diff --git a/nextflow_schema.json b/nextflow_schema.json
index f429d1b..d3878c1 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -10,7 +10,10 @@
             "type": "object",
             "fa_icon": "fas fa-terminal",
             "description": "Define where the pipeline should find input data and save output data.",
-            "required": ["input", "outdir"],
+            "required": [
+                "input",
+                "outdir"
+            ],
             "properties": {
                 "input": {
                     "type": "string",
@@ -173,7 +176,14 @@
                     "description": "Method used to save pipeline results to output directory.",
                     "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
                     "fa_icon": "fas fa-copy",
-                    "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
+                    "enum": [
+                        "symlink",
+                        "rellink",
+                        "link",
+                        "copy",
+                        "copyNoFollow",
+                        "move"
+                    ],
                     "hidden": true
                 },
                 "email_on_fail": {
@@ -294,7 +304,10 @@
         "shortread_clipmerge_tool": {
             "type": "string",
             "default": "fastp",
-            "enum": ["fastp", "adapterremoval"]
+            "enum": [
+                "fastp",
+                "adapterremoval"
+            ]
         },
         "shortread_clipmerge_skipadaptertrim": {
             "type": "boolean"
@@ -335,7 +348,10 @@
         "shortread_complexityfilter_prinseqplusplus_mode": {
             "type": "string",
             "default": "entropy",
-            "enum": ["entropy", "dust"]
+            "enum": [
+                "entropy",
+                "dust"
+            ]
         },
         "shortread_complexityfilter_prinseqplusplus_dustscore": {
             "type": "number",
@@ -388,7 +404,14 @@
         "kaiju_taxon_name": {
             "type": "string",
             "default": "species",
-            "enum": ["phylum", "class", "order", "family", "genus", "species"]
+            "enum": [
+                "phylum",
+                "class",
+                "order",
+                "family",
+                "genus",
+                "species"
+            ]
         },
         "run_diamond": {
             "type": "boolean"
@@ -396,7 +419,39 @@
         "diamond_output_format": {
             "type": "string",
             "default": "tsv",
-            "enum": ["blast", "xml", "txt", "daa", "sam", "tsv", "paf"]
+            "enum": [
+                "blast",
+                "xml",
+                "txt",
+                "daa",
+                "sam",
+                "tsv",
+                "paf"
+            ]
+        },
+        "longread_hostremoval_index": {
+            "type": "string",
+            "default": null
+        },
+        "save_minimap2_hostremoval_index": {
+            "type": "string",
+            "default": "false",
+            "description": "Flag for publishing minimap2 host removal index"
+        },
+        "save_minimap2_hostremoval_mapped": {
+            "type": "string",
+            "default": "false",
+            "description": "Flag for publishinig bam file with all long reads mapped to a reference"
+        },
+        "save_samtools_unmapped_bam": {
+            "type": "string",
+            "default": "false",
+            "description": "Flag for publishing bam for reads that did not map to the host reference"
+        },
+        "save_minimap2_unmapped_fq": {
+            "type": "string",
+            "default": "false",
+            "description": "Flag for publishing fastq files for reads that did not map to the host reference"
         }
     }
 }