From 086a8767be7831b393c6a79a46e0bde48f29779e Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 9 Jun 2023 09:56:53 +0200
Subject: [PATCH] split plot from the analysis
---
src/bin/kmerclust.R | 11 ++---------
src/main.nf | 6 ++++--
src/modules/kmerclust.nf | 27 ++++++++++++++++++++++++++-
3 files changed, 32 insertions(+), 12 deletions(-)
diff --git a/src/bin/kmerclust.R b/src/bin/kmerclust.R
index 786f1dd..582d80d 100644
--- a/src/bin/kmerclust.R
+++ b/src/bin/kmerclust.R
@@ -8,15 +8,8 @@ data <- readr::read_tsv(args[2], show_col_types = FALSE)
format(object.size(data), units = "Mb")
annotation <- parse_annotation(args[1])
count <- annotate_counts(annotation, data, args[3])
-save(count, file = paste0(args[3], ".Rdata"))
res <- compare_models(count %>% dplyr::ungroup(), nboot = 100, bootsize = 0.1, core = as.numeric(args[4]))
+
+save(count, file = paste0(args[3], ".Rdata"))
save(res, file = paste0(args[3], "_boot.Rdata"))
-res %>%
- ggplot(aes(x = name, y = BIC)) +
- geom_violin()
-ggsave(paste0(args[3], "_BIC.pdf"))
-res %>%
- ggplot(aes(x = name, y = WSS_f / BSS)) +
- geom_violin()
-ggsave(paste0(args[3], "_WSS_BSS.pdf"))
diff --git a/src/main.nf b/src/main.nf
index bbafd2e..d747c7a 100644
--- a/src/main.nf
+++ b/src/main.nf
@@ -8,8 +8,9 @@ params.kmer_size = 12
include { SPLIT } from "./modules/split"
include { FASTKMERS } from "./modules/fastkmers"
include { MERGEKMER } from "./modules/mergekmer"
-include { COLLATEKMER} from "./modules/mergekmer"
-include { KMERCLUST} from "./modules/kmerclust"
+include { COLLATEKMER } from "./modules/mergekmer"
+include { KMERCLUST } from "./modules/kmerclust"
+include { KMERCLUST_PLOT } from "./modules/kmerclust"
Channel.fromPath( file(params.csv) )
@@ -30,4 +31,5 @@ workflow {
MERGEKMER(FASTKMERS.out.csv.groupTuple())
COLLATEKMER(MERGEKMER.out.csv.map{it -> [it[0].specie, it[1]] }.groupTuple())
KMERCLUST(COLLATEKMER.out.csv, params_csv.collect())
+ KMERCLUST_PLOT(KMERCLUST.out.rdata)
}
diff --git a/src/modules/kmerclust.nf b/src/modules/kmerclust.nf
index 31e0fa5..7a7090f 100644
--- a/src/modules/kmerclust.nf
+++ b/src/modules/kmerclust.nf
@@ -10,7 +10,6 @@ process KMERCLUST {
path params_csv
output:
- tuple val(specie), path("*.pdf"), emit: pdf
tuple val(specie), path("*.Rdata"), emit: rdata
path "versions.yml" , emit: versions
@@ -25,3 +24,29 @@ process KMERCLUST {
END_VERSIONS
"""
}
+
+process KMERCLUST_PLOT {
+ tag "$specie"
+ label 'big_mem_mono_cpus'
+
+ container "lbmc/kmerclust:0.0.2"
+ publishDir "results/${params.kmer_size}/${specie}/", mode: 'copy'
+
+ input:
+ tuple val(specie), path(rdata)
+
+ output:
+ tuple val(specie), path("*.pdf"), emit: pdf
+ path "versions.yml" , emit: versions
+
+ script:
+ def args = task.ext.args ?: ''
+ """
+ Rscript ${projectDir}/bin/kmerclust_plot.R ${specie}
+
+ cat <<-END_VERSIONS > versions.yml
+ "${task.process}":
+ Rkmerclust: 0.0.1
+ END_VERSIONS
+ """
+}
--
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