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apptainer to execute nextflow #33

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ms-bacino opened this issue Mar 5, 2024 · 0 comments
Open

apptainer to execute nextflow #33

ms-bacino opened this issue Mar 5, 2024 · 0 comments

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@ms-bacino
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ms-bacino commented Mar 5, 2024

I am trying to run epi2me on an HPC but keep running into nextflow trying to run through docker instead of apptainer. I added apptainer to the profile list (see below) but it will not run
profiles {
// the "standard" profile is used implicitly by nextflow
// if no other profile is given on the CLI
standard {
docker {
enabled = true
// this ensures the container is run as the host user and group, but
// also adds the host user to the within-container group
runOptions = "--user $(id -u):$(id -g) --group-add 100"
}
}

// using singularity instead of docker
singularity {
singularity {
enabled = true
autoMounts = true
}
}

// using Apptainer instead of Docker
apptainer {
apptainer {
enabled = true
autoMounts = true
container = "/path to /nextflow_latest.sif"
}
}

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