update json and usage files

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

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"
                 }
             }
         }