Test run does not work

[olkap]

Description of the bug

I run the rnafusion test analysis, and it gives the error: "No such file: /data/tmpnfs/nextflow_output/test_rnafusion/references/ensembl/Homo_sapiens.GRCh38.102.all.fa"

The test analyses for sarek and rnaseq work ok. Should I download some reference files before running an rnafusion test analysis?

Command used and terminal output

Command:
nextflow run nf-core/rnafusion -profile test,singularity --outdir /data/tmpnfs/nextflow_output/test_rnafusion

Output:
N E X T F L O W  ~  version 22.04.4
Pulling nf-core/rnafusion ...
 downloaded from https://github.com/nf-core/rnafusion.git
Launching `https://github.com/nf-core/rnafusion` [reverent_austin] DSL2 - revision: 6ffe30435b [master]


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        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/rnafusion v2.1.0
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Core Nextflow options
  revision                          : master
  runName                           : reverent_austin
  containerEngine                   : singularity
  launchDir                         : /data/tmpnfs/nextflow_running
  workDir                           : /data/tmpnfs/nextflow_running/work
  projectDir                        : /home/aleksandra/.nextflow/assets/nf-core/rnafusion
  userName                          : aleksandra
  profile                           : test,singularity
  configFiles                       : /home/aleksandra/.nextflow/assets/nf-core/rnafusion/nextflow.config

Input/output options
  input                             : https://raw.githubusercontent.com/nf-core/test-datasets/rnafusion/testdata/human/samplesheet_valid.csv
  outdir                            : /data/tmpnfs/nextflow_output/test_rnafusion
  genomes_base                      : /data/tmpnfs/nextflow_output/test_rnafusion/references
  ensembl_version                   : 102
  starfusion_build                  : true
  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
  ensembl_ref                       : /data/tmpnfs/nextflow_output/test_rnafusion/references/ensembl
  fusioncatcher_limitSjdbInsertNsj  : 2000000
  fusioncatcher_ref                 : /data/tmpnfs/nextflow_output/test_rnafusion/references/fusioncatcher/human_v102
  fusioninspector_limitSjdbInsertNsj: 1000000
  fusionreport_ref                  : /data/tmpnfs/nextflow_output/test_rnafusion/references/fusion_report_db
  pizzly_ref                        : /data/tmpnfs/nextflow_output/test_rnafusion/references/pizzly/kallisto
  squid_ref                         : /data/tmpnfs/nextflow_output/test_rnafusion/references/squid
  starfusion_ref                    : /data/tmpnfs/nextflow_output/test_rnafusion/references/starfusion/ctat_genome_lib_build_dir
  starindex_ref                     : /data/tmpnfs/nextflow_output/test_rnafusion/references/star

Reference genome options
  genome                            : GRCh38
  fasta                             : /data/tmpnfs/nextflow_output/test_rnafusion/references/ensembl/Homo_sapiens.GRCh38.102.all.fa
  gtf                               : /data/tmpnfs/nextflow_output/test_rnafusion/references/ensembl/Homo_sapiens.GRCh38.102.gtf
  chrgtf                            : /data/tmpnfs/nextflow_output/test_rnafusion/references/ensembl/Homo_sapiens.GRCh38.102.chr.gtf
  transcript                        : /data/tmpnfs/nextflow_output/test_rnafusion/references/ensembl/Homo_sapiens.GRCh38.102.cdna.all.fa.gz
  refflat                           : /data/tmpnfs/nextflow_output/test_rnafusion/references/ensembl/Homo_sapiens.GRCh38.102.chr.gtf.refflat

Institutional config options
  config_profile_name               : Test profile
  config_profile_description        : Minimal test dataset to check pipeline function

Max job request options
  max_cpus                          : 2
  max_memory                        : 6 GB
  max_time                          : 6h

!! Only displaying parameters that differ from the pipeline defaults !!
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If you use nf-core/rnafusion for your analysis please cite:

* The pipeline
  https://doi.org/10.5281/zenodo.151721952

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
  https://github.com/nf-core/rnafusion/blob/master/CITATIONS.md
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No such file: /data/tmpnfs/nextflow_output/test_rnafusion/references/ensembl/Homo_sapiens.GRCh38.102.all.fa

 -- Check script '/home/aleksandra/.nextflow/assets/nf-core/rnafusion/./workflows/rnafusion.nf' at line: 31 or see '.nextflow.log' file for more details

Relevant files

No response

System information

Nextflow version: 22.04.4 Hardware: HPC Executor: local Container engine: Singularity OS: (Ubuntu Linux) Version of nf-core/rnafusion (2.1.0)

[apeltzer]

See here - you need to build the references first: https://github.com/nf-core/rnafusion#build-references