diff --git a/modules/bwa/index/main.nf b/modules/bwa/index/main.nf
index 3affbf16bc3..d99ae090c1b 100644
--- a/modules/bwa/index/main.nf
+++ b/modules/bwa/index/main.nf
@@ -11,7 +11,7 @@ process BWA_INDEX {
     path fasta
 
     output:
-    path "bwa"         , emit: index
+    path "bwa/*"       , emit: index
     path "versions.yml", emit: versions
 
     when:
diff --git a/modules/bwa/mem/main.nf b/modules/bwa/mem/main.nf
index 27ea6f42e5e..79bc44b0d45 100644
--- a/modules/bwa/mem/main.nf
+++ b/modules/bwa/mem/main.nf
@@ -26,13 +26,11 @@ process BWA_MEM {
     def read_group = meta.read_group ? "-R ${meta.read_group}" : ""
     def samtools_command = sort_bam ? 'sort' : 'view'
     """
-    INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'`
-
     bwa mem \\
         $args \\
         $read_group \\
         -t $task.cpus \\
-        \$INDEX \\
+        ${index[0].baseName} \\
         $reads \\
         | samtools $samtools_command $args2 --threads $task.cpus -o ${prefix}.bam -
 
diff --git a/modules/bwamem2/index/main.nf b/modules/bwamem2/index/main.nf
index 900f27d472a..71352dbd997 100644
--- a/modules/bwamem2/index/main.nf
+++ b/modules/bwamem2/index/main.nf
@@ -11,8 +11,8 @@ process BWAMEM2_INDEX {
     path fasta
 
     output:
-    path "bwamem2"      , emit: index
-    path "versions.yml" , emit: versions
+    path "bwamem2/*"   , emit: index
+    path "versions.yml", emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -24,7 +24,8 @@ process BWAMEM2_INDEX {
     bwa-mem2 \\
         index \\
         $args \\
-        $fasta -p bwamem2/${fasta}
+        -p bwamem2/${fasta} \\
+        $fasta
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/bwamem2/mem/main.nf b/modules/bwamem2/mem/main.nf
index e3a3d164eaa..8dc4df4ea4c 100644
--- a/modules/bwamem2/mem/main.nf
+++ b/modules/bwamem2/mem/main.nf
@@ -26,14 +26,12 @@ process BWAMEM2_MEM {
     def read_group = meta.read_group ? "-R ${meta.read_group}" : ""
     def samtools_command = sort_bam ? 'sort' : 'view'
     """
-    INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'`
-
     bwa-mem2 \\
         mem \\
         $args \\
         $read_group \\
         -t $task.cpus \\
-        \$INDEX \\
+        ${index[0].baseName} \\
         $reads \\
         | samtools $samtools_command $args2 -@ $task.cpus -o ${prefix}.bam -