Prepare release 1.5.8-genotek

Genotek · May 31, 2021 · b6caea3 · b6caea3
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diff --git a/README.md b/README.md
@@ -1,38 +1,4 @@
 ![Imputationserver Logo](logo.png)
 
-[![Publication](https://img.shields.io/badge/Published-Nature%20Genetics-26af64.svg?colorB=26af64&style=popout)](https://www.nature.com/articles/ng.3656)
-[![Build Status](https://travis-ci.org/genepi/imputationserver.svg?branch=master)](https://travis-ci.org/genepi/imputationserver)
-[![codecov](https://codecov.io/gh/genepi/imputationserver/branch/master/graph/badge.svg)](https://codecov.io/gh/genepi/imputationserver)
- <a href="https://twitter.com/intent/follow?screen_name=umimpute"> <img src="https://img.shields.io/twitter/follow/umimpute.svg?style=social" alt="follow on Twitter"></a>
 
-This repository includes the complete source code for the [Michigan Imputation Server](https://imputationserver.sph.umich.edu) workflow based on Minimac4.
-The workflow itself is executed with the [Cloudgene workflow system](https://github.com/genepi/cloudgene) for Hadoop MapReduce.
-
-Michigan Imputation Server consists of several parallelized pipeline steps:
-
-- Quality Control
-- QC Report
-- Phasing and Imputation
-- Compression and Encryption
-
-## Documentation
-The documentation is available at http://imputationserver.readthedocs.io.
-
-## Citation
-Please cite this paper if you use Michigan Imputation Server:
-
-> Das S, Forer L, Schönherr S, Sidore C, Locke AE, Kwong A, Vrieze S, Chew EY, Levy S, McGue M, Schlessinger D, Stambolian D, Loh PR, Iacono WG, Swaroop A, Scott LJ, Cucca F, Kronenberg F, Boehnke M, Abecasis GR, Fuchsberger C. [Next-generation genotype imputation service and methods](https://www.ncbi.nlm.nih.gov/pubmed/27571263). Nature Genetics 48, 1284–1287 (2016).
-
-## Contact
-
-Feel free to contact [us](https://imputationserver.sph.umich.edu/index.html#!pages/contact) in case of any problems.
-
-## Contributors
-
-- Lukas Forer
-- Sebastian Schönherr
-- Sayantan Das
-- Christian Fuchsberger
-
-## Contributing
-Project contributions are more than welcome! See our [CONTRIBUTING.md](CONTRIBUTING.md) file for details.
+This repository is a fork of https://github.com/genepi/imputationserver
diff --git a/files/minimac4.yaml b/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: 1.5.8
+version: 1.5.8-genotek
 website: https://imputationserver.readthedocs.io
 category:
 

diff --git a/pom.xml b/pom.xml
@@ -5,7 +5,7 @@
 
 	<groupId>genepi</groupId>
 	<artifactId>imputationserver</artifactId>
-	<version>1.5.8</version>
+	<version>1.5.8-genotek</version>
 	<packaging>jar</packaging>
 
 	<name>University of Michigan Imputation Server</name>

diff --git a/src/main/java/genepi/imputationserver/steps/imputation/ImputationPipeline.java b/src/main/java/genepi/imputationserver/steps/imputation/ImputationPipeline.java
@@ -23,7 +23,7 @@
 
 public class ImputationPipeline {
 
-	public static final String PIPELINE_VERSION = "michigan-imputationserver-1.5.8";
+	public static final String PIPELINE_VERSION = "michigan-imputationserver-1.5.8-genotek";
 
 	public static final String IMPUTATION_VERSION = "minimac4-1.0.2";
 

diff --git a/src/main/java/genepi/imputationserver/util/DefaultPreferenceStore.java b/src/main/java/genepi/imputationserver/util/DefaultPreferenceStore.java
@@ -71,13 +71,15 @@ public static Properties defaults() {
 		defaults.setProperty("chunksize", "20000000");
 		defaults.setProperty("phasing.window", "5000000");
 		defaults.setProperty("minimac.window", "500000");
+		defaults.setProperty("minimac.vcores", "1");
+		defaults.setProperty("eagle.vcores", "1");
 		defaults.setProperty("minimac.sendmail", "no");
 		defaults.setProperty("server.url", "https://imputationserver.sph.umich.edu");
 		defaults.setProperty("minimac.tmp", "/tmp");
 		defaults.setProperty("minimac.command",
 				"--refHaps ${ref} --haps ${vcf} --start ${start} --end ${end} --window ${window} --prefix ${prefix} --chr ${chr} --cpus 1 --noPhoneHome --format GT,DS,GP --allTypedSites --meta --minRatio 0.00001 ${chr =='MT' ? '--myChromosome ' + chr : ''} ${unphased ? '--unphasedOutput' : ''} ${mapMinimac != null ? '--referenceEstimates --map ' + mapMinimac : ''}");
 		defaults.setProperty("eagle.command",
-				"--vcfRef ${ref} --vcfTarget ${vcf} --geneticMapFile ${map} --outPrefix ${prefix} --bpStart ${start} --bpEnd ${end} --allowRefAltSwap --vcfOutFormat z --keepMissingPloidyX");
+				"--numThreads ${eagle.vcores} --vcfRef ${ref} --vcfTarget ${vcf} --geneticMapFile ${map} --outPrefix ${prefix} --bpStart ${start} --bpEnd ${end} --allowRefAltSwap --vcfOutFormat z --keepMissingPloidyX");
 		defaults.setProperty("beagle.command",
 				"-jar ${beagle} ref=${ref} gt=${vcf} out=${prefix} nthreads=1 chrom=${chr}:${start}-${end} map=${map} impute=false");
 		defaults.setProperty("ref.fasta", "v37");