From f5686750876c425bbc35db8a2d30a2edafd9d9e5 Mon Sep 17 00:00:00 2001
From: nservant <nicolas.servant@curie.fr>
Date: Wed, 4 Jan 2023 13:54:15 +0100
Subject: [PATCH] Add comments in bowtie call
---
subworkflows/local/hicpro_mapping.nf | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/subworkflows/local/hicpro_mapping.nf b/subworkflows/local/hicpro_mapping.nf
index 06d579b..0f889e9 100644
--- a/subworkflows/local/hicpro_mapping.nf
+++ b/subworkflows/local/hicpro_mapping.nf
@@ -46,7 +46,7 @@ workflow HICPRO_MAPPING {
ch_reads_r2 = reads.map{ it -> pairToSingle(it,"R2") }
ch_reads = ch_reads_r1.concat(ch_reads_r2)
- // bowtie2
+ // bowtie2 - save_unaligned=true - sort_bam=false
BOWTIE2_ALIGN(
ch_reads,
index.collect(),
@@ -63,7 +63,7 @@ workflow HICPRO_MAPPING {
)
ch_versions = ch_versions.mix(TRIM_READS.out.versions)
- // bowtie2 on trimmed reads
+ // bowtie2 on trimmed reads - save_unaligned=false - sort_bam=false
BOWTIE2_ALIGN_TRIMMED(
TRIM_READS.out.fastq,
index.collect(),
--
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