From e7e81d53b41e34b12679e3b3f3a00d3162a58d31 Mon Sep 17 00:00:00 2001
From: aliarifki <aliarifki@outlook.fr>
Date: Fri, 26 May 2023 10:57:51 +0200
Subject: [PATCH] =?UTF-8?q?Mise=20=C3=A0=20jour=20des=20scripts=20R?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
---
.../{HBV_RNAs_count_2.R => HBV_RNAs_count.R} | 6 ++---
...anoSplicer_2.R => Junctions_NanoSplicer.R} | 6 ++---
...ions_individuals_2.R => Start_positions.R} | 6 ++---
src/nf_modules/junction_nanosplicer/main.nf | 4 +--
src/nf_modules/rna_count/main.nf | 25 +++++++++++++++++++
src/nf_modules/start_positions/main.nf | 4 +--
6 files changed, 38 insertions(+), 13 deletions(-)
rename src/.docker_modules/r-scripts/1.0/{HBV_RNAs_count_2.R => HBV_RNAs_count.R} (98%)
rename src/.docker_modules/r-scripts/1.0/{Junctions_NanoSplicer_2.R => Junctions_NanoSplicer.R} (99%)
rename src/.docker_modules/r-scripts/1.0/{start_positions_individuals_2.R => Start_positions.R} (98%)
diff --git a/src/.docker_modules/r-scripts/1.0/HBV_RNAs_count_2.R b/src/.docker_modules/r-scripts/1.0/HBV_RNAs_count.R
similarity index 98%
rename from src/.docker_modules/r-scripts/1.0/HBV_RNAs_count_2.R
rename to src/.docker_modules/r-scripts/1.0/HBV_RNAs_count.R
index 0010d51..ea15c73 100755
--- a/src/.docker_modules/r-scripts/1.0/HBV_RNAs_count_2.R
+++ b/src/.docker_modules/r-scripts/1.0/HBV_RNAs_count.R
@@ -1,5 +1,5 @@
#!/bin/Rscript
-# Packages installation
+# Packages loading
library(ggplot2, quietly = TRUE)
library(tidyr, quietly = TRUE)
library(plyr, quietly = TRUE)
@@ -60,7 +60,7 @@ palette_complete <- rbind.data.frame(palette_TSS,
stringsAsFactors = FALSE)
# Load Start_positions_count files:
-identified_SP <- read.table(file = opt$SPvariants[1],
+identified_SP <- read.table(file = opt$SPvariants,
header = TRUE)
clean_SP <- identified_SP[!duplicated(identified_SP$id),] %>%
@@ -108,7 +108,7 @@ ggsave(file = "SP_proportion.png",
dpi = 300)
# TSS not spliced:
-classified_reads <- read.table(file = opt$classification[1],
+classified_reads <- read.table(file = opt$classification,
header = TRUE)
not_spliced <- classified_reads[!(classified_reads$read_ID %in% clean_SP$id),]
diff --git a/src/.docker_modules/r-scripts/1.0/Junctions_NanoSplicer_2.R b/src/.docker_modules/r-scripts/1.0/Junctions_NanoSplicer.R
similarity index 99%
rename from src/.docker_modules/r-scripts/1.0/Junctions_NanoSplicer_2.R
rename to src/.docker_modules/r-scripts/1.0/Junctions_NanoSplicer.R
index 720226d..bce3845 100644
--- a/src/.docker_modules/r-scripts/1.0/Junctions_NanoSplicer_2.R
+++ b/src/.docker_modules/r-scripts/1.0/Junctions_NanoSplicer.R
@@ -12,19 +12,19 @@ library(optparse)
# Load classification per promoter:
option_list = list(
- make_option(c("-c", "--classification"), type="character", default=NULL,
+ make_option(c("-c", "--classification"), type="character", default="./classification.txt",
help="input classification or reads file (.txt)", metavar="character"),
make_option(c("-j", "--jwr"), type="character", default=NULL,
help="input nanosplicer results table (.csv)", metavar="character"))
opt_parser = OptionParser(option_list=option_list)
opt = parse_args(opt_parser)
-reads_pos <- read.table(opt$classification[1],
+reads_pos <- read.table(opt$classification,
sep = "\t")
colnames(reads_pos) <- c("id", reads_pos[1,2:length(reads_pos[1,])])
reads_pos <- reads_pos[2:length(reads_pos$id),]
# Load Nanosplicer results:
-df <- read.csv(opt$jwr[1])
+df <- read.csv(opt$jwr)
colnames(df)[1] <- "juncNumber"
# split donor and acceptor positions:
diff --git a/src/.docker_modules/r-scripts/1.0/start_positions_individuals_2.R b/src/.docker_modules/r-scripts/1.0/Start_positions.R
similarity index 98%
rename from src/.docker_modules/r-scripts/1.0/start_positions_individuals_2.R
rename to src/.docker_modules/r-scripts/1.0/Start_positions.R
index 31b4e61..683336e 100755
--- a/src/.docker_modules/r-scripts/1.0/start_positions_individuals_2.R
+++ b/src/.docker_modules/r-scripts/1.0/Start_positions.R
@@ -1,5 +1,5 @@
#!/bin/Rscript
-# Packages installation
+# Packages loading
library(dplyr)
library(ggplot2)
library(RColorBrewer)
@@ -25,8 +25,8 @@ opt = parse_args(opt_parser)
# pattern="*.txt",
# all.files=FALSE,
# full.names=FALSE)
-file_to_load <- opt$input[1]
-splitted <- strsplit(opt$input[1], split = "[/]")[[1]]
+file_to_load <- opt$input
+splitted <- strsplit(opt$input, split = "[/]")[[1]]
filename <- strsplit(splitted[length(splitted)], split = "[.]")[[1]][1]
sam_bc01 <- read.table(file_to_load, header = F)
diff --git a/src/nf_modules/junction_nanosplicer/main.nf b/src/nf_modules/junction_nanosplicer/main.nf
index 8598562..4af81e2 100644
--- a/src/nf_modules/junction_nanosplicer/main.nf
+++ b/src/nf_modules/junction_nanosplicer/main.nf
@@ -11,8 +11,8 @@ process junctions_nanosplicer{
}
input:
+ path(txt)
path(csv)
- path(classification_of_reads_per_RNA)
output:
path("Rplots.pdf")
@@ -21,6 +21,6 @@ process junctions_nanosplicer{
script:
"""
- Rscript /Junctions_NanoSplicer/Junctions_NanoSplicer_2.R
+ Rscript Junctions_NanoSplicer.R -c txt -j csv
"""
}
\ No newline at end of file
diff --git a/src/nf_modules/rna_count/main.nf b/src/nf_modules/rna_count/main.nf
index e69de29..5899f2e 100644
--- a/src/nf_modules/rna_count/main.nf
+++ b/src/nf_modules/rna_count/main.nf
@@ -0,0 +1,25 @@
+version = "1.0"
+container_url = "xgrand/r-scripts:${version}"
+
+params.rna_count_out = ""
+process rna_count{
+ container = "${container_url}"
+ label "small_mem_mono_cpus"
+ tag "RNA quantification"
+ if (params.rna_count_out != "") {
+ publishDir "results/${params.rna_count_out}", mode: 'copy'
+ }
+
+ input:
+ path(spvariants)
+ path(classification)
+
+ output:
+ path("*.csv")
+ path("*.pdf")
+
+ script:
+ """
+ Rscript HBV_RNAs_count.R -s spvariants -c classification
+ """
+}
diff --git a/src/nf_modules/start_positions/main.nf b/src/nf_modules/start_positions/main.nf
index 06e2e4f..4a29e9f 100644
--- a/src/nf_modules/start_positions/main.nf
+++ b/src/nf_modules/start_positions/main.nf
@@ -5,7 +5,7 @@ params.start_position_counts_out = ""
process start_position_individuals{
container = "${container_url}"
label "small_mem_mono_cpus"
- tag "identification de variants d'épissage"
+ tag "start positions"
if (params.start_position_counts_out != "") {
publishDir "results/${params.start_position_counts_out}", mode: 'copy'
}
@@ -20,6 +20,6 @@ process start_position_individuals{
script:
"""
- Rscript start_positions_individuals.R -i start_position_counts
+ Rscript start_positions.R -i start_position_counts
"""
}
\ No newline at end of file
--
GitLab