From 9489f360f17061ec141a870ff34f8070e2b8f8f6 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Mon, 16 Aug 2021 10:25:00 +0200
Subject: [PATCH] Merge branch 'crey02-master-patch-25149' into 'master'
Crey02 master patch 25149
See merge request LBMC/nextflow!24
---
src/nf_modules/minimap2/main.nf | 6 ++----
1 file changed, 2 insertions(+), 4 deletions(-)
diff --git a/src/nf_modules/minimap2/main.nf b/src/nf_modules/minimap2/main.nf
index 5ac89820..9dbe5a57 100644
--- a/src/nf_modules/minimap2/main.nf
+++ b/src/nf_modules/minimap2/main.nf
@@ -16,7 +16,6 @@ process index_fasta {
output:
tuple val(file_id), path("${fasta}"), path("*.mmi*"), emit: index
- path "*_report.txt", emit: report
script:
memory = "${task.memory}" - ~/\s*GB/
@@ -41,7 +40,6 @@ process mapping_fastq {
output:
tuple val(file_id), path("*.bam"), emit: bam
- path "*_report.txt", emit: report
script:
if (file_id instanceof List){
@@ -50,7 +48,7 @@ process mapping_fastq {
file_prefix = file_id
}
memory = "${task.memory}" - ~/\s*GB/
- memory = memory / (task.cpus + 1.0)
+ memory = memory.toInteger() / (task.cpus + 1.0)
if (reads.size() == 2)
"""
minimap2 ${params.mapping_fastq} -t ${task.cpus} -K ${memory} ${fasta} ${reads[0]} ${reads[1]} |
@@ -61,4 +59,4 @@ process mapping_fastq {
minimap2 ${params.mapping_fastq} -t ${task.cpus} -K ${memory} ${fasta} ${reads} |
samtools view -Sb - > ${pair_id}.bam
"""
-}
\ No newline at end of file
+}
--
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