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Delete MS2 GWT code. Switch to simple job launcher #479

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Merged
labkey-jeckels merged 6 commits into from
Feb 14, 2025
Merged

Delete MS2 GWT code. Switch to simple job launcher #479

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2fccf51
Delete MS2 GWT code. Switch to simple job launcher
labkey-jeckels Dec 19, 2024
45fbe0d
Fix CometTest. Trim now unused code
labkey-jeckels Dec 22, 2024
357dca7
Merge branch 'develop' into fb_deleteMs2Gwt
labkey-jeckels Jan 2, 2025
6135386
Merge branch 'develop' into fb_deleteMs2Gwt
labkey-jeckels Jan 10, 2025
89000aa
Merge branch 'develop' into fb_deleteMs2Gwt
labkey-jeckels Jan 21, 2025
0f5d5fc
Merge branch 'develop' into fb_deleteMs2Gwt
labkey-jeckels Feb 7, 2025
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7 changes: 3 additions & 4 deletions nextflow/src/org/labkey/nextflow/pipeline/NextFlowProtocol.java
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Original file line number Diff line number Diff line change
@@ -1,14 +1,13 @@
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;
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;
Expand Down Expand Up @@ -42,7 +41,7 @@ public AbstractFileAnalysisProtocolFactory<NextFlowProtocol> 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();
}
Expand All @@ -62,7 +61,7 @@ public String getName()
}

@Override
public NextFlowPipelineJob createPipelineJob(ViewBackgroundInfo info, PipeRoot root, List<File> filesInput, File fileParameters, @Nullable Map<String, String> variableMap) throws IOException
public NextFlowPipelineJob createPipelineJob(ViewBackgroundInfo info, PipeRoot root, List<Path> filesInput, Path fileParameters, @Nullable Map<String, String> variableMap)
{
throw new UnsupportedOperationException();
}
Expand Down