From b6b7aeba6635088bdc4825bd3d36ce616534e8a3 Mon Sep 17 00:00:00 2001
From: nservant <nicolas.servant@curie.fr>
Date: Fri, 7 Aug 2020 18:36:08 +0200
Subject: [PATCH] Lint with new template
---
main.nf | 1 +
nextflow.config | 7 ++++---
nextflow_schema.json | 9 ++++++---
3 files changed, 11 insertions(+), 6 deletions(-)
diff --git a/main.nf b/main.nf
index 0cfcbc6..5f7e943 100644
--- a/main.nf
+++ b/main.nf
@@ -244,6 +244,7 @@ summary['Restriction Motif']= params.restriction_site
summary['Ligation Motif'] = params.ligation_site
summary['DNase Mode'] = params.dnase
summary['Remove Dup'] = params.rm_dup
+summary['Remove MultiHits'] = params.rm_multi
summary['Min MAPQ'] = params.min_mapq
summary['Min Fragment Size']= params.min_restriction_fragment_size
summary['Max Fragment Size']= params.max_restriction_fragment_size
diff --git a/nextflow.config b/nextflow.config
index c598df9..edb8038 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -39,9 +39,10 @@ params {
min_insert_size = false
max_insert_size = false
dnase = false
- rm_dup = false
- rm_singleton = false
- rm_multi = false
+ min_cis_dist = false
+ rm_dup = true
+ rm_singleton = true
+ rm_multi = true
bin_size = '1000000,500000'
ice_max_iter = 100
ice_filer_low_count_perc = 0.02
diff --git a/nextflow_schema.json b/nextflow_schema.json
index bb45295..ed2f701 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -132,15 +132,18 @@
},
"rm_dup": {
"type": "boolean",
- "description": "Remove duplicates"
+ "description": "Remove duplicates",
+ "default": true
},
"rm_multi": {
"type": "boolean",
- "description": "Remove multi-mapped reads"
+ "description": "Remove multi-mapped reads",
+ "default": true
},
"rm_singleton": {
"type": "boolean",
- "description": "Remove singleton"
+ "description": "Remove singleton",
+ "default": true
},
"min_mapq": {
"type": "integer",
--
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