From 11ae71a40582d44a95fe27ee033de44196f0359d Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 26 Apr 2023 14:13:39 +0200
Subject: [PATCH] add mergekmer module
---
src/main.nf | 4 +++-
src/modules/fastkmers.nf | 3 ---
src/modules/mergekmer.nf | 26 ++++++++++++++++++++++++++
3 files changed, 29 insertions(+), 4 deletions(-)
create mode 100644 src/modules/mergekmer.nf
diff --git a/src/main.nf b/src/main.nf
index 5034df4..4d13e99 100644
--- a/src/main.nf
+++ b/src/main.nf
@@ -4,8 +4,9 @@ nextflow.enable.dsl=2
Testing pipeline for marseq scRNASeq analysis
*/
-include { FASTKMERS } from "./modules/fastkmers"
include { SPLIT } from "./modules/split"
+include { FASTKMERS } from "./modules/fastkmers"
+include { MERGEKMER } from "./modules/mergekmer"
Channel.fromPath( file(params.csv) )
@@ -21,4 +22,5 @@ Channel.fromPath( file(params.csv) )
workflow {
SPLIT(fastq.r1.mix(fastq.r2))
FASTKMERS(SPLIT.out.fastq.transpose())
+ MERGEKMER(FASTKMERS.out.csv.view())
}
diff --git a/src/modules/fastkmers.nf b/src/modules/fastkmers.nf
index ebbdf45..c2b0028 100644
--- a/src/modules/fastkmers.nf
+++ b/src/modules/fastkmers.nf
@@ -1,6 +1,3 @@
-/*
- * normalize bam file
- */
process FASTKMERS {
tag "$meta.id"
label 'big_mem_mono_cpus'
diff --git a/src/modules/mergekmer.nf b/src/modules/mergekmer.nf
new file mode 100644
index 0000000..d8c4c7d
--- /dev/null
+++ b/src/modules/mergekmer.nf
@@ -0,0 +1,26 @@
+process MERGEKMER {
+ tag "$meta.id"
+ label 'big_mem_mono_cpus'
+ publishDir "results/${meta.specie}/${meta.sex}/${meta.read}/", mode: 'copy'
+
+ container "lbmc/mergekmer:0.1.0"
+
+ input:
+ tuple val(meta), path(csv)
+
+ output:
+ tuple val(meta), path("*.csv"), emit: csv
+ path "versions.yml" , emit: versions
+
+ script:
+ def args = task.ext.args ?: ''
+ """
+ mergekmer --csv ${csv} -output ${meta.id}.csv
+
+
+ cat <<-END_VERSIONS > versions.yml
+ "${task.process}":
+ mergekmer: \$(echo \$(mergekmer --version 2>&1))
+ END_VERSIONS
+ """
+}
--
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