From 2fccf5196ae13c7ceadbece0990c87cd145b48c3 Mon Sep 17 00:00:00 2001 From: labkey-jeckels Date: Thu, 19 Dec 2024 15:30:06 -0800 Subject: [PATCH 1/2] Delete MS2 GWT code. Switch to simple job launcher --- .../src/org/labkey/nextflow/pipeline/NextFlowProtocol.java | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/nextflow/src/org/labkey/nextflow/pipeline/NextFlowProtocol.java b/nextflow/src/org/labkey/nextflow/pipeline/NextFlowProtocol.java index 2faf82b1..494e012a 100644 --- a/nextflow/src/org/labkey/nextflow/pipeline/NextFlowProtocol.java +++ b/nextflow/src/org/labkey/nextflow/pipeline/NextFlowProtocol.java @@ -7,8 +7,6 @@ import org.labkey.api.util.FileType; import org.labkey.api.view.ViewBackgroundInfo; -import java.io.File; -import java.io.IOException; import java.nio.file.Path; import java.util.List; import java.util.Map; @@ -62,7 +60,7 @@ public String getName() } @Override - public NextFlowPipelineJob createPipelineJob(ViewBackgroundInfo info, PipeRoot root, List filesInput, File fileParameters, @Nullable Map variableMap) throws IOException + public NextFlowPipelineJob createPipelineJob(ViewBackgroundInfo info, PipeRoot root, List filesInput, Path fileParameters, @Nullable Map variableMap) { throw new UnsupportedOperationException(); } From 45fbe0db4eb3d5e98f7be77419a51401c6548eda Mon Sep 17 00:00:00 2001 From: labkey-jeckels Date: Sun, 22 Dec 2024 12:31:26 -0800 Subject: [PATCH 2/2] Fix CometTest. Trim now unused code --- .../src/org/labkey/nextflow/pipeline/NextFlowProtocol.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/nextflow/src/org/labkey/nextflow/pipeline/NextFlowProtocol.java b/nextflow/src/org/labkey/nextflow/pipeline/NextFlowProtocol.java index 494e012a..29544bed 100644 --- a/nextflow/src/org/labkey/nextflow/pipeline/NextFlowProtocol.java +++ b/nextflow/src/org/labkey/nextflow/pipeline/NextFlowProtocol.java @@ -1,6 +1,7 @@ package org.labkey.nextflow.pipeline; import org.jetbrains.annotations.Nullable; +import org.labkey.api.data.Container; import org.labkey.api.pipeline.PipeRoot; import org.labkey.api.pipeline.file.AbstractFileAnalysisProtocol; import org.labkey.api.pipeline.file.AbstractFileAnalysisProtocolFactory; @@ -40,7 +41,7 @@ public AbstractFileAnalysisProtocolFactory getFactory() return new AbstractFileAnalysisProtocolFactory<>() { @Override - public NextFlowProtocol createProtocolInstance(String name, String description, String xml) + public NextFlowProtocol createProtocolInstance(String name, String description, String xml, Container container) { return new NextFlowProtocol(); }