test data failing about airrflow HOT 3 CLOSED

Hi, this issue has been fixed in the dev branch now and it will be included in the next release

from airrflow.

Hi @andreiprodan , thank you for opening the issue. We have investigated this with @ssnn-airr and it seems like this error occurs only when using the singularity container and not with the docker container. I am working on a more permanent fix, but as as a workaround, could you try whether running the same command but with the following configuration file works:

nextflow run nf-core/airrflow -r 3.1.0 <other parameters you are using> -c custom.config

with the custom.config file containing the following:

process{
  withName: DOWSER_LINEAGES {
    container = 'quay.io/biocontainers/r-enchantr:0.1.3--r42hdfd78af_0'
  }
}

This forces pulling the docker container which currently works and converting it to singularity at runtime. We are also working towards a fix for the singularity container itself.

Edit: please provide this container instead of the singularity_pull_docker_containers option.

from airrflow.

I'm seeing the same error, also running Slurm + Singularity.
Pulling the docker container doesn't seem help.
I'm not too familiar with airrflow yet, so still trying to narrow down the issue.

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