diff --git a/modules/samtools/index/main.nf b/modules/samtools/index/main.nf
index b033e225..74ae15df 100644
--- a/modules/samtools/index/main.nf
+++ b/modules/samtools/index/main.nf
@@ -11,10 +11,13 @@ process SAMTOOLS_INDEX {
     tuple val(meta), path(input)
 
     output:
-    tuple val(meta), path("*.bai") , optional:true, emit: bai
-    tuple val(meta), path("*.crai"), optional:true, emit: crai
-    tuple val(meta), path("*.csi") , optional:true, emit: csi
-    path  "versions.yml"           , emit: versions
+    tuple val(meta), path("*.bam" , includeInputs:true), path("*.bai") , optional:true, emit: bam_bai
+    tuple val(meta), path("*.bai")                                     , optional:true, emit: bai
+    tuple val(meta), path("*.bam" , includeInputs:true), path("*.csi") , optional:true, emit: bam_csi
+    tuple val(meta), path("*.csi")                                     , optional:true, emit: csi
+    tuple val(meta), path("*.cram", includeInputs:true), path("*.crai"), optional:true, emit: cram_crai
+    tuple val(meta), path("*.crai")                                    , optional:true, emit: crai
+    path  "versions.yml"                                                              , emit: versions
 
     script:
     def args = task.ext.args ?: ''