diff --git a/conf/modules.config b/conf/modules.config
index 0d3b9cbe..2fc42b22 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -238,7 +238,11 @@ if (params.aligner == 'cellrangermulti') {
             publishDir = [
                 path: "${params.outdir}/${params.aligner}/count",
                 mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                saveAs: { filename ->
+                    if (filename.equals('versions.yml')) null
+                    else if (filename.equals('cellranger_multi_config.csv')) "${meta.id}/${filename}"
+                    else filename
+                }
             ]
         }
         withName: 'GUNZIP*' {