diff --git a/src/nf_modules/deeptools/main.nf b/src/nf_modules/deeptools/main.nf
index 52a8728942e0f1a3fc2905dfa3b469878fa73167..2e658d1cdd74abd9e1a532f7e8a99e73d6ce1341 100644
--- a/src/nf_modules/deeptools/main.nf
+++ b/src/nf_modules/deeptools/main.nf
@@ -15,7 +15,7 @@ process index_bam {
     tuple val(file_id), path(bam)
 
   output:
-    tuple val(file_id), path("*.bam*"), emit: bam
+    tuple val(file_id), path("${bam}"), path("*.bam*"), emit: bam_idx
 
   script:
 """
@@ -74,8 +74,8 @@ computeMatrix scale-regions -S ${bw} \
 """
 }
 
-params.compute_matrix = ""
-params.compute_matrix_out = ""
+params.plot_profile = ""
+params.plot_profile_out = ""
 process plot_profile {
   container = "${container_url}"
   label "big_mem_mono_cpus"
diff --git a/src/nf_modules/samtools/main.nf b/src/nf_modules/samtools/main.nf
index 4d5c931391f2d43e3f28cb2134baba34d42981a3..4228dc5f272a7a118ef36efe1f2562fdb5b4ce94 100644
--- a/src/nf_modules/samtools/main.nf
+++ b/src/nf_modules/samtools/main.nf
@@ -125,8 +125,7 @@ process index_bam {
     tuple val(file_id), path(bam)
 
   output:
-    tuple val(file_id), path(bam), emit: bam
-    tuple val(file_id), path("*.bam.bai"), emit: bam_idx
+    tuple val(file_id), path("${bam}"), path("*.bam.bai"), emit: bam_idx
 
   script:
 """