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Patch: Azure compatible docker.userEmulation replacement #26

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merged 8 commits into from
Nov 5, 2024
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Patch comes from the PR

Summary of change

The setting in the docker profile docker.userEmulation was removed from Nextflow in this PR 4596.

Following this issue I had implemented this at the process level as in this PR

process.containerOptions = '-u $(id -u):$(id -g)'

This caused problems when running on Azure but not locally, and was missed in tests.

However the correct solution, as seen in the nf-core template, here is to put it in the docker profile as via docker.runOptions = '-u $(id -u):$(id -g)'
e.g,

docker {
        docker.enabled         = true
        conda.enabled          = false
        singularity.enabled    = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
        apptainer.enabled      = false
        docker.runOptions      = '-u $(id -u):$(id -g)'
    }

@sgsutcliffe sgsutcliffe merged commit ef4a918 into main Nov 5, 2024
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