diff --git a/conf/modules.config b/conf/modules.config
index f593dada7312c5690b7fcc2d4ad71743915b8d02..25fb8d3188ab14379a698a05a5e7e2c112824a59 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -432,8 +432,7 @@ process {
         ext.output_rev = { "${meta2.id}_${meta2.chunk}_${meta2.mates}_digested.fastq" }
         ext.args = { [
             " -m ${params.cutsite_mode}",
-            " -s ${params.cutsite_seed}",
-            " -c ${params.cutsite_cpu}"
+            " -s ${params.cutsite_seed}"
             ].join('').trim()
         }
         publishDir = [
@@ -447,7 +446,6 @@ process {
         ext.prefix = { "${meta.id}_${meta.chunk}_${meta.mates}" }
         ext.args = { [
             " -t ${params.hicstuff_tmp_dir}",
-            " -n ${params.hicstuff_cpu}",
             " -m ${params.hicstuff_min_qual}",
             " -l ${params.hicstuff_read_len}"
             ].join('').trim()
diff --git a/docs/hicstuff_usage.md b/docs/hicstuff_usage.md
index a89057ece8b1d4e9c56e522ef475e46c416793dd..f7b4b3e572c29b1dd07aaf7961fa0da3c4c854cd 100644
--- a/docs/hicstuff_usage.md
+++ b/docs/hicstuff_usage.md
@@ -280,16 +280,9 @@ Common name of matrix files. Default: 'abs_fragments_contacts_weighted.txt'
 --hicstuff_matrix '[Name of matrix file]'
 ```
 
-#### `--hicstuff_bin`
-Binsize for plotting matrix. Default: 10000
-
-```bash
---hicstuff_bin [binsize]
-```
-
-> :warning: **Warning**: Depending of the size of your input, the bin size may not correspond and make the pipeline fail
->>10000 is default for human genome.
->>For yeast for example you may want to use a smaller bin
+> :warning: **Warning**: Hicstuff builds matrices based on the fragments file
+>> For matrices build with fixed bin size, it's done in the COOLER subworkflow.
+>> See [bin_size](usage.md#bin_size) to change the size of the bin for fixed bin matrices.
 
 ### `--skip_plot_matrix`
 
diff --git a/nextflow.config b/nextflow.config
index 3c268a40751d01392fdb5c2354d78954acd55649..a9d73c30e6fc43c6293231d1df2df7a670d08d65 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -149,7 +149,6 @@ params {
     hicstuff_valid_idx = 'valid_idx.pairs'
     hicstuff_min_qual = 30
     hicstuff_matrix = 'abs_fragments_contacts_weighted.txt'
-    hicstuff_bin = 10000
     hicstuff_valid_idx_filtered = 'valid_idx_filtered.pairs'
     hicstuff_plot_events = 'false'
     hicstuff_pie_plot = 'distrib'
@@ -162,7 +161,6 @@ params {
     hicstuff_distance_out_plot = 'plot_distance_law.pdf'
     hicstuff_filter_pcr_out_file = 'valid_idx_pcrfree.pairs'
     hicstuff_read_len = 'None'
-    hicstuff_cpu = 4
     hicstuff_tmp_dir = 'None'
 
     //Hicstuff optional modules
@@ -176,7 +174,6 @@ params {
     //Cutsite
     cutsite_mode = 'for_vs_rev'
     cutsite_seed = 0
-    cutsite_cpu = 4
     save_digested = false
     cutsite = false
 
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 2067b795e4a10ad13114d5aede58eb81e03344d8..3568326a34f4f2c16c158ab8181046039cf013fe 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -579,12 +579,6 @@
                     "default": false,
                     "fa_icon": "fas fa-cogs"
                 },
-                "hicstuff_bin": {
-                    "type": "integer",
-                    "description": "Binsize for plotting matrix",
-                    "default": 10000,
-                    "fa_icon": "fas fa-cogs"
-                },
                 "hicstuff_output_contigs": {
                     "type": "string",
                     "description": "Name of info contigs file",
@@ -723,10 +717,6 @@
                     "type": "boolean",
                     "description": "If true, do cutsite process to pre digest reads"
                 },
-                "cutsite_cpu": {
-                    "type": "integer",
-                    "description": "Number of cpu to use for cutsite"
-                },
                 "cutsite_seed": {
                     "type": "integer",
                     "description": "Minimum size of a fragment (i.e. seed size used in mapping as reads smaller won't be mapped.)"
@@ -744,10 +734,6 @@
                     "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"