Building Ref

[ZWael]

Description of the bug

Hello, nf-core team It is more a how to question

i was using nf-core for some fusion analysis like this,

1. creating conda env for nf-core

conda create --name nf-core python=3.7 nf-core nextflow

2. downloading the pipeline

conda activate nf-core
nf-core download rnafusion

so i have now a directory nf-core-rnafusion-2.1.0/workflow with main.nf file

2. building ref (the singularity module is loaded)

nextflow run nf-core-rnafusion-2.1.0/workflow \
--build_references --all\
--outdir outdir \
--genomes_base  genomes_base \
--cosmic_username xxx@xxx --cosmic_passwd xxxxx
-profile singularity

in this step a genome_base folder is created with ensembl, fusion_report_db, fusioncatcher, pizzy, star, and starfusion subfolders as noticed no arriba subfolder is created so running the pipeline i have an error with the arriba step mount source /usr/local/var/lib/arriba doesn't exist and in the Input/output options i have this

arriba_ref : /usr/local/var/lib/arriba arriba_ref_blacklist : /usr/local/var/lib/arriba/blacklist_hg38_GRCh38_v2.3.0.tsv.gz arriba_ref_protein_domain : /usr/local/var/lib/arriba/protein_domains_hg38_GRCh38_v2.3.0.gff3

how to fix the arriba buiding ref step ?

Command used and terminal output

No response

Relevant files

No response

System information

No response

[BarryDigby]

https://github.com/nf-core/rnafusion/blob/6ffe30435b611339999145e4b71ac59158cf1182/nextflow.config#L64

[rannick]

The next release is going to contain arriba references again. In the meantime, you can follow these steps:

• Download arriba tar.gz file from https://github.com/suhrig/arriba/releases/latest
• Extract
• Start rnafusion pipeline with:

nextflow run nf-core/rnafusion \
  --<arriba> (--<tool2> ... OR --all) \
  --input <SAMPLE_SHEET.CSV> \
  --genomes_base <PATH/TO/REFERENCES> \
  --outdir <OUTPUT/PATH> \
  --arriba_ref_blacklist <PATH/TO/ARRIBA/BLACKLIST/FILE> \
  --arriba_protein_domain <PATH/TO/ARRIBA/PROTEIN/DOMAIN/FILE> \
  --arriba_ref <PATH/TO/ARRIBA/REFERENCES/FOLDER>

[YeHW]

The next release is going to contain arriba references again. In the meantime, you can follow these steps:

• Download arriba tar.gz file from https://github.com/suhrig/arriba/releases/latest
• Extract
• Start rnafusion pipeline with:

nextflow run nf-core/rnafusion \
  --<arriba> (--<tool2> ... OR --all) \
  --input <SAMPLE_SHEET.CSV> \
  --genomes_base <PATH/TO/REFERENCES> \
  --outdir <OUTPUT/PATH> \
  --arriba_ref_blacklist <PATH/TO/ARRIBA/BLACKLIST/FILE> \
  --arriba_protein_domain <PATH/TO/ARRIBA/PROTEIN/DOMAIN/FILE> \
  --arriba_ref <PATH/TO/ARRIBA/REFERENCES/FOLDER>

--arriba_ref_protein_domain instead of --arriba_protein_domain