Maxime U Garcia

Can you try with that? [Samplesheet.csv](https://github.com/nf-core/rnavar/files/13230993/Samplesheet.csv) I'm not sure about the space in the sample id

> I'll try. I didn't realize there was space in my sample id. Thank you so much! there should be an error for that anyway, so thanks for finding out

Hi @bounlu, This pipeline is due for some refactoring. I'm updating the ENSEMBLVEP/SNPEFF modules and Subworkflows in Sarek. Once it's done, I'll refactor that part here as well.

@PBMCHUGA and you have the issue only with this process?

Hi all, I'm currently working on updating the pipeline with the the latest template sync, once this is done, I will work on adding extra features towards a release. Current...

can you share what's in your `cluster` profile or in your custom config file?

I can see that you have: ``` withName: 'SAMTOOLS.*' { container = '/data/projects/ptdom/pipelines/rnavar/sifs/samtools-1.15.1--h1170115_0.sif ' } ``` In your `conf/singularity.config`, so I think it should cover `SAMTOOL_FAIDX`, can you remove the...

ok, I honestly have no idea why this idea fixed your problem, but I think we can close this issue then, right?

I see. I think the proper way to deal with it, is indeed to use `singularity.cacheDir` or `NXF_SINGULARITY_CACHE_DIR`. Which should allow you not to set up such custom files to...

Hi @bounlu thanks for reporting that, this WARNING is a known bug, but the pipeline should run its course. https://github.com/nextflow-io/nextflow/issues/3560 We'll fix that in the coming release.