt to re-identify or contact research participants.
  type: terms_checkbox
- 
+
  - id: check2
  description: I will report any inadvertent data release, security breach or other data management incident of which I become aware.
- type: terms_checkbox 
+ type: terms_checkbox
+
 
-
  outputs:
 
  - id: qcreport
@@ -163,7 +163,7 @@ workflow:
  mergeOutput: true
  removeHeader: false
  zip: false
- 
+
  - id: chunksDir
  description: Actual chunk files
  type: local-folder
@@ -201,13 +201,13 @@ workflow:
  type: local-folder
  download: true
  temp: true
- 
+
  - id: logfile
  description: Logs
  type: local-folder
  download: true
  temp: false
- 
+
  - id: hadooplogs
  description: Hadoop Task Logs
  type: local-folder