From 324f550545360e6f883c32032c379d9fea3921b6 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Mon, 15 Mar 2021 12:17:19 +0100
Subject: [PATCH] minimap2: add main.nf
---
src/nf_modules/minimap2/main.nf | 50 +++++++++++++++++++++++++++++++++
1 file changed, 50 insertions(+)
create mode 100644 src/nf_modules/minimap2/main.nf
diff --git a/src/nf_modules/minimap2/main.nf b/src/nf_modules/minimap2/main.nf
new file mode 100644
index 00000000..73dc0e34
--- /dev/null
+++ b/src/nf_modules/minimap2/main.nf
@@ -0,0 +1,50 @@
+version = "2.17"
+container_url = "lbmc/minimap2:${version}"
+
+process index_fasta {
+ container = "${container_url}"
+ label "big_mem_multi_cpus"
+ tag "$fasta.baseName"
+
+ input:
+ path fasta
+
+ output:
+ tuple path("${fasta}"), path("*.mmi*"), emit: index
+ path "*_report.txt", emit: report
+
+ script:
+ memory = "${task.memory}" - ~/\s*GB/
+"""
+minimap2 -t ${task.cpus} -I ${memory}G -d ${fasta.baseName}.mmi ${fasta}
+"""
+}
+
+
+process mapping_fastq {
+ container = "${container_url}"
+ label "big_mem_multi_cpus"
+ tag "$pair_id"
+
+ input:
+ tuple path(fasta), path(index)
+ tuple val(pair_id), path(reads)
+
+ output:
+ tuple val(pair_id), path("*.bam"), emit: bam
+ path "*_report.txt", emit: report
+
+ script:
+ memory = "${task.memory}" - ~/\s*GB/
+ memory = memory / (task.cpus + 1.0)
+if (reads instanceof List)
+"""
+minimap2 -ax sr -t ${task.cpus} -K ${memory} ${fasta} ${reads[0]} ${reads[1]} |
+ samtools view -Sb - > ${pair_id}.bam
+"""
+else
+"""
+minimap2 -ax sr -t ${task.cpus} -K ${memory} ${fasta} ${reads} |
+ samtools view -Sb - > ${reads.baseName}.bam
+"""
+}
\ No newline at end of file
--
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