Merge pull request #799 from AlexsLemonade/jashapiro/filter-more

Increase minimum cells to 3
AlexsLemonade · Nov 4, 2024 · cc50b09 · cc50b09
2 parents e609162 + 1501058
commit cc50b09
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/modules/export-anndata.nf b/modules/export-anndata.nf
@@ -61,7 +61,7 @@ workflow sce_to_anndata {
         // number of cells are stored in each metadata.json file
         .filter{
           def cells = Utils.getMetaVal(file(it[3]), "${it[2]}_cells");
-          cells == '' || cells > 1  // if no cell count, keep file for testing, otherwise require at least 2 cells
+          cells == '' || cells > 2  // if no cell count, keep file for testing, otherwise require at least 3 cells
         }
         // remove metadata.json file from tuple
         .map{it.dropRight(1)}

diff --git a/nextflow.config b/nextflow.config
@@ -78,7 +78,7 @@ profiles {
   standard {
     process.executor = 'local'
     docker.enabled = true
-    docker.userEmulation = true
+    docker.fixOwnership = true
   }
   // AWS batch profile with autoscaling disk
   batch {