delete hicstuff_min_mapq and use min_qual instead

conf/modules.config

@@ -208,7 +208,7 @@ process {
         ext.pairs = params.hicstuff_valid_pairs
         ext.index = params.hicstuff_valid_idx
         ext.args = { [
-            " -q ${params.hicstuff_min_qual}",
+            " -q ${params.min_mapq}",
             " -c ${params.hicstuff_circular}"
         ].join('').trim() }
         publishDir = [
@@ -446,7 +446,7 @@ process {
         ext.prefix = { "${meta.id}_${meta.chunk}_${meta.mates}" }
         ext.args = { [
             " -t ${params.hicstuff_tmp_dir}",
-            " -m ${params.hicstuff_min_qual}",
+            " -m ${params.min_mapq}",
             " -l ${params.hicstuff_read_len}"
             ].join('').trim()
         }

docs/hicstuff_usage.md

@@ -166,7 +166,7 @@ Default: false
 --iteralign
 ```
 
-Use [`--hicstuff_min_qual`](#hicstuff_min_qual) to set the minimum quality for the iterative alignment.
+Use [`--min_mapq`](usage.md#min_mapq) to set the minimum quality for the iterative alignment.
 
 #### `--hicstuff_read_len`
 
@@ -239,6 +239,8 @@ If specified, save fragments file. Default: false
 
 ### Bam2pairs
 
+Use [`--min_mapq`](usage.md#min_mapq) to set the minimum quality for the iterative alignment.
+
 #### `--hicstuff_valid_pairs`
 Name of valid pairs file. Default: 'valid.pairs'
 
@@ -253,13 +255,6 @@ Name of valid pairs index file. Default: 'valid_idx.pairs'
 --hicstuff_valid_idx '[Name of valid pairs index file]'
 ```
 
-#### `--hicstuff_min_qual`
-Minimum mapping quality required to keep a pair of Hi-C reads. Default:30
-
-```bash
---hicstuff_min_qual '[Minimum quality value]'
-```
-
 [#### `--hicstuff_circular`](#hicstuff_circular)
 
 #### `--save_pairs`

nextflow.config

@@ -147,7 +147,6 @@ params {
     hicstuff_frags_plot_path = 'frags_hist.pdf'
     hicstuff_valid_pairs = 'valid.pairs'
     hicstuff_valid_idx = 'valid_idx.pairs'
-    hicstuff_min_qual = 30
     hicstuff_matrix = 'abs_fragments_contacts_weighted.txt'
     hicstuff_valid_idx_filtered = 'valid_idx_filtered.pairs'
     hicstuff_plot_events = 'false'

nextflow_schema.json

@@ -567,12 +567,6 @@
                     "default": 0,
                     "fa_icon": "fas fa-cogs"
                 },
-                "hicstuff_min_qual":{
-                    "type": "integer",
-                    "description": "Minimum mapping quality required to keep a pair of Hi-C reads",
-                    "default": 30,
-                    "fa_icon": "fas fa-cogs"
-                },
                 "hicstuff_circular": {
                     "type": "boolean",
                     "description": "Use if the genome is circular",