changed groupClones -> assembleCells

mizraelson · mizraelson · commit 645b973d003d · 2025-06-21T12:56:40.000-04:00
diff --git a/docs/mixcr/reference/mixcr-assembleCells.md b/docs/mixcr/reference/mixcr-assembleCells.md
@@ -1,10 +1,10 @@
-# `mixcr groupClones`
+# `mixcr assembleCells`
 
 Groups clones in .clna/.clns files by Cell tags. Grouped clones can be exported using [`mixcr exportCloneGroups`](./mixcr-export.md#clone-groups-by-cell). Each group represents a reliable set of clones (chains) present in all cells within the group. Some clones cannot be assigned to any group and will be labeled as `undefined`. Additionally, some clones may be labeled as `contamination` if they are evenly spread across multiple different cell groups. See the detailed explanation below.
 
 
 ```
-mixcr groupClones 
+mixcr assembleCells 
     [-O <key=value>]
     [--report <path>] 
     [--json-report <path>] 
diff --git a/docs/mixcr/reference/mixcr-export.md b/docs/mixcr/reference/mixcr-export.md
@@ -147,7 +147,7 @@ mixcr exportCloneGroups
     [table.tsv]
 ```
 
-Exports information about clonotypes combined by Cell tag. Input .clns/.clna files have to be grouped with [`mixcr groupClones`](./mixcr-groupClones.md).
+Exports information about clonotypes combined by Cell tag. Input .clns/.clna files have to be grouped with [`mixcr assembleCells`](./mixcr-assembleCells.md).
 
 Command line options:
 
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -175,7 +175,7 @@ nav:
         - 'exportTables': mixcr/reference/mixcr-exportTables.md
         - 'exportPreprocTables': mixcr/reference/mixcr-exportPreprocTables.md
         - 'exportClonesOverlap': mixcr/reference/mixcr-exportClonesOverlap.md
-        - 'groupClones': mixcr/reference/mixcr-groupClones.md
+        - 'assembleCells': mixcr/reference/mixcr-assembleCells.md
         - 'mergeAlignments': mixcr/reference/mixcr-mergeAlignments.md
         - 'overlapScatterPlot': mixcr/reference/mixcr-overlapScatterPlot.md
         - 'postanalysis': mixcr/reference/mixcr-postanalysis.md
