From 9f24674dc6590b76c3fa1a49860ce8f99f4a50a2 Mon Sep 17 00:00:00 2001
From: nservant <nicolas.servant@curie.fr>
Date: Mon, 1 Feb 2021 19:14:51 +0100
Subject: [PATCH] fix bug
---
main.nf | 1 +
nextflow.config | 17 +++++------------
2 files changed, 6 insertions(+), 12 deletions(-)
diff --git a/main.nf b/main.nf
index 4c03cdf..b6a66d3 100644
--- a/main.nf
+++ b/main.nf
@@ -106,6 +106,7 @@ if (params.genomes && params.genome && !params.genomes.containsKey(params.genome
if (params.digest && params.digestion && !params.digest.containsKey(params.digestion)) {
exit 1, "Unknown digestion protocol. Currently, the available digestion options are ${params.digest.keySet().join(", ")}. Please set manually the '--restriction_site' and '--ligation_site' parameters."
}
+
params.restriction_site = params.digestion ? params.digest[ params.digestion ].restriction_site ?: false : false
params.ligation_site = params.digestion ? params.digest[ params.digestion ].ligation_site ?: false : false
diff --git a/nextflow.config b/nextflow.config
index 782a1c1..8cca554 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -17,10 +17,6 @@ params {
restriction_fragments = false
save_reference = false
- // Dnase Hi-C
- dnase = false
- min_cis_dist = 0
-
// Mapping
split_fastq = false
fastq_chunks_size = 20000000
@@ -34,14 +30,7 @@ params {
// Digestion Hi-C
- digestion = 'hindiii'
- restriction_site = ''
- ligation_site = ''
- min_restriction_fragment_size = 0
- max_restriction_fragment_size = 0
- min_insert_size = 0
- max_insert_size =0
-
+ digestion = false
digest {
'hindiii'{
restriction_site='A^AGCTT'
@@ -60,6 +49,10 @@ params {
ligation_site='GATCGATC,GATCGANT,GANTGATC,GANTGANT'
}
}
+ min_restriction_fragment_size = 0
+ max_restriction_fragment_size = 0
+ min_insert_size = 0
+ max_insert_size = 0
// Dnase Hi-C
dnase = false
--
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