diff --git a/docs/hicstuff_usage.md b/docs/hicstuff_usage.md
index c084b0c6c03441588c4fedcbf2cc9704d60b84ff..a89057ece8b1d4e9c56e522ef475e46c416793dd 100644
--- a/docs/hicstuff_usage.md
+++ b/docs/hicstuff_usage.md
@@ -168,6 +168,15 @@ Default: false
 
 Use [`--hicstuff_min_qual`](#hicstuff_min_qual) to set the minimum quality for the iterative alignment.
 
+#### `--hicstuff_read_len`
+
+Read length in the fasta file. If set to None, the length of the first read is used. Set this value to the longest read length in the file if you have different read lengths.
+Default: None
+
+```bash
+--hicstuff_read_len '[Wanted read length]'
+```
+
 #### `--save_bam`
 
 If specified, save BAM files after mapping (works for normal and iterative mode). Default: false
diff --git a/nextflow_schema.json b/nextflow_schema.json
index f5f0617db10277a1ab2df9d0ef06e4340dd5fc4e..2067b795e4a10ad13114d5aede58eb81e03344d8 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -735,6 +735,22 @@
                     "type": "string",
                     "description": "Mode to use to make the digestion.",
                     "enum": ["all", "for_vs_rev", "pile"]
+                },
+                "iteralign": {
+                    "type": "boolean",
+                    "description": "If true, do iterative alignment"
+                },
+                "hicstuff_tmp_dir": {
+                    "type": "string",
+                    "description": "Path where temporary files should be written"
+                },
+                "hicstuff_cpu": {
+                    "type": "integer",
+                    "description": "The number of CPUs to use for the iterative alignment"
+                },
+                "hicstuff_read_len": {
+                    "type": "integer",
+                    "description": "Read length in the fasta file. If set to None, the first read is used. Set this value to the longest read length in the file if you have different read lengths"
                 }
             }
         }