From 88d2a3552cf4a095443ad538cdd93bad87870cd1 Mon Sep 17 00:00:00 2001 From: seppinho Date: Thu, 23 Sep 2021 15:36:25 +0200 Subject: [PATCH 01/17] Update pgs-calc to 0.9.4 --- pom.xml | 2 +- .../imputationserver/steps/CompressionEncryption.java | 6 ------ .../steps/imputation/ImputationPipeline.java | 8 ++------ .../genepi/imputationserver/steps/ImputationTest.java | 2 +- 4 files changed, 4 insertions(+), 14 deletions(-) diff --git a/pom.xml b/pom.xml index 562beb6a..6b245017 100644 --- a/pom.xml +++ b/pom.xml @@ -296,7 +296,7 @@ lukfor pgs-calc - 0.9.2 + 0.9.4 diff --git a/src/main/java/genepi/imputationserver/steps/CompressionEncryption.java b/src/main/java/genepi/imputationserver/steps/CompressionEncryption.java index c9b12c11..6d22677a 100644 --- a/src/main/java/genepi/imputationserver/steps/CompressionEncryption.java +++ b/src/main/java/genepi/imputationserver/steps/CompressionEncryption.java @@ -304,12 +304,6 @@ public boolean run(WorkflowContext context) { MetaFile metaFile = MetaFile.load(FileUtil.path(folder, "pgs-catalog.json")); report.mergeWithMeta(metaFile); - CreateHtmlReportTask htmlReport = new CreateHtmlReportTask(); - htmlReport.setReport(report); - htmlReport.setData(mergeScore.getResult()); - htmlReport.setOutput(outputFileHtml); - TaskService.run(htmlReport); - String fileName = "scores.zip"; String filePath = FileUtil.path(localOutput, fileName); File file = new File(filePath); diff --git a/src/main/java/genepi/imputationserver/steps/imputation/ImputationPipeline.java b/src/main/java/genepi/imputationserver/steps/imputation/ImputationPipeline.java index eb203426..6acf68f9 100644 --- a/src/main/java/genepi/imputationserver/steps/imputation/ImputationPipeline.java +++ b/src/main/java/genepi/imputationserver/steps/imputation/ImputationPipeline.java @@ -344,16 +344,12 @@ private boolean runPgsCalc(VcfChunkOutput output) { task.setVcfFilename(output.getImputedVcfFilename()); task.setChunk(scoreChunk); task.setRiskScoreFilenames(scores); + task.setOutputReportFilename(output.getScoreFilename() + ".json"); + task.setOutput(output.getScoreFilename()); TaskService.setAnsiSupport(false); TaskService.run(task); - OutputFile outputFile = new OutputFile(task.getRiskScores(), task.getSummaries()); - outputFile.save(output.getScoreFilename()); - - ReportFile reportFile = new ReportFile(task.getSummaries()); - reportFile.save(output.getScoreFilename() + ".json"); - return true; } catch (Exception e) { diff --git a/src/test/java/genepi/imputationserver/steps/ImputationTest.java b/src/test/java/genepi/imputationserver/steps/ImputationTest.java index 5fd434aa..c0a3db64 100644 --- a/src/test/java/genepi/imputationserver/steps/ImputationTest.java +++ b/src/test/java/genepi/imputationserver/steps/ImputationTest.java @@ -757,7 +757,7 @@ public void testPipelineWithEagleAndScores() throws IOException, ZipException { } readerExpected.close(); readerActual.close(); - // FileUtil.deleteDirectory("test-data/tmp"); + FileUtil.deleteDirectory("test-data/tmp"); } From cdc19f10ac6fdf2082475fdd0c25672f5e0e316b Mon Sep 17 00:00:00 2001 From: seppinho Date: Thu, 23 Sep 2021 15:43:36 +0200 Subject: [PATCH 02/17] Prepare release candidate 1.6.0-rc3 --- files/imputationserver-beagle.yaml | 2 +- files/imputationserver-hla.yaml | 2 +- files/imputationserver-pgs.yaml | 2 +- files/minimac4.yaml | 2 +- pom.xml | 2 +- .../imputationserver/steps/imputation/ImputationPipeline.java | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/files/imputationserver-beagle.yaml b/files/imputationserver-beagle.yaml index 9f6ad520..5ec65fd5 100644 --- a/files/imputationserver-beagle.yaml +++ b/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 Minimac4. Documentation can be found here.

If your input data is GRCh37/hg19 please ensure chromosomes are encoded without prefix (e.g. 20).
If your input data is GRCh38hg38 please ensure chromosomes are encoded with prefix 'chr' (e.g. chr20). -version: 1.5.8 +version: 1.6.0-rc3 website: https://imputationserver.readthedocs.io category: diff --git a/files/imputationserver-hla.yaml b/files/imputationserver-hla.yaml index 64a14846..f51ee3ce 100644 --- a/files/imputationserver-hla.yaml +++ b/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 Minimac4. Documentation can be found here.

If your input data is GRCh37/hg19 please ensure chromosomes are encoded without prefix (e.g. 20).
If your input data is GRCh38hg38 please ensure chromosomes are encoded with prefix 'chr' (e.g. chr20). -version: 1.5.8 +version: 1.6.0-rc3 website: https://imputationserver.readthedocs.io category: diff --git a/files/imputationserver-pgs.yaml b/files/imputationserver-pgs.yaml index 93f34f85..33e674f2 100644 --- a/files/imputationserver-pgs.yaml +++ b/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 Minimac4. Documentation can be found here.

If your input data is GRCh37/hg19 please ensure chromosomes are encoded without prefix (e.g. 20).
If your input data is GRCh38hg38 please ensure chromosomes are encoded with prefix 'chr' (e.g. chr20). -version: 1.5.8 +version: 1.6.0-rc3 website: https://imputationserver.readthedocs.io category: diff --git a/files/minimac4.yaml b/files/minimac4.yaml index fe2eb10e..bb134f29 100644 --- 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 Minimac4. Documentation can be found here.

If your input data is GRCh37/hg19 please ensure chromosomes are encoded without prefix (e.g. 20).
If your input data is GRCh38hg38 please ensure chromosomes are encoded with prefix 'chr' (e.g. chr20). -version: 1.6.0-rc2 +version: 1.6.0-rc3 website: https://imputationserver.readthedocs.io category: diff --git a/pom.xml b/pom.xml index 6b245017..1b1677be 100644 --- a/pom.xml +++ b/pom.xml @@ -5,7 +5,7 @@ genepi imputationserver - 1.6.0-rc2 + 1.6.0-rc3 jar University of Michigan Imputation Server diff --git a/src/main/java/genepi/imputationserver/steps/imputation/ImputationPipeline.java b/src/main/java/genepi/imputationserver/steps/imputation/ImputationPipeline.java index 6acf68f9..2836fc50 100644 --- 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-1.6.0-rc2"; + public static final String PIPELINE_VERSION = "michigan-imputationserver-1.6.0-rc3"; public static final String IMPUTATION_VERSION = "minimac4-1.0.2"; From c044ce6b64e736577a8ebf059a07827875b6de88 Mon Sep 17 00:00:00 2001 From: seppinho Date: Thu, 23 Sep 2021 17:03:53 +0200 Subject: [PATCH 03/17] Fix package name --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 1b1677be..1fb3f821 100644 --- a/pom.xml +++ b/pom.xml @@ -79,7 +79,7 @@ org.codehaus.plexus:plexus-classworlds:*:* org.codehaus.groovy:groovy-all:*:* lukfor:pgs-calc:*:* - lukfor:magic-progress:*:* + com.github.lukfor:magic-progress:*:* com.samskivert:jmustache:*:* com.google.code.gson:gson:*:* com.github.tommyettinger:blazingchain:*:* From 9e1235eae80bd70cafdf78ce8c7d031a6fd36e32 Mon Sep 17 00:00:00 2001 From: seppinho Date: Thu, 23 Sep 2021 17:05:58 +0200 Subject: [PATCH 04/17] Add missing package --- pom.xml | 1 + 1 file changed, 1 insertion(+) diff --git a/pom.xml b/pom.xml index 1fb3f821..bc3bf389 100644 --- a/pom.xml +++ b/pom.xml @@ -80,6 +80,7 @@ org.codehaus.groovy:groovy-all:*:* lukfor:pgs-calc:*:* com.github.lukfor:magic-progress:*:* + com.github.lukfor:magic-reports:*:* com.samskivert:jmustache:*:* com.google.code.gson:gson:*:* com.github.tommyettinger:blazingchain:*:* From 0be5c6cb145bb9d5c8a174254f3b2080bf6b622b Mon Sep 17 00:00:00 2001 From: seppinho Date: Thu, 23 Sep 2021 17:07:56 +0200 Subject: [PATCH 05/17] Prepare release candidate 1.6.0-rc4 --- files/imputationserver-beagle.yaml | 2 +- files/imputationserver-hla.yaml | 2 +- files/imputationserver-pgs.yaml | 2 +- files/minimac4.yaml | 2 +- pom.xml | 2 +- .../imputationserver/steps/imputation/ImputationPipeline.java | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/files/imputationserver-beagle.yaml b/files/imputationserver-beagle.yaml index 5ec65fd5..27e18f3a 100644 --- a/files/imputationserver-beagle.yaml +++ b/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 Minimac4. Documentation can be found here.

If your input data is GRCh37/hg19 please ensure chromosomes are encoded without prefix (e.g. 20).
If your input data is GRCh38hg38 please ensure chromosomes are encoded with prefix 'chr' (e.g. chr20). -version: 1.6.0-rc3 +version: 1.6.0-rc4 website: https://imputationserver.readthedocs.io category: diff --git a/files/imputationserver-hla.yaml b/files/imputationserver-hla.yaml index f51ee3ce..3ad55fee 100644 --- a/files/imputationserver-hla.yaml +++ b/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 Minimac4. Documentation can be found here.

If your input data is GRCh37/hg19 please ensure chromosomes are encoded without prefix (e.g. 20).
If your input data is GRCh38hg38 please ensure chromosomes are encoded with prefix 'chr' (e.g. chr20). -version: 1.6.0-rc3 +version: 1.6.0-rc4 website: https://imputationserver.readthedocs.io category: diff --git a/files/imputationserver-pgs.yaml b/files/imputationserver-pgs.yaml index 33e674f2..93dda1fd 100644 --- a/files/imputationserver-pgs.yaml +++ b/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 Minimac4. Documentation can be found here.

If your input data is GRCh37/hg19 please ensure chromosomes are encoded without prefix (e.g. 20).
If your input data is GRCh38hg38 please ensure chromosomes are encoded with prefix 'chr' (e.g. chr20). -version: 1.6.0-rc3 +version: 1.6.0-rc4 website: https://imputationserver.readthedocs.io category: diff --git a/files/minimac4.yaml b/files/minimac4.yaml index bb134f29..ed89eaee 100644 --- 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 Minimac4. Documentation can be found here.

If your input data is GRCh37/hg19 please ensure chromosomes are encoded without prefix (e.g. 20).
If your input data is GRCh38hg38 please ensure chromosomes are encoded with prefix 'chr' (e.g. chr20). -version: 1.6.0-rc3 +version: 1.6.0-rc4 website: https://imputationserver.readthedocs.io category: diff --git a/pom.xml b/pom.xml index bc3bf389..bc0f71ae 100644 --- a/pom.xml +++ b/pom.xml @@ -5,7 +5,7 @@ genepi imputationserver - 1.6.0-rc3 + 1.6.0-rc4 jar University of Michigan Imputation Server diff --git a/src/main/java/genepi/imputationserver/steps/imputation/ImputationPipeline.java b/src/main/java/genepi/imputationserver/steps/imputation/ImputationPipeline.java index 2836fc50..9a05285c 100644 --- 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-1.6.0-rc3"; + public static final String PIPELINE_VERSION = "michigan-imputationserver-1.6.0-rc4"; public static final String IMPUTATION_VERSION = "minimac4-1.0.2"; From 2e6c01c5ab02c6df2ec19f2080bad31cd2a4cfe8 Mon Sep 17 00:00:00 2001 From: Lukas Forer Date: Tue, 5 Oct 2021 15:54:40 +0200 Subject: [PATCH 06/17] Handle errors of pgs-calc --- .../steps/imputation/ImputationPipeline.java | 16 ++++++++++++---- 1 file changed, 12 insertions(+), 4 deletions(-) diff --git a/src/main/java/genepi/imputationserver/steps/imputation/ImputationPipeline.java b/src/main/java/genepi/imputationserver/steps/imputation/ImputationPipeline.java index 9a05285c..7e4d1d64 100644 --- a/src/main/java/genepi/imputationserver/steps/imputation/ImputationPipeline.java +++ b/src/main/java/genepi/imputationserver/steps/imputation/ImputationPipeline.java @@ -3,6 +3,7 @@ import java.io.File; import java.io.IOException; import java.util.HashMap; +import java.util.List; import java.util.Map; import org.apache.commons.io.FileUtils; @@ -13,13 +14,12 @@ import genepi.imputationserver.steps.vcf.VcfChunkOutput; import genepi.io.FileUtil; import genepi.riskscore.io.Chunk; -import genepi.riskscore.io.OutputFile; import genepi.riskscore.io.PGSCatalog; -import genepi.riskscore.io.ReportFile; import genepi.riskscore.tasks.ApplyScoreTask; import groovy.text.SimpleTemplateEngine; import htsjdk.samtools.util.StopWatch; import lukfor.progress.TaskService; +import lukfor.progress.tasks.Task; public class ImputationPipeline { @@ -171,7 +171,7 @@ public boolean execute(VcfChunk chunk, VcfChunkOutput output) throws Interrupted return false; } - if (scores != null && !scores.equals("no_score")) { + if (scores != null && scores.length >= 0) { System.out.println(" Starting PGS calculation '" + scores + "'..."); @@ -348,7 +348,15 @@ private boolean runPgsCalc(VcfChunkOutput output) { task.setOutput(output.getScoreFilename()); TaskService.setAnsiSupport(false); - TaskService.run(task); + List runningTasks = TaskService.run(task); + + for (Task runningTask : runningTasks) { + if (!runningTask.getStatus().isSuccess()) { + System.out.println("PGS-Calc failed: " + runningTask.getStatus().getThrowable()); + runningTask.getStatus().getThrowable().printStackTrace(); + return false; + } + } return true; From afccfd1f193e496d347db80504954f503998aef6 Mon Sep 17 00:00:00 2001 From: Lukas Forer Date: Tue, 5 Oct 2021 16:49:20 +0200 Subject: [PATCH 07/17] Update pgs-calc to 0.9.6 --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index bc0f71ae..b360bd96 100644 --- a/pom.xml +++ b/pom.xml @@ -297,7 +297,7 @@ lukfor pgs-calc - 0.9.4 + 0.9.6 From f438d59e513792faa285b71364f3bb4c24902ecf Mon Sep 17 00:00:00 2001 From: seppinho Date: Tue, 5 Oct 2021 17:45:09 +0200 Subject: [PATCH 08/17] Prepare release candidate 1.6.0-rc5 --- files/imputationserver-beagle.yaml | 2 +- files/imputationserver-hla.yaml | 2 +- files/minimac4.yaml | 2 +- pom.xml | 2 +- .../imputationserver/steps/imputation/ImputationPipeline.java | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/files/imputationserver-beagle.yaml b/files/imputationserver-beagle.yaml index 27e18f3a..423f011b 100644 --- a/files/imputationserver-beagle.yaml +++ b/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 Minimac4. Documentation can be found here.

If your input data is GRCh37/hg19 please ensure chromosomes are encoded without prefix (e.g. 20).
If your input data is GRCh38hg38 please ensure chromosomes are encoded with prefix 'chr' (e.g. chr20). -version: 1.6.0-rc4 +version: 1.6.0-rc5 website: https://imputationserver.readthedocs.io category: diff --git a/files/imputationserver-hla.yaml b/files/imputationserver-hla.yaml index 3ad55fee..d4aa362d 100644 --- a/files/imputationserver-hla.yaml +++ b/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 Minimac4. Documentation can be found here.

If your input data is GRCh37/hg19 please ensure chromosomes are encoded without prefix (e.g. 20).
If your input data is GRCh38hg38 please ensure chromosomes are encoded with prefix 'chr' (e.g. chr20). -version: 1.6.0-rc4 +version: 1.6.0-rc5 website: https://imputationserver.readthedocs.io category: diff --git a/files/minimac4.yaml b/files/minimac4.yaml index ed89eaee..bff72f85 100644 --- 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 Minimac4. Documentation can be found here.

If your input data is GRCh37/hg19 please ensure chromosomes are encoded without prefix (e.g. 20).
If your input data is GRCh38hg38 please ensure chromosomes are encoded with prefix 'chr' (e.g. chr20). -version: 1.6.0-rc4 +version: 1.6.0-rc5 website: https://imputationserver.readthedocs.io category: diff --git a/pom.xml b/pom.xml index b360bd96..4dfc4ab7 100644 --- a/pom.xml +++ b/pom.xml @@ -5,7 +5,7 @@ genepi imputationserver - 1.6.0-rc4 + 1.6.0-rc5 jar University of Michigan Imputation Server diff --git a/src/main/java/genepi/imputationserver/steps/imputation/ImputationPipeline.java b/src/main/java/genepi/imputationserver/steps/imputation/ImputationPipeline.java index 7e4d1d64..36b74017 100644 --- 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-1.6.0-rc4"; + public static final String PIPELINE_VERSION = "michigan-imputationserver-1.6.0-rc5"; public static final String IMPUTATION_VERSION = "minimac4-1.0.2"; From 87774c2ad570fdfb39a705fc315324095aab5f50 Mon Sep 17 00:00:00 2001 From: seppinho Date: Tue, 5 Oct 2021 17:53:19 +0200 Subject: [PATCH 09/17] Commit missing yaml file --- files/imputationserver-pgs.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/files/imputationserver-pgs.yaml b/files/imputationserver-pgs.yaml index 93dda1fd..d94498e5 100644 --- a/files/imputationserver-pgs.yaml +++ b/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 Minimac4. Documentation can be found here.

If your input data is GRCh37/hg19 please ensure chromosomes are encoded without prefix (e.g. 20).
If your input data is GRCh38hg38 please ensure chromosomes are encoded with prefix 'chr' (e.g. chr20). -version: 1.6.0-rc4 +version: 1.6.0-rc5 website: https://imputationserver.readthedocs.io category: From 78d62051784881bad222bc2a2528be6551205a52 Mon Sep 17 00:00:00 2001 From: Lukas Forer Date: Tue, 1 Feb 2022 13:12:05 +0100 Subject: [PATCH 10/17] Update pgs-calc to 0.9.12 --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index b852140b..786e85ab 100644 --- a/pom.xml +++ b/pom.xml @@ -299,7 +299,7 @@ lukfor pgs-calc - 0.9.6 + 0.9.12 From ba25cc2f58fc0f6b9fbfacafa6591f060743f6fc Mon Sep 17 00:00:00 2001 From: seppinho Date: Mon, 7 Feb 2022 09:38:23 +0100 Subject: [PATCH 11/17] Prepare release candidate v1.6.2-rc1 --- files/imputationserver-pgs.yaml | 4 ++-- pom.xml | 2 +- .../imputationserver/steps/imputation/ImputationPipeline.java | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/files/imputationserver-pgs.yaml b/files/imputationserver-pgs.yaml index 8f3f3958..f84d216c 100644 --- a/files/imputationserver-pgs.yaml +++ b/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 Minimac4. Documentation can be found here.

If your input data is GRCh37/hg19 please ensure chromosomes are encoded without prefix (e.g. 20).
If your input data is GRCh38hg38 please ensure chromosomes are encoded with prefix 'chr' (e.g. chr20). -version: 1.6.1 +description: This is the new Michigan Imputation Server Pipeline using Minimac4. Documentation can be found here.

If your input data is GRCh37/hg19 please ensure chromosomes are encoded without prefix (e.g. 20).
If your input data is GRCh38hg38 please ensure chromosomes are encoded with prefix 'chr' (e.g. chr20). +version: 1.6.2-rc1 website: https://imputationserver.readthedocs.io category: diff --git a/pom.xml b/pom.xml index 786e85ab..07bb7051 100644 --- a/pom.xml +++ b/pom.xml @@ -6,7 +6,7 @@ genepi imputationserver - 1.6.1 + 1.6.2-rc1 jar diff --git a/src/main/java/genepi/imputationserver/steps/imputation/ImputationPipeline.java b/src/main/java/genepi/imputationserver/steps/imputation/ImputationPipeline.java index c2abb46e..5712f335 100644 --- 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-1.6.1"; + public static final String PIPELINE_VERSION = "michigan-imputationserver-1.6.2-rc1"; public static final String IMPUTATION_VERSION = "minimac4-1.0.2"; From 34cdaadd549ef3d480c21322db927c70636977c0 Mon Sep 17 00:00:00 2001 From: Lukas Forer Date: Thu, 10 Feb 2022 15:32:24 +0100 Subject: [PATCH 12/17] Remove groovy-all and update groovy-templates to 3.0.9 --- pom.xml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/pom.xml b/pom.xml index 83fbfe3e..c49f6483 100644 --- a/pom.xml +++ b/pom.xml @@ -289,10 +289,10 @@ org.codehaus.groovy - groovy-all - 2.4.14 + groovy-templates + 3.0.9 - + lukfor pgs-calc From 371b3ffc3d3db53ad75db42e3fc9d77e27025040 Mon Sep 17 00:00:00 2001 From: Lukas Forer Date: Thu, 10 Feb 2022 15:33:21 +0100 Subject: [PATCH 13/17] Update htsjdk to 2.24.1 --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index c49f6483..d0fcc5da 100644 --- a/pom.xml +++ b/pom.xml @@ -226,7 +226,7 @@ com.github.samtools htsjdk - 2.21.3 + 2.24.1 From 7db0c15da47b7fbf65d7b655faeb18aec56049aa Mon Sep 17 00:00:00 2001 From: Lukas Forer Date: Thu, 10 Feb 2022 15:34:00 +0100 Subject: [PATCH 14/17] Update genepi-io 1.2.0 --- pom.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pom.xml b/pom.xml index d0fcc5da..faefa6c8 100644 --- a/pom.xml +++ b/pom.xml @@ -214,9 +214,9 @@ genepi genepi-io - 1.0.12 + 1.2.0 - + genepi genepi-hadoop From ce4978da11fd74c8581f84dc8e60b8c361e54f4c Mon Sep 17 00:00:00 2001 From: Lukas Forer Date: Thu, 10 Feb 2022 15:35:19 +0100 Subject: [PATCH 15/17] Update zip4j to 2.9.1 --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index faefa6c8..84c37385 100644 --- a/pom.xml +++ b/pom.xml @@ -202,7 +202,7 @@ net.lingala.zip4j zip4j - 2.5.2 + 2.9.1 From 661e3cb95ff42a93ebd7cc28acfc9380c95d8bd6 Mon Sep 17 00:00:00 2001 From: Lukas Forer Date: Thu, 10 Feb 2022 15:39:46 +0100 Subject: [PATCH 16/17] Update junit to 4.13.2 --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 84c37385..01e77ba7 100644 --- a/pom.xml +++ b/pom.xml @@ -195,7 +195,7 @@ junit junit - 4.13.1 + 4.13.2 test From 8732011557e5cff2ca2ebb15c27179a95c474eba Mon Sep 17 00:00:00 2001 From: Lukas Forer Date: Thu, 10 Feb 2022 15:40:34 +0100 Subject: [PATCH 17/17] Update yamlbeans to 1.15 --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 01e77ba7..c72a50d7 100644 --- a/pom.xml +++ b/pom.xml @@ -208,7 +208,7 @@ com.esotericsoftware.yamlbeans yamlbeans - 1.14 + 1.15