diff --git a/modules.json b/modules.json
index e9af665..10d6c74 100644
--- a/modules.json
+++ b/modules.json
@@ -119,8 +119,7 @@
                     },
                     "minimap2/index": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
-                        "patch": "modules/nf-core/minimap2/index/minimap2-index.diff"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
                     },
                     "motus/merge": {
                         "branch": "master",
diff --git a/modules/nf-core/minimap2/index/main.nf b/modules/nf-core/minimap2/index/main.nf
index 3dfeb86..25e9429 100644
--- a/modules/nf-core/minimap2/index/main.nf
+++ b/modules/nf-core/minimap2/index/main.nf
@@ -7,11 +7,11 @@ process MINIMAP2_INDEX {
         'quay.io/biocontainers/minimap2:2.21--h5bf99c6_0' }"
 
     input:
-    path fasta
+    tuple val(meta), path(fasta)
 
     output:
-    path "*.mmi"        , emit: index
-    path "versions.yml" , emit: versions
+    tuple val(meta), path("*.mmi"), emit: index
+    path "versions.yml"           , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/nf-core/minimap2/index/minimap2-index.diff b/modules/nf-core/minimap2/index/minimap2-index.diff
deleted file mode 100644
index de306d5..0000000
--- a/modules/nf-core/minimap2/index/minimap2-index.diff
+++ /dev/null
@@ -1,20 +0,0 @@
-Changes in module 'nf-core/minimap2/index'
---- modules/nf-core/minimap2/index/main.nf
-+++ modules/nf-core/minimap2/index/main.nf
-@@ -7,11 +7,11 @@
-         'quay.io/biocontainers/minimap2:2.21--h5bf99c6_0' }"
- 
-     input:
--    tuple val(meta), path(fasta)
-+    path fasta
- 
-     output:
--    tuple val(meta), path("*.mmi"), emit: index
--    path "versions.yml"           , emit: versions
-+    path "*.mmi"        , emit: index
-+    path "versions.yml" , emit: versions
- 
-     when:
-     task.ext.when == null || task.ext.when
-
-************************************************************
diff --git a/subworkflows/local/longread_hostremoval.nf b/subworkflows/local/longread_hostremoval.nf
index 751f4e1..82ea8ca 100644
--- a/subworkflows/local/longread_hostremoval.nf
+++ b/subworkflows/local/longread_hostremoval.nf
@@ -18,7 +18,7 @@ workflow LONGREAD_HOSTREMOVAL {
     ch_multiqc_files  = Channel.empty()
 
     if ( !params.longread_hostremoval_index ) {
-        ch_minimap2_index = MINIMAP2_INDEX ( reference ).index
+        ch_minimap2_index = MINIMAP2_INDEX ( [ [], reference ] ).index.map { it[1] }
         ch_versions       = ch_versions.mix( MINIMAP2_INDEX.out.versions )
     } else {
         ch_minimap2_index = index