From a7d6630733f4cfe9ce250fee11df91cfbf719e01 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 28 Apr 2023 15:39:39 +0200
Subject: [PATCH] fix collatekmer
---
src/main.nf | 2 +-
src/modules/mergekmer.nf | 6 +++---
2 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/src/main.nf b/src/main.nf
index ea10ec8..f0214c9 100644
--- a/src/main.nf
+++ b/src/main.nf
@@ -27,5 +27,5 @@ workflow {
FASTKMERS(SPLIT.out.fastq.transpose())
MERGEKMER(FASTKMERS.out.csv.groupTuple(size: 10))
MERGEKMER2(MERGEKMER.out.csv.groupTuple())
- COLLATEKMER(MERGEKMER2.out.csv)
+ COLLATEKMER(MERGEKMER2.out.csv.map{it -> it[1]}.collect())
}
diff --git a/src/modules/mergekmer.nf b/src/modules/mergekmer.nf
index 83368cc..cc5b7d4 100644
--- a/src/modules/mergekmer.nf
+++ b/src/modules/mergekmer.nf
@@ -28,12 +28,12 @@ process MERGEKMER {
process COLLATEKMER {
tag "$meta.id"
label 'big_mem_mono_cpus'
- publishDir "results/${meta.specie}/${meta.sex}/${meta.read}/", mode: 'copy'
+ publishDir "results/", mode: 'copy'
container "lbmc/mergekmer:0.1.1"
input:
- tuple val(meta), path(csv)
+ path(csv)
output:
tuple val(meta), path("*.csv"), emit: csv
@@ -42,7 +42,7 @@ process COLLATEKMER {
script:
def args = task.ext.args ?: ''
"""
- mergekmer --csv ${csv} --output ${meta.id}.csv --collate
+ mergekmer --csv ${csv} --output final.csv --collate
cat <<-END_VERSIONS > versions.yml
--
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