From 2c07085207ed9882c0e222d3fddebe2b43b9488c Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 27 Apr 2023 16:45:43 +0200
Subject: [PATCH] add collatekmer step
---
src/main.nf | 2 ++
src/modules/mergekmer.nf | 31 +++++++++++++++++++++++++++++--
2 files changed, 31 insertions(+), 2 deletions(-)
diff --git a/src/main.nf b/src/main.nf
index c73b10d..e60107b 100644
--- a/src/main.nf
+++ b/src/main.nf
@@ -7,6 +7,7 @@ Testing pipeline for marseq scRNASeq analysis
include { SPLIT } from "./modules/split"
include { FASTKMERS } from "./modules/fastkmers"
include { MERGEKMER } from "./modules/mergekmer"
+include { COLLATEKMER } from "./modules/mergekmer"
Channel.fromPath( file(params.csv) )
@@ -23,4 +24,5 @@ workflow {
SPLIT(fastq.r1.mix(fastq.r2))
FASTKMERS(SPLIT.out.fastq.transpose())
MERGEKMER(FASTKMERS.out.csv.groupTuple())
+ COLLATEKMER(MERGEKMER.out.csv)
}
diff --git a/src/modules/mergekmer.nf b/src/modules/mergekmer.nf
index d8c4c7d..83368cc 100644
--- a/src/modules/mergekmer.nf
+++ b/src/modules/mergekmer.nf
@@ -3,7 +3,7 @@ process MERGEKMER {
label 'big_mem_mono_cpus'
publishDir "results/${meta.specie}/${meta.sex}/${meta.read}/", mode: 'copy'
- container "lbmc/mergekmer:0.1.0"
+ container "lbmc/mergekmer:0.1.1"
input:
tuple val(meta), path(csv)
@@ -15,7 +15,34 @@ process MERGEKMER {
script:
def args = task.ext.args ?: ''
"""
- mergekmer --csv ${csv} -output ${meta.id}.csv
+ mergekmer --csv ${csv} --output ${meta.id}.csv
+
+
+ cat <<-END_VERSIONS > versions.yml
+ "${task.process}":
+ mergekmer: \$(echo \$(mergekmer --version 2>&1))
+ END_VERSIONS
+ """
+}
+
+process COLLATEKMER {
+ tag "$meta.id"
+ label 'big_mem_mono_cpus'
+ publishDir "results/${meta.specie}/${meta.sex}/${meta.read}/", mode: 'copy'
+
+ container "lbmc/mergekmer:0.1.1"
+
+ 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 --collate
cat <<-END_VERSIONS > versions.yml
--
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