diff --git a/conf/modules.config b/conf/modules.config
index b0e5d61..5b9a815 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -133,20 +133,34 @@ process {
     }
 
     withName: BOWTIE2_BUILD {
-        ext.prefix = { "${meta.id}_${meta.run_accession}" }
         publishDir = [
             path: { "${params.outdir}/bowtie2/build" },
             mode: params.publish_dir_mode,
-            pattern: '*.bt2'
+            enabled: params.save_hostremoval_index,
+            pattern: 'bowtie2'
         ]
     }
 
     withName: BOWTIE2_ALIGN {
         ext.prefix = { "${meta.id}_${meta.run_accession}" }
         publishDir = [
+            [
             path: { "${params.outdir}/bowtie2/align" },
             mode: params.publish_dir_mode,
-            pattern: '*.{fastq.gz,bam}'
+            pattern: '*.log'
+            ],
+            [
+            path: { "${params.outdir}/bowtie2/align" },
+            mode: params.publish_dir_mode,
+            enabled: params.save_hostremoval_mapped,
+            pattern: '*.bam'
+            ],
+            [
+            path: { "${params.outdir}/bowtie2/align" },
+            mode: params.publish_dir_mode,
+            enabled: params.save_hostremoval_unmapped,
+            pattern: '*.fastq.gz'
+            ]
         ]
     }
 
diff --git a/nextflow.config b/nextflow.config
index fce21ad..43aaae8 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -82,8 +82,11 @@ params {
 
     // Host Removal
     perform_shortread_hostremoval     = false
-    shortread_hostremoval_reference = null
-    shortread_hostremoval_index     = null
+    shortread_hostremoval_reference   = null
+    shortread_hostremoval_index       = null
+    save_hostremoval_index            = false
+    save_hostremoval_mapped           = false
+    save_hostremoval_unmapped         = false
 
     // MALT
     run_malt                   = false
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 3d3ad96..2181cce 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -370,6 +370,15 @@
             "type": "string",
             "default": "None"
         },
+        "save_hostremoval_index": {
+            "type": "boolean"
+        },
+        "save_hostremoval_mapped": {
+            "type": "boolean"
+        },
+        "save_hostremoval_unmapped": {
+            "type": "boolean"
+        },
         "run_kaiju": {
             "type": "boolean"
         },