Ensembl version is not supported by squid and fusion catcher doesn't update its directory name /fusioncatcher/human_v*ensembl*

[ZheFrench]

Description of the bug

I'm trying to run rnafusion and I wanted to change the ensembl reference version for the --build_references .
I clone the nf-core/rnafusion
I changed nextflow.config for all stuffs relative to ensembl. Actual version setting for ensembl is 102, and I want to use the 109. I also tried by passing as parameter --ensembl_version 109.
Finaly I get "Ensembl version is not supported by squid".

Command used and terminal output

nextflow clone nf-core/rnafusion 

nextflow run rnafusion  -profile test  --build_references --ensembl_version 109 --all --cosmic_username XXX --cosmic_passwd XXX --genomes_base /data/ --outdir /pathTo/fusion -stub

Relevant files

nextflow.log.gz

System information

N E X T F L O W ~ version 23.10.0
nf-core/rnafusion 2.4.0
Ubuntu 18.04
Hardware HPC without job scheduler
local
Singularity

[ZheFrench]

Just notice that in the version 2.3 ChangeLog

Exit with error when using squid in combination with any ensembl version different from 102

Could you explain why ?

Finally it works when I bypass Squid :

nextflow run rnafusion -profile singularity --build_references --arriba --pizzly --fusioncatcher --starindex --starfusion --stringtie --fusionreport --cosmic_username XXX --cosmic_passwd XXX --genomes_base /data/fusion --outdir /data/fusion

[ZheFrench]

Try to bypass squid and finally end up removing parameters --all. Seems to work for test profile but not for singularity profile.

nextflow run rnafusion -profile test --build_references --cosmic_username XXX --cosmic_passwd XXX --genomes_base /data/ --outdir /data2/villemin/Myelome/fusion -stub

nextflow run rnafusion -profile singularity --build_references --cosmic_username XXX --cosmic_passwd XXX --genomes_base /data/ --outdir /data2/villemin/Myelome/fusion -stub

Pulling Singularity image https://depot.galaxyproject.org/singularity/gnu-wget:1.18--h5bf99c6_5 [cache /data2/USERS/villemin/Myelome/fusion/work/singularity/depot.galaxyproject.org-singularity-gnu-wget-1.18--h5bf99c6_5.img]
WARN: There's no process matching config selector: REFORMAT
WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /data2/USERS/villemin/Myelome/fusion/work/singularity -- Use the environment variable NXF_SINGULARITY_CACHEDIR to specify a different location
ERROR ~ Error executing process > 'NFCORE_RNAFUSION:BUILD_REFERENCES:ENSEMBL_DOWNLOAD'

Caused by:
  Failed to pull singularity image
  command: singularity pull  --name depot.galaxyproject.org-singularity-gnu-wget-1.18--h5bf99c6_5.img.pulling.1697717276738 https://depot.galaxyproject.org/singularity/gnu-wget:1.18--h5bf99c6_5 > /dev/null
  status : 255
  message:
    ERROR: pull is only supported for shub URIs



 -- Check '.nextflow.log' file for details

UPDATE : Due to the fact that singularity was very old 2.4, it was not working. After an update to 3.8.6, it works now. I let it here because it could help others.

[rannick]

Indeed, as you noticed, other ensembl versions are not compatible with squid and --all includes squid. Squid will be removed from future version so I will not improve documentation on this. Can be closed with the next release

[ZheFrench]

I found a similar bug with fusioncatcher which will create a directory called human_v102 even if you change fusioncatcher_ref in netflow.config to human_v109
fusioncatcher_ref = "${params.genomes_base}/fusioncatcher/human_v109"

build_references will works but then it complains when you try to execute the pipeline to detect fusion.

[rannick]

Unfortunatly, the references for fusioncatcher only exist for ensembl 102: https://sourceforge.net/projects/fusioncatcher/files/data/
This is why human_v102 is created. That will not be influenced by the ensembl_version parameter