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gene-fusions-nf
A nextflow pipeline to call somatic rna fusions from RNA-seq data using arriba
Dependencies
- Nextflow : for common installation procedures see the IARC-nf repository.
- arriba
A conda receipe, and docker and singularity containers are available with all the tools needed to run the pipeline (see "Usage")
Input
| Type | Description |
|---|
| reads | Path to input data |
| bams | Path to folder containing BAM files for processing |
Parameters
| Name | Example value | Description |
|---|
| ref_fa | ref.fa | Path to fasta reference |
| ref_gtf | annot.gtf | Path to GTF annotation |
| star_index | index/ | Path to STAR-Index reference |
| Name | Default value | Description |
|---|
| reads_csv | NULL | file with tabular data for each sample to process |
| svs | NULL | file with tabular data for each sample with structural variants in bedpe format |
Flags are special parameters without value.
| Name | Description |
|---|
| --arriba_plot | by default plot all the gene fusions detected by arriba. set to false to deactivate |
| --help | Display help |
Usage
nextflow run iarc/nf-gene-fusions -r v1.1 -profile singularity --reads 'test_dataset/reads/*.R{1,2}.fastq.gz' --ref_fa test_dataset/genome.fa --ref_gtf test_dataset/genome.gtf
or
nextflow run iarc/nf-gene-fusions -r v1.1 -profile singularity --bams '/path/to/bams/' --ref_fa test_dataset/genome.fa --ref_gtf test_dataset/genome.gtf
To run the pipeline without singularity just remove "-profile singularity". Alternatively, one can run the pipeline using a docker container (-profile docker) the conda receipe containing all required dependencies (-profile conda).
Output
| Type | Description |
|---|
| outdir | Folder with fusion genes file |
<!--- ## Detailed description (optional section) --->
Contributions
| Name | Email | Description |
|---|
| Alex Di Genova | | Developer |
References
Sebastian Uhrig, Julia Ellermann, Tatjana Walther, Pauline Burkhardt, Martina Fröhlich, Barbara Hutter, Umut H. Toprak, Olaf Neumann, Albrecht Stenzinger, Claudia Scholl, Stefan Fröhling and Benedikt Brors: Accurate and efficient detection of gene fusions from RNA sequencing data. Genome Research. March 2021 31: 448-460; Published in Advance January 13, 2021. doi: 10.1101/gr.257246.119