From f9892e169628023427acea6c327a516dc6001a8e Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 28 Apr 2023 09:42:09 +0200
Subject: [PATCH] add kmersize parameter
---
src/main.nf | 1 +
src/modules/fastkmers.nf | 2 +-
2 files changed, 2 insertions(+), 1 deletion(-)
diff --git a/src/main.nf b/src/main.nf
index cb1609e..ea10ec8 100644
--- a/src/main.nf
+++ b/src/main.nf
@@ -3,6 +3,7 @@ nextflow.enable.dsl=2
/*
Testing pipeline for marseq scRNASeq analysis
*/
+params.kmer_size = 31
include { SPLIT } from "./modules/split"
include { FASTKMERS } from "./modules/fastkmers"
diff --git a/src/modules/fastkmers.nf b/src/modules/fastkmers.nf
index c2b0028..5a6ea26 100644
--- a/src/modules/fastkmers.nf
+++ b/src/modules/fastkmers.nf
@@ -15,7 +15,7 @@ process FASTKMERS {
script:
def args = task.ext.args ?: ''
"""
- fastkmers -k 31 ${fastq} > ${fastq.simpleName}.csv
+ fastkmers -k ${params.kmer_size} ${fastq} > ${fastq.simpleName}.csv
cat <<-END_VERSIONS > versions.yml
--
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