Resolve merge conflicts

Author: bbimber

.github/workflows/sync-repos.yml

@@ -4,8 +4,7 @@ on:
     - cron:  "10 */3 * * *"
 jobs:
   sync-release-branches:
-    # github.head_ref should only be set on forked repos, meaning this action should only run on the primary fork
-    if: github.head_ref == ''
+    if: github.repository == 'BimberLab/DiscvrLabkeyModules'
     runs-on: ubuntu-latest
     steps:
       - name: "Sync Release Branches"
@@ -17,7 +16,7 @@ jobs:
           destination_branch_prefix: "discvr-"
           github_token: ${{ secrets.GITHUB_TOKEN }}
   sync-develop:
-    if: github.head_ref == ''
+    if: github.repository == 'BimberLab/DiscvrLabkeyModules'
     runs-on: ubuntu-latest
     steps:
       - name: "Sync Develop Branch"

.gitignore

@@ -4,4 +4,6 @@
 /intellijBuild
 /travisSettings.sh
 
-dependencies.txt
+# Created by npm install
+/jbrowse/jb_run.js
+/jbrowse/jb_setup.js

SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/CellHashingHandler.java

@@ -268,6 +268,9 @@ public void processFilesRemote(List<Readset> readsets, JobContext ctx) throws Un
                 {
                     ctx.getLogger().warn("None of the edit distances produced results");
                 }
+
+                //clear info field
+                ctx.getJob().setStatus(PipelineJob.TaskStatus.running);
             }
         }
     }
@@ -277,7 +280,7 @@ private Map<String, Object> executeCiteSeqCount(JobContext ctx, RecordedAction a
         CiteSeqCountWrapper wrapper = new CiteSeqCountWrapper(ctx.getLogger());
         ReadData rd = rs.getReadData().get(0);
 
-        //ctx.getJob().setStatus(PipelineJob.TaskStatus.running, "Running CITE-seq-count with edit distance: " + editDistance);
+        ctx.getJob().setStatus(PipelineJob.TaskStatus.running, "Running CITE-seq-count with edit distance: " + editDistance);
         List<String> args = new ArrayList<>();
 
         args.addAll(getClientCommandArgs(ctx.getParams()));
@@ -326,6 +329,7 @@ private Map<String, Object> executeCiteSeqCount(JobContext ctx, RecordedAction a
         }
         ctx.getFileManager().addIntermediateFile(doneFile);
 
+        ctx.getJob().setStatus(PipelineJob.TaskStatus.running, "Generating HTO calls for edit distance: " + editDistance);
         File htoCalls = generateFinalCalls(outputMatrix.getParentFile(), ctx.getOutputDir(), outputBasename, ctx.getLogger(), null, true, minCountPerCell, ctx.getSourceDirectory());
         File html = new File(htoCalls.getParentFile(), outputBasename + ".html");