# nf-core/rnafusion references

This document contains a POC of the S3 structure for the rnafusion references

Words in `<>` should be replaced by a corresponding value:
e.g. <gencode_version> could be `46`

<details>
<summary><b><organism>_v<gencode_version>/</b></summary>
This directory contains the root of all references that are built with the specified gencode annotation for a specific organism.
<details>
<summary><b>gencode/</b></summary>
This directory contains some common reference files used in the pipeline
<details>
<summary><b><organism>_<genome>_<gencode_version>_dna_primary_assembly.fa</b></summary>
The FASTA reference file
</details>
<details>
<summary><b><organism>_<genome>_<gencode_version>_dna_primary_assembly.fa.fai</b></summary>
The FASTA reference file index
</details>
<details>
<summary><b><organism>_<genome>_<gencode_version>.gtf</b></summary>
The gene annotation file
</details>
<details>
<summary><b><organism>_<genome>_<gencode_version>.gtf_refflat</b></summary>
The refflat file
</details>
<details>
<summary><b><organism>_<genome>_<gencode_version>.interval_list</b></summary>
The interval list file
</details>
</details>
<details>
<summary><b>arriba/</b></summary>
This directory contains the files needed to run Arriba
<details>
<summary><b>blacklist_<genome>_<arriba_version>.tsv.gz</b></summary>
A file containing blacklists for Arriba
</details>
<details>
<summary><b>cytobands_<genome>_<arriba_version>.tsv</b></summary>
A file containing cytobands for Arriba
</details>
<details>
<summary><b>known_fusions_<genome>_<arriba_version>.tsv.gz</b></summary>
A file containing known fusions for Arriba
</details>
<details>
<summary><b>protein_domains<genome>_<arriba_version>.gff3</b></summary>
A file containing protein domains for Arriba
</details>
</details>
<details>
<summary><b>fusioncatcher/</b></summary>
This directory contains the files needed to run Fusioncatcher
<details>
<summary><b><organism>_v<gencode_version>/</b></summary>
A directory with all fusioncatcher references
</details>
</details>
<details>
<summary><b>hgnc/</b></summary>
This directory contains HGNC files
<details>
<summary><b>hgnc_complete_set.txt</b></summary>
The HGNC complete set
</details>
<details>
<summary><b>HGNC-DB-timestamp.txt</b></summary>
The HGNC DB timestamp
</details>
</details>
<details>
<summary><b>salmon/</b></summary>
This directory contains the files needed to run Salmon
<details>
<summary><b>salmon/</b></summary>
A directory with all Salmon references
</details>
</details>
<details>
<summary><b>starfusion/</b></summary>
This directory contains the files needed to run StarFusion
<details>
<summary><b>ctat_genome_lib_build_dir/</b></summary>
A directory with all StarFusion references
</details>
</details>
<details>
<summary><b>star/</b></summary>
This directory contains the files needed to run Star
</details>
<details>
<summary><b>fusion_report_db/</b></summary>
This directory contains the files needed to run FusionReport
</details>
</details>