A nextflow pipeline to call somatic rna fusions from RNA-seq data using arriba
- 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")
| Type |
Description |
| reads |
Path to input data |
| bams |
Path to folder containing BAM files for processing |
| 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 |
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
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).
| Type |
Description |
| outdir |
Folder with fusion genes file |
| Name |
Email |
Description |
| Alex Di Genova |
|
Developer |
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
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