From fba1fce0de316eefa5c127792f3fc50b1f78c54b Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 7 Jun 2023 16:04:50 +0200
Subject: [PATCH] add cpu args to kmerclust
---
src/bin/kmerclust.R | 21 +++++++++++++++++++++
src/kmerclust | 2 +-
src/modules/kmerclust.nf | 2 +-
3 files changed, 23 insertions(+), 2 deletions(-)
create mode 100644 src/bin/kmerclust.R
diff --git a/src/bin/kmerclust.R b/src/bin/kmerclust.R
new file mode 100644
index 0000000..31507a1
--- /dev/null
+++ b/src/bin/kmerclust.R
@@ -0,0 +1,21 @@
+library(kmerclust)
+library(ggplot2)
+
+args <- commandArgs(trailingOnly = TRUE)
+
+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(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/kmerclust b/src/kmerclust
index fa43261..bd49510 160000
--- a/src/kmerclust
+++ b/src/kmerclust
@@ -1 +1 @@
-Subproject commit fa432617ab1e7b8eea3c4d671ce9e8948653e6f6
+Subproject commit bd49510e4e4931796e2ed7811333479e74f52269
diff --git a/src/modules/kmerclust.nf b/src/modules/kmerclust.nf
index 8967ea7..3f652da 100644
--- a/src/modules/kmerclust.nf
+++ b/src/modules/kmerclust.nf
@@ -16,7 +16,7 @@ process KMERCLUST {
script:
def args = task.ext.args ?: ''
"""
- Rscript ../bin/kmerclust.R ${params.csv} ${csv} ${specie}
+ Rscript ../bin/kmerclust.R ${params.csv} ${csv} ${specie} ${task.cpus}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
--
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