diff --git a/modules/cliquesnv/main.nf b/modules/cliquesnv/main.nf
index f22ffa1..f00d979 100644
--- a/modules/cliquesnv/main.nf
+++ b/modules/cliquesnv/main.nf
@@ -5,7 +5,7 @@ process CLIQUESNV {
     container 'quay.io/biocontainers/cliquesnv:2.0.3--hdfd78af_0'
 
     input:
-    tuple val(prefix), path(bam)
+    tuple val(prefix), path(bam), path(bai)
     val(method)
 
     output:
diff --git a/modules/haplink/haplotypes/main.nf b/modules/haplink/haplotypes/main.nf
index e4b96e8..e178112 100644
--- a/modules/haplink/haplotypes/main.nf
+++ b/modules/haplink/haplotypes/main.nf
@@ -5,7 +5,7 @@ process HAPLINK_HAPLOTYPES {
     container 'quay.io/biocontainers/haplink:1.0.0--h031d066_0'
 
     input:
-    tuple val(prefix), path(bam), path(bai)
+    tuple val(prefix), path(bam), path(bai), path(vcf)
     path reference
 
     output:
diff --git a/modules/predicthaplo/main.nf b/modules/predicthaplo/main.nf
index 71d2fc1..2c14476 100644
--- a/modules/predicthaplo/main.nf
+++ b/modules/predicthaplo/main.nf
@@ -5,7 +5,7 @@ process PREDICTHAPLO {
     container 'quay.io/biocontainers/predicthaplo:2.1.4--h9b88814_5'
 
     input:
-    tuple val(prefix), path(bam)
+    tuple val(prefix), path(bam), path(bai)
     path(reference)
 
     output:
diff --git a/modules/quasirecomb/main.nf b/modules/quasirecomb/main.nf
index e2896c0..085122e 100644
--- a/modules/quasirecomb/main.nf
+++ b/modules/quasirecomb/main.nf
@@ -5,7 +5,7 @@ process QUASIRECOMB {
     container 'quay.io/biocontainers/quasirecomb:1.2--hdfd78af_1'
 
     input:
-    tuple val(prefix), path(bam)
+    tuple val(prefix), path(bam), path(bai)
 
     output:
     tuple val(prefix), path("*.fasta")
diff --git a/modules/shorah/amplicon/main.nf b/modules/shorah/amplicon/main.nf
index d35961a..171cf6b 100644
--- a/modules/shorah/amplicon/main.nf
+++ b/modules/shorah/amplicon/main.nf
@@ -5,7 +5,7 @@ process SHORAH_AMPLICON {
     container 'quay.io/biocontainers/shorah:1.99.2--py38h73782ee_8'
 
     input:
-    tuple val(prefix), path(bam)
+    tuple val(prefix), path(bam), path(bai)
     path(reference)
 
     output:
diff --git a/modules/shorah/shotgun/main.nf b/modules/shorah/shotgun/main.nf
index 224dca9..9f2ece9 100644
--- a/modules/shorah/shotgun/main.nf
+++ b/modules/shorah/shotgun/main.nf
@@ -5,7 +5,7 @@ process SHORAH_SHOTGUN {
     container 'quay.io/biocontainers/shorah:1.99.2--py38h73782ee_8'
 
     input:
-    tuple val(prefix), path(bam)
+    tuple val(prefix), path(bam), path(bai)
     path(reference)
 
     output: