From 0a3203a15b32ed16e2607cd9a62b7fcdba7e765f Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 10 May 2023 09:47:01 +0200
Subject: [PATCH] split COLLATEKMER in 2 steps
---
src/main.nf | 6 ++++--
src/modules/mergekmer.nf | 4 ++--
2 files changed, 6 insertions(+), 4 deletions(-)
diff --git a/src/main.nf b/src/main.nf
index f8524d8..251ad36 100644
--- a/src/main.nf
+++ b/src/main.nf
@@ -8,7 +8,8 @@ params.kmer_size = 31
include { SPLIT } from "./modules/split"
include { FASTKMERS } from "./modules/fastkmers"
include { MERGEKMER } from "./modules/mergekmer"
-include { COLLATEKMER } from "./modules/mergekmer"
+include { COLLATEKMER as COLLATEKMER1 } from "./modules/mergekmer"
+include { COLLATEKMER as COLLATEKMER2} from "./modules/mergekmer"
Channel.fromPath( file(params.csv) )
@@ -25,5 +26,6 @@ workflow {
SPLIT(fastq.r1.mix(fastq.r2))
FASTKMERS(SPLIT.out.fastq.transpose())
MERGEKMER(FASTKMERS.out.csv.groupTuple())
- COLLATEKMER(MERGEKMER.out.csv.map{it -> it[1]}.collect())
+ COLLATEKMER1(MERGEKMER.out.csv.map{it -> it[1]}.collate(5))
+ COLLATEKMER2(COLLATEKMER1.out.csv.map{it -> it[1]}.collect())
}
diff --git a/src/modules/mergekmer.nf b/src/modules/mergekmer.nf
index cc5b7d4..35fd56d 100644
--- a/src/modules/mergekmer.nf
+++ b/src/modules/mergekmer.nf
@@ -36,8 +36,8 @@ process COLLATEKMER {
path(csv)
output:
- tuple val(meta), path("*.csv"), emit: csv
- path "versions.yml" , emit: versions
+ tuple path("*.csv"), emit: csv
+ path "versions.yml", emit: versions
script:
def args = task.ext.args ?: ''
--
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