From a433d102ece884b976cdf2015460f4cde95e28da Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 16 Apr 2021 17:53:51 +0200
Subject: [PATCH] minimap2: fix single-end handling
---
src/nf_modules/minimap2/main.nf | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/src/nf_modules/minimap2/main.nf b/src/nf_modules/minimap2/main.nf
index d404ac79..5ac89820 100644
--- a/src/nf_modules/minimap2/main.nf
+++ b/src/nf_modules/minimap2/main.nf
@@ -56,7 +56,7 @@ process mapping_fastq {
minimap2 ${params.mapping_fastq} -t ${task.cpus} -K ${memory} ${fasta} ${reads[0]} ${reads[1]} |
samtools view -Sb - > ${pair_id}.bam
"""
- else if (reads.size() == 1)
+ else
"""
minimap2 ${params.mapping_fastq} -t ${task.cpus} -K ${memory} ${fasta} ${reads} |
samtools view -Sb - > ${pair_id}.bam
--
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