From b67793d5b182445c3c2311f31be108621a8df52e Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 23 May 2023 10:16:07 +0200
Subject: [PATCH] change collate step to collate by species
---
src/main.nf | 4 ++--
src/modules/fastkmers.nf | 1 -
src/modules/kmc.nf | 1 -
src/modules/mergekmer.nf | 9 ++++-----
4 files changed, 6 insertions(+), 9 deletions(-)
diff --git a/src/main.nf b/src/main.nf
index 563a087..5198b79 100644
--- a/src/main.nf
+++ b/src/main.nf
@@ -3,7 +3,7 @@ nextflow.enable.dsl=2
/*
Testing pipeline for marseq scRNASeq analysis
*/
-params.kmer_size = 31
+params.kmer_size = 12
include { SPLIT } from "./modules/split"
include { FASTKMERS } from "./modules/fastkmers"
@@ -24,5 +24,5 @@ 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())
+ COLLATEKMER(MERGEKMER.out.csv.map{it -> [it[0].specie, it[1]] }.groupTuple())
}
diff --git a/src/modules/fastkmers.nf b/src/modules/fastkmers.nf
index 5a6ea26..469883c 100644
--- a/src/modules/fastkmers.nf
+++ b/src/modules/fastkmers.nf
@@ -1,7 +1,6 @@
process FASTKMERS {
tag "$meta.id"
label 'big_mem_mono_cpus'
- publishDir "results/${meta.specie}/${meta.sex}/${meta.read}/", mode: 'copy'
container "lbmc/fastkmers:025efdf"
diff --git a/src/modules/kmc.nf b/src/modules/kmc.nf
index d89b1be..61a555f 100644
--- a/src/modules/kmc.nf
+++ b/src/modules/kmc.nf
@@ -4,7 +4,6 @@
process KMC {
tag "$meta.id"
label 'process_single'
- publishDir "results/${meta.specie}/${meta.sex}/${meta.read}/", mode: 'copy'
container "lbmc/kmc:3.2.2"
diff --git a/src/modules/mergekmer.nf b/src/modules/mergekmer.nf
index 3885cc7..1ecd27e 100644
--- a/src/modules/mergekmer.nf
+++ b/src/modules/mergekmer.nf
@@ -1,7 +1,6 @@
process MERGEKMER {
tag "$meta.id"
label 'big_mem_mono_cpus'
- publishDir "results/${meta.specie}/${meta.sex}/${meta.read}/", mode: 'copy'
container "lbmc/mergekmer:0.1.2"
@@ -26,14 +25,14 @@ process MERGEKMER {
}
process COLLATEKMER {
- tag "$csv"
+ tag "$specie"
label 'big_mem_mono_cpus'
- publishDir "results/", mode: 'copy'
+ publishDir "results/${specie}/", mode: 'copy'
container "lbmc/mergekmer:0.1.2"
input:
- path(csv)
+ tuple val(specie), path(csv)
output:
path("*.csv"), emit: csv
@@ -42,7 +41,7 @@ process COLLATEKMER {
script:
def args = task.ext.args ?: ''
"""
- mergekmer --csv ${csv} --output fusion.csv --collate
+ mergekmer --csv ${csv} --output ${specie}.csv --collate
cat <<-END_VERSIONS > versions.yml
--
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