RNA-FUSION-NFCORE (⚠ FOREIGN IMPORTATION)

Version: nf-core/rnafusion:1.0 Tags: rna-seq / rnaseq / rna / fusion / nf-core / nfcore / rnafusion / nextflow

Metacaller for detection of gene-fusions in RNA-seq data developped by nf-core community (https://nf-co.re/) that has been set up for Gustave Roussy clusters.

This pipeline uses following tools:

• [STAR-Fusion](https://github.com/STAR-Fusion/STAR-Fusion/wiki)

• [FusionCatcher](https://github.com/ndaniel/fusioncatcher/blob/master/doc/manual.md)

• [EricScript](https://sites.google.com/site/bioericscript/getting-started)

• [Pizzly](https://github.com/pmelsted/pizzly)

• [Squid](https://github.com/Kingsford-Group/squid)

• [FusionInspector](https://github.com/FusionInspector/FusionInspector/wiki)

More informations at:

• https://github.com/nf-core/rnafusion/tree/1.0

• https://github.com/gustaveroussy/rnafusion/releases

Pipeline dependencies

This pipeline requires the following packages to be run. Any other additional requirements are being installed dynamically.

Conda:

• bioconda::nextflow ==19.07.0

• git ==2.20.1

Additionally, the following prerequisites are non-optional:

• Conda

• Singularity

• References for each tool (Genome sequence and annotations)

Input files

Please find below the list of required input files:

• Fastq files (paired-end or single-end) from one sample

Output files

Please find below the list of expected output files:

• FastQC - read quality control

• MultiQC - aggregate report, describing results of the whole pipeline

• Summary report in html format containing the list of all detected fusions

• List of gene-fusions identified by each tool (STAR-Fusion, FusionCatcher, EricScript, Pizzly and Squid)

Installation

While installing the workflow, you may run the following commands (order matters):

Case	Command line
nextflow	conda env create --force --file "${STRONGR_DIR:?}/workflows/fusion/rna-fusion-nfcore/environment.yaml" conda activate rna-fusion-nfcore

Preparation

In order to prepare a run, you may try the following commands:

Case	Command line
singularity	module load singularity
nextflow_venv	export NXF_TEMP=./tmp export NXF_OPTS='-Xms100m -Xmx200m'
single_end_design	export SINGLE_END="--singleEnd"
paired_end_design	export SINGLE_END=""

Execution

In order to execute the pipeline, you may run the following commands:

Case	Command line(s)
cigogne_mode	nextflow run -r v1.0.cigogne.190913 gustaveroussy/rnafusion --reads ${FASTQ_DIR:?}/${SAMPLE:?}*{1,2}.fastq.gz --read_length ${READ_LENGTH:?} $SINGLE_END --outdir ${OUT_DIR:?}/${SAMPLE:?}/results --genome GRCh37 --tool_cutoff 2 -profile singularity --star_fusion --fusioncatcher --ericscript --pizzly --squid --fusion_inspector -with-report -with-trace -with-timeline -with-dag
flamingo_mode	nextflow run -r v1.0.flamingo.191011 gustaveroussy/rnafusion --reads ${FASTQ_DIR:?}/${SAMPLE:?}*{1,2}.fastq.gz --read_length ${READ_LENGTH:?} $SINGLE_END --outdir ${OUT_DIR:?}/${SAMPLE:?}/results --genome GRCh37 --tool_cutoff 2 -profile singularity --star_fusion --fusioncatcher --ericscript --pizzly --squid --fusion_inspector -with-report -with-trace -with-timeline -with-dag