From 804cd499de60d3d4ca1ed610970422462ae87286 Mon Sep 17 00:00:00 2001
From: nservant <nicolas.servant@curie.fr>
Date: Tue, 2 Apr 2019 23:26:48 +0200
Subject: [PATCH] update igenomes
---
conf/hicpro.config | 8 ++++----
conf/test.config | 2 +-
main.nf | 9 +++++----
3 files changed, 10 insertions(+), 9 deletions(-)
diff --git a/conf/hicpro.config b/conf/hicpro.config
index 268d4d4..a68bad7 100644
--- a/conf/hicpro.config
+++ b/conf/hicpro.config
@@ -9,9 +9,9 @@
params {
- // Genome Reference
- bwt2_index =
- chromosome_size =
+ // Reference
+ chromosome_size = false
+ bwt2_index = false
// Alignment options
bwt2_opts_end2end = '--very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder'
@@ -20,7 +20,7 @@ params {
// Digestion Hi-C
restriction_site = 'A^AGGCT'
- restriction_fragments =
+ restrictiong_fragments = false
ligation_site = 'AAGCTAGCTT'
min_restriction_fragment_size = 0
max_restriction_fragment_size = 100
diff --git a/conf/test.config b/conf/test.config
index e13858c..78c37e9 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -24,5 +24,5 @@ params {
]
// Annotations
- genome = 'GRch37'
+ genome = 'GRCh37'
}
diff --git a/main.nf b/main.nf
index ee1945d..a891d4e 100644
--- a/main.nf
+++ b/main.nf
@@ -49,15 +49,15 @@ def helpMessage() {
--bwt2_index Path to Bowtie2 index
--fasta Path to Fasta reference
--chromosome_size Path to chromosome size file
- --restriction_fragment_bed Path to restriction fragment file (bed)
+ --restriction_fragments Path to restriction fragment file (bed)
Options:
--bwt2_opts_end2end Options for bowtie2 end-to-end mappinf (first mapping step)
--bwt2_opts_trimmed Options for bowtie2 mapping after ligation site trimming
--min_mapq Minimum mapping quality values to consider
- --restriction-site Cutting motif(s) of restriction enzyme(s) (comma separated)
- --ligation-site Ligation motifs to trim (comma separated)
+ --restriction_site Cutting motif(s) of restriction enzyme(s) (comma separated)
+ --ligation_site Ligation motifs to trim (comma separated)
--min_restriction_fragment_size Minimum size of restriction fragments to consider
--max_restriction_framgnet_size Maximum size of restriction fragmants to consider
@@ -210,6 +210,7 @@ else if ( params.fasta && params.restriction_site ){
Channel.fromPath(params.fasta)
.ifEmpty { exit 1, "Fasta file not found: ${params.fasta}" }
.set { fasta_for_resfrag }
+}
else {
exit 1, "No restriction fragments file specified!"
}
@@ -344,7 +345,7 @@ if(!params.chromosome_size && params.fasta){
}
}
-if(!params.bwt2_index && params.fasta){
+if(!params.restriction_fragments && params.fasta){
process makeRestrictionFragments {
tag "$fasta"
publishDir path: { params.saveReference ? "${params.outdir}/reference_genome" : params.outdir },
--
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