Skip to content
Snippets Groups Projects
Verified Commit 2894bcf4 authored by Mia Croiset's avatar Mia Croiset
Browse files

delete hicstuff_min_mapq and use min_qual instead

parent 966011bb
No related branches found
No related tags found
No related merge requests found
......@@ -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()
}
......
......@@ -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`
......
......@@ -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'
......
......@@ -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",
......
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment