From 5f1c445f122e01cb5bc88c2c05187725f1d95c33 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 8 Jun 2023 14:30:05 +0200
Subject: [PATCH] pass params.csv as a channel to kmerclust
---
src/main.nf | 4 +++-
src/modules/kmerclust.nf | 3 ++-
2 files changed, 5 insertions(+), 2 deletions(-)
diff --git a/src/main.nf b/src/main.nf
index 6a5799f..7b3aadc 100644
--- a/src/main.nf
+++ b/src/main.nf
@@ -22,10 +22,12 @@ Channel.fromPath( file(params.csv) )
}
.set{ fastq }
+Channel.fromPath("params.csv").set{params_csv}
+
workflow {
SPLIT(fastq.r1.mix(fastq.r2))
FASTKMERS(SPLIT.out.fastq.transpose())
MERGEKMER(FASTKMERS.out.csv.groupTuple())
COLLATEKMER(MERGEKMER.out.csv.map{it -> [it[0].specie, it[1]] }.groupTuple())
- KMERCLUST(COLLATEKMER.out.csv)
+ KMERCLUST(COLLATEKMER.out.csv, params_csv.collect())
}
diff --git a/src/modules/kmerclust.nf b/src/modules/kmerclust.nf
index 74a5fbf..9a9e51a 100644
--- a/src/modules/kmerclust.nf
+++ b/src/modules/kmerclust.nf
@@ -7,6 +7,7 @@ process KMERCLUST {
input:
tuple val(specie), path(csv)
+ path params_csv
output:
tuple val(specie), path("*.pdf"), emit: pdf
@@ -16,7 +17,7 @@ process KMERCLUST {
script:
def args = task.ext.args ?: ''
"""
- Rscript ${projectDir}/bin/kmerclust.R ${params.csv} ${csv} ${specie} ${task.cpus}
+ Rscript ${projectDir}/bin/kmerclust.R ${params_csv} ${csv} ${specie} ${task.cpus}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
--
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