Nextflow integration with pipeline #453
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labkey-jeckels
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Oct 31, 2024
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labkey-jeckels
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labkey-jeckels
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Some requests but no need for another review unless you want it.
| btnTxt = "Enable NextFlow"; | ||
| } | ||
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| return new HtmlView("Enable/Disable Nextflow", DIV("Enable/Disable Nextflow", |
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These kinds of UIs can be confusing about what's the current vs future state.
In addition to the button, let's clearly state "NextFlow is currently enabled in this folder" (or disabled).
| { | ||
| PropertyStore store = PropertyManager.getNormalStore(); | ||
| PropertyManager.PropertyMap map = store.getWritableProperties(NextFlowManager.NEXTFLOW_ENABLE, false); | ||
| if (map == null || !"true".equals(map.get("enabled"))) |
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Boolean.parseBoolean()
| @Override | ||
| public void addNavTrail(NavTree navTree) | ||
| { | ||
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Append to the nav trail to give the page a title
| this._apiKey = apiKey; | ||
| try | ||
| { | ||
| setLogFile(FileUtil.createTempFile("NextFlowPipelineJob", ".log")); |
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This shouldn't be a temp file. Create a file based on the current date/time in the pipeline root. See MaintenancePipelineJob for an example.
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Rationale
This PR adds a new Nextflow module to easily initiate DIA (data independent analysis) through the LK pipelines, both pulling data from PanoramaWeb and uploading the results back into PanoramaWeb.
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