Hi! I'm new to this pipeline but it looks very promising. Thank you for developing it. I'm stuck at reference creation, though. With the following command:

nextflow run nf-core/rnafusion \
-revision dev \
-latest \
-profile docker \
--tools all \
--references_only \
--cosmic_username 'szymon.baluszek@***' --cosmic_passwd '***' \
--genomes_base '/mnt/data/szymon_rstudio_data/genomes' \
--outdir '/mnt/data/szymon_rstudio_data/genomes/refFusions' \
-work-dir '/mnt/data/szymon_rstudio_data/genomes'

I get: `You have selected

fusioncatcher

in

--tools

, but did not provide an existing path to the fusioncatcher reference files with

--fusioncatcher_ref

.` Also, the project that I'm working on is with Ensembl genome references (

gtf

influsive). How do I supply these into the reference build?

Hi did you download the references as specified in the documentation of the pipeline? My guess is that the correct files are missing from

--genomes_base

Thank you, Nicolas. This was exactly the case. Now I got an error in fusioncatcher that seems to be related to run time. I run:

nextflow run nf-core/rnafusion \
  --tools all \
  --input ~/CCA/CCAsamplesheet.csv \
  --genomes_base ~/genomes/refFusionsNULL/ \
  --outdir ~/CCA/fusionsBulk \
  -r dev -profile docker -c fusions.config

and despite specifying run time of 24h in the config I get this runtime error (8h limit):

Error executing process > 'RNAFUSION:FUSIONCATCHER_WORKFLOW:FUSIONCATCHER_FUSIONCATCHER (CC15)'

Caused by:
  Process exceeded running time limit (8h)


Command executed:

  fusioncatcher \
      --input=CC15_1.fastp.fastq.gz,CC15_2.fastp.fastq.gz \
      --output=. \
      --data=fusioncatcher \
      --threads=6 \
      --Xmx=29491M \
      --limitSjdbInsertNsj 2000000 --skip-blat 
  
  mv final-list_candidate-fusion-genes.txt CC15.fusion-genes.txt
  mv summary_candidate_fusions.txt CC15.summary.txt
  mv fusioncatcher.log CC15.log
  
  cat <<-END_VERSIONS > versions.yml
  "RNAFUSION:FUSIONCATCHER_WORKFLOW:FUSIONCATCHER_FUSIONCATCHER":
      fusioncatcher: "$(fusioncatcher --version 2>&1 | awk '{print $2}')"
  END_VERSIONS

Do you have any tips on how to deal with it?

The process is called

FUSIONCATCHER_FUSIONCATCHER

and not

FUSIONCATCHER

if you put the correct process in the config, then it should work

Thank you! I got a bit further. There is another error, now in fusionreport:

Caused by:
  Process `RNAFUSION:FUSIONREPORT_DETECT (CC10)` terminated with an error exit status (1)


Command executed:

  fusion_report run CC10 . fusion_report_db --arriba CC10.arriba.fusions.tsv --starfusion CC10.starfusion.fusion_predictions.tsv --fusioncatcher CC10.fusion-genes.txt  --allow-multiple-gene-symbols --tool-cutoff 1  --export csv
  
  mv fusion_list.tsv CC10.fusionreport.tsv
  mv fusion_list_filtered.tsv CC10.fusionreport_filtered.tsv
  mv index.html CC10_fusionreport_index.html
  [ ! -f fusions.csv ] || mv fusions.csv CC10.fusions.csv
  [ ! -f fusions.json ] || mv fusions.json CC10.fusions.json
  
  cat <<-END_VERSIONS > versions.yml
  "RNAFUSION:FUSIONREPORT_DETECT":
      fusion_report: $(fusion_report --version | sed 's/fusion-report //')
      fusion_report DB retrieval: $(cat fusion_report_db/DB-timestamp.txt)
  END_VERSIONS

Could you show me the full log of the process?