More informative job status

Author: bbimber

singlecell/src/org/labkey/singlecell/run/AbstractCellRangerDependentStep.java

@@ -3,6 +3,7 @@
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.jetbrains.annotations.Nullable;
+import org.labkey.api.pipeline.PipelineJob;
 import org.labkey.api.pipeline.PipelineJobException;
 import org.labkey.api.sequenceanalysis.model.Readset;
 import org.labkey.api.sequenceanalysis.pipeline.AlignmentOutputImpl;
@@ -29,6 +30,8 @@ public IndexOutput createIndex(ReferenceGenome referenceGenome, File outputDir)
 
     protected File runCellRanger(AlignmentOutputImpl output, Readset rs, List<File> inputFastqs1, @Nullable List<File> inputFastqs2, File outputDirectory, ReferenceGenome referenceGenome, String basename, String readGroupId, @Nullable String platformUnit) throws PipelineJobException
     {
+        getPipelineCtx().getJob().setStatus(PipelineJob.TaskStatus.running, "Running Cellranger GEX");
+
         File localBam = new File(outputDirectory, basename + ".cellranger.bam");
         File localBamIdx = new File(localBam.getPath() + ".bai");
 

singlecell/src/org/labkey/singlecell/run/NimbleHelper.java

@@ -12,6 +12,7 @@
 import org.labkey.api.data.SimpleFilter;
 import org.labkey.api.data.TableInfo;
 import org.labkey.api.data.TableSelector;
+import org.labkey.api.pipeline.PipelineJob;
 import org.labkey.api.pipeline.PipelineJobException;
 import org.labkey.api.query.FieldKey;
 import org.labkey.api.query.QueryService;
@@ -151,6 +152,8 @@ public void doNimbleAlign(File bam, PipelineStepOutput output, Readset rs, Strin
     {
         for (NimbleGenome genome : getGenomes())
         {
+            getPipelineCtx().getJob().setStatus(PipelineJob.TaskStatus.running, "Running Nimble for: " + genome.genomeId);
+
             File genomeCsv = getGenomeCsv(genome.getGenomeId());
             File genomeFasta = getGenomeFasta(genome.getGenomeId());