From 2894bcf47d4c29ddba687730eb8115f212af1c9f Mon Sep 17 00:00:00 2001
From: Mia Croiset <mia.croiset@ens-lyon.fr>
Date: Mon, 26 Feb 2024 14:56:44 +0100
Subject: [PATCH] delete hicstuff_min_mapq and use min_qual instead
---
conf/modules.config | 4 ++--
docs/hicstuff_usage.md | 11 +++--------
nextflow.config | 1 -
nextflow_schema.json | 6 ------
4 files changed, 5 insertions(+), 17 deletions(-)
diff --git a/conf/modules.config b/conf/modules.config
index 25fb8d3..2001ddd 100644
--- a/conf/modules.config
+++ b/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()
}
diff --git a/docs/hicstuff_usage.md b/docs/hicstuff_usage.md
index f7b4b3e..07abb2c 100644
--- a/docs/hicstuff_usage.md
+++ b/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`
diff --git a/nextflow.config b/nextflow.config
index a9d73c3..738613a 100644
--- a/nextflow.config
+++ b/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'
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 3568326..d26c093 100644
--- a/nextflow_schema.json
+++ b/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",
--
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