From 82e6907d1add1d5fd1761e3ae16ccd7da183f822 Mon Sep 17 00:00:00 2001
From: xgrand <xavier.grand@inserm.fr>
Date: Wed, 31 May 2023 15:14:26 +0200
Subject: [PATCH] Add deseq2-wrapper
---
.../deseq2-wrapper/1.0.0/Dockerfile | 17 +++++++
.../deseq2-wrapper/1.0.0/deseq2-wrapper.R | 5 ++
.../deseq2-wrapper/1.0.0/docker_init.sh | 5 ++
.../1.0.0/install_deseq2-wrapper.R | 4 ++
src/arriba_fusion.nf | 11 +++++
src/nf_modules/concatenate/main.nf | 48 +++++++++++++++++++
src/nf_modules/fusion_parser/main.nf | 1 +
7 files changed, 91 insertions(+)
create mode 100644 src/.docker_modules/deseq2-wrapper/1.0.0/Dockerfile
create mode 100755 src/.docker_modules/deseq2-wrapper/1.0.0/deseq2-wrapper.R
create mode 100755 src/.docker_modules/deseq2-wrapper/1.0.0/docker_init.sh
create mode 100644 src/.docker_modules/deseq2-wrapper/1.0.0/install_deseq2-wrapper.R
create mode 100755 src/nf_modules/concatenate/main.nf
diff --git a/src/.docker_modules/deseq2-wrapper/1.0.0/Dockerfile b/src/.docker_modules/deseq2-wrapper/1.0.0/Dockerfile
new file mode 100644
index 0000000..bf24a2d
--- /dev/null
+++ b/src/.docker_modules/deseq2-wrapper/1.0.0/Dockerfile
@@ -0,0 +1,17 @@
+FROM rocker/r-base:4.2.3
+
+LABEL MAINTAINER "Xavier Grand <xavier.grand@ens-lyon.fr>"
+
+RUN apt update && apt-get install -y apt-transport-https
+RUN apt install -y pandoc libfontconfig1-dev libcurl4-openssl-dev \
+ libssl-dev libssh2-1-dev libxml2-dev zlib1g-dev \
+ libharfbuzz-dev libfribidi-dev libfreetype6-dev \
+ libpng-dev libtiff5-dev libjpeg-dev && \
+ R -e "install.packages(c('devtools', 'testthat', 'roxygen2', 'BiocManager', 'plotly'))" && \
+ R -e "BiocManager::install('DESeq2')"
+
+COPY *.R .
+
+RUN Rscript install_deseq2-wrapper.R
+
+CMD [ "bash" ]
\ No newline at end of file
diff --git a/src/.docker_modules/deseq2-wrapper/1.0.0/deseq2-wrapper.R b/src/.docker_modules/deseq2-wrapper/1.0.0/deseq2-wrapper.R
new file mode 100755
index 0000000..62b9783
--- /dev/null
+++ b/src/.docker_modules/deseq2-wrapper/1.0.0/deseq2-wrapper.R
@@ -0,0 +1,5 @@
+# deseq2-wrapper.R
+
+#!/bin/Rscript
+library(DESeqwrapper)
+cli_run_deseq2()
diff --git a/src/.docker_modules/deseq2-wrapper/1.0.0/docker_init.sh b/src/.docker_modules/deseq2-wrapper/1.0.0/docker_init.sh
new file mode 100755
index 0000000..d581461
--- /dev/null
+++ b/src/.docker_modules/deseq2-wrapper/1.0.0/docker_init.sh
@@ -0,0 +1,5 @@
+#!/bin/sh
+# docker pull xgrand/deseq2-wrapper:1.0.0
+docker build src/.docker_modules/deseq2-wrapper/1.0.0 -t 'xgrand/deseq2-wrapper:1.0.0'
+docker push xgrand/deseq2-wrapper:1.0.0
+# docker buildx build --platform linux/amd64,linux/arm64 -t "xgrand/deseq2-wrapper:1.0.0" --push src/.docker_modules/deseq2-wrapper/1.0.0
\ No newline at end of file
diff --git a/src/.docker_modules/deseq2-wrapper/1.0.0/install_deseq2-wrapper.R b/src/.docker_modules/deseq2-wrapper/1.0.0/install_deseq2-wrapper.R
new file mode 100644
index 0000000..9db139e
--- /dev/null
+++ b/src/.docker_modules/deseq2-wrapper/1.0.0/install_deseq2-wrapper.R
@@ -0,0 +1,4 @@
+#!/usr/bin/env Rscript
+install.packages("devtools")
+library(devtools)
+install_gitlab("LBMC/regards/deseq2-wrapper", host = "https://gitbio.ens-lyon.fr", quiet = FALSE)
diff --git a/src/arriba_fusion.nf b/src/arriba_fusion.nf
index 0d5c7db..f183a87 100644
--- a/src/arriba_fusion.nf
+++ b/src/arriba_fusion.nf
@@ -31,6 +31,7 @@ def helpMessage() {
Input:
--fastq [path] Path to fastq folder.
--bam [path] Path to the bam folder (indexed and sorted).
+ --design [path] Path to the design file.
References: Can be downloaded with download_references.sh (not implemented in pipeline).
--genome [path] Path to genome reference fasta file.
@@ -83,6 +84,8 @@ params.star_mapping2fusion_out = "06_mapping2fusion"
params.filter_bam_quality_out = "07_Filtered_bam"
params.arriba_out = "10_Arriba_results"
params.draw_fusions_out = "11_drawn_fusions"
+params.concat_fusion_out = "12_concat_fusions"
+params.fusion_out = "13_DFG"
/*
****************************************************************
@@ -122,6 +125,10 @@ Channel
.fromPath( params.gtf )
.set { gtf_file }
+Channel
+ .fromPath( params.design )
+ .set { design }
+
if(params.bam) {
Channel
.fromPath( bam_list )
@@ -162,6 +169,8 @@ include { index_bam } from './nf_modules/samtools/main.nf'
include { htseq_count } from './nf_modules/htseq/main.nf' addParams(htseq_out: '09_htseq_count', htseq_param: "${params.htseq_param}" )
include { arriba } from "./nf_modules/arriba/main.nf"
include { draw_fusions } from "./nf_modules/arriba/main.nf"
+include { concat_fusion } from "./nf_modules/concatenate/main.nf"
+include { parsefusion } from "./nf_modules/fusion_parser/main.nf"
/*
****************************************************************
@@ -232,4 +241,6 @@ workflow {
****************************************************************
*/
+ concat_fusion(arriba.out.fusions, arriba.out.discarded)
+ parsefusion(concat_fusion.out.concatenated_fusions)
}
\ No newline at end of file
diff --git a/src/nf_modules/concatenate/main.nf b/src/nf_modules/concatenate/main.nf
new file mode 100755
index 0000000..c67cf8a
--- /dev/null
+++ b/src/nf_modules/concatenate/main.nf
@@ -0,0 +1,48 @@
+version = "3.15.4"
+container_url = "xgrand/alpine:${version}"
+
+
+params.fastq_out = ""
+process concatenate {
+ tag "fastq_folder"
+ label "big_mem_mono_cpus"
+
+ if (params.fastq_out != "") {
+ publishDir "results/${params.fastq_out}", mode: 'copy'
+ }
+
+ input:
+ path fastq
+
+ output:
+ path "merged.fastq.gz", emit: merged_fastq
+
+ script:
+"""
+zcat ${fastq}/*.fastq.gz > merged.fastq
+gzip --quiet merged.fastq
+"""
+}
+
+params.concat_fusion_out = ""
+process concat_fusion {
+ tag "concat_fusion"
+ label "big_mem_mono_cpus"
+
+ if (params.fastq_out != "") {
+ publishDir "results/${concat_fusion_out}", mode: 'copy'
+ }
+
+ input:
+ path fusions
+ path discarded_fusions
+
+ output:
+ path "*_fusions.tsv", emit: concatenated_fusions
+
+ script:
+"""
+cat ${fusions} > res_fusions.tsv
+tail +2 ${discarded_fusions} >> res_fusions.tsv
+"""
+}
\ No newline at end of file
diff --git a/src/nf_modules/fusion_parser/main.nf b/src/nf_modules/fusion_parser/main.nf
index ceac664..6023c3d 100644
--- a/src/nf_modules/fusion_parser/main.nf
+++ b/src/nf_modules/fusion_parser/main.nf
@@ -1,6 +1,7 @@
version = "1.0"
container_url = "xgrand/fusion_parser:${version}"
+params.fusion_out = ""
process parsefusion{
container = "${container_url}"
label "big_mem_multi_cpus"
--
GitLab