AccessDeniedException with docker + slurm on AWS

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Hi all,
I’m running the nf-core/rnaseq pipeline on AWS using -profile docker and running with a config specifying executor = 'slurm'.

I have had trouble with permission at various steps of the pipeline (mostly SALMON_QUANT & STAR_ALIGN ) and I’ve tried various different combinations of docker params in the config that I’m using.

The error I see now comes from NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN:

Caused by:
  /path/to/nf-work-dir/work/b3/48b4e8.../sampleID._STARpass1
java.nio.file.AccessDeniedException: /path/to/nf-work-dir/work/b3/48b4e8.../sampleID._STARpass1

The docker section of my config looks like this:

docker {
    docker.enabled    = true
    runOptions        = "--user root -v /var/run/docker.sock:/var/run/docker.sock"
    docker.mountFlags = 'shared'
}

I’ve seen a few other posts here and elsewhere that touch on this, but I haven’t managed to find a solution that works for me.

Would love any advice or suggestions on how we can get this running!

Thanks in advance,

Nick

2

Hi @Nick_Riddiford.

Can you share more detail about your AWS setup?

It’s not clear to me why you’d have permission issues with nf-core/rnaseq.