From a8f12adcc88ae79041feca5c604d3c4e1008a957 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 18 Apr 2023 14:52:55 +0200
Subject: [PATCH] add kmc module
---
src/modules/kmc.nf | 30 ++++++++++++++++++++++++++++++
1 file changed, 30 insertions(+)
create mode 100644 src/modules/kmc.nf
diff --git a/src/modules/kmc.nf b/src/modules/kmc.nf
new file mode 100644
index 0000000..a0f4997
--- /dev/null
+++ b/src/modules/kmc.nf
@@ -0,0 +1,30 @@
+/*
+ * normalize bam file
+ */
+process FASTKMERS {
+ tag "$meta.id"
+ label 'process_single'
+ publishDir "results/${meta.specie}/${meta.sex}/${meta.read}/", mode: 'copy'
+
+ container "lbmc/kmc:3.2.2"
+
+ input:
+ tuple val(meta), path(fastq)
+
+ output:
+ tuple val(meta), path("*.csv"), emit: csv
+ path "versions.yml" , emit: versions
+
+ script:
+ def args = task.ext.args ?: ''
+ """
+ kmc -k31 ${fastq} 31mers .
+ kmc_tools transform 27mers dump ${fastq.simpleName}.txt
+
+
+ cat <<-END_VERSIONS > versions.yml
+ "${task.process}":
+ kmc: \$(echo \$(kmc --version 2>&1))
+ END_VERSIONS
+ """
+}
--
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