From bcbb832e7cb62e9c156930197acd0675d7b58182 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 5 Dec 2023 16:52:13 +0100
Subject: [PATCH] COLLATEKMER: ensure to have male / female columns
---
src/main.nf | 11 ++++++++++-
src/modules/mergekmer.nf | 4 ++--
2 files changed, 12 insertions(+), 3 deletions(-)
diff --git a/src/main.nf b/src/main.nf
index e65bd25..4e0898d 100644
--- a/src/main.nf
+++ b/src/main.nf
@@ -32,7 +32,16 @@ workflow {
SPLIT(SUBSAMPLE_READ.out.fastq)
FASTKMERS(SPLIT.out.fastq.transpose())
MERGEKMER(FASTKMERS.out.csv.map{it -> [[it[0][0], it[0][1], it[0][2]], it[1]]}.groupTuple())
- COLLATEKMER(MERGEKMER.out.csv.map{it -> [it[0].specie, it[1]] }.groupTuple())
+ COLLATEKMER(
+ MERGEKMER.out.csv
+ .filter{ it[0].sex == "male" }
+ .map{ it -> [it[0].specice, it[1]]}
+ .join(
+ MERGEKMER.out.csv
+ .filter{ it[0].sex == "female" }
+ .map{ it -> [it[0].specice, it[1]]}
+ )
+ )
KMERCLUST_LOAD(COLLATEKMER.out.csv, params_csv.collect())
KMERCLUST_BOOT(Channel.of(1..params.bootstrap).combine(KMERCLUST_LOAD.out.rdata))
KMERCLUST_CLUST(Channel.from(["XY", "XO", "OO"]).combine(KMERCLUST_LOAD.out.rdata))
diff --git a/src/modules/mergekmer.nf b/src/modules/mergekmer.nf
index ed09d1c..02f3882 100644
--- a/src/modules/mergekmer.nf
+++ b/src/modules/mergekmer.nf
@@ -31,7 +31,7 @@ process COLLATEKMER {
container "lbmc/mergekmer:0.1.2"
input:
- tuple val(specie), path(csv)
+ tuple val(specie), path(male_csv), path(female_csv)
output:
tuple val(specie), path("*.csv"), emit: csv
@@ -40,7 +40,7 @@ process COLLATEKMER {
script:
def args = task.ext.args ?: ''
"""
- mergekmer --csv ${csv} --output ${specie}.csv --collate
+ mergekmer --csv ${male_csv} ${female_csv} --output ${specie}.csv --collate
cat <<-END_VERSIONS > versions.yml
--
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