Permission Denied Issue with Network-Mounted FASTQ Files in Nextflow

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I found a workaround!

Originally, my process was using a Docker container labeled wf_common. Below is an excerpt from my nextflow.config:

wf {
    common_sha = "sha338caea0a2532dc0ea8f46638ccc322bb8f9af48"
}

process {
    withLabel:wf_common {
        container = "ontresearch/wf-common:${params.wf.common_sha}"
    }
}

To resolve the issue, I changed the label to point to a custom Conda environment that I created, rather than using a Docker container. This change solved the problem. I got the idea after reading this issue on the Nextflow GitHub.

I’m not entirely sure why this fixed the problem, especially considering that the issue occurred with the mounted directory but not with my home directory. If anyone has a good explanation, I’d love to hear more insights on this!

Hopefully, this saves someone else some time :slight_smile: