.. _`rna-fusion-nfcore (⚠ Foreign importation)`:

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


.. role:: bash(code)
  :language: bash

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):

.. list-table::
  :widths: 10 80
  :header-rows: 1
  :align: left

  * - Case
    - Command line
  * - nextflow
    - .. code-block:: bash 

        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:

.. list-table::
  :widths: 10 80
  :header-rows: 1
  :align: left

  * - Case
    - Command line
  * - singularity
    - .. code-block:: bash 

        module load singularity
  * - nextflow_venv
    - .. code-block:: bash 

        export NXF_TEMP=./tmp

        export NXF_OPTS='-Xms100m -Xmx200m'
  * - single_end_design
    - .. code-block:: bash 

        export SINGLE_END="--singleEnd"
  * - paired_end_design
    - .. code-block:: bash 

        export SINGLE_END=""



Execution
---------

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

.. list-table::
  :widths: 10 80
  :header-rows: 1
  :align: left

  * - Case
    - Command line(s)
  * - cigogne_mode
    - .. code-block:: bash 

        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
    - .. code-block:: bash 

        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