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feat: Replace hard-coded singularity with profile-based containers

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This commit is contained in:
Thomas A. Christensen II 2023-09-25 18:16:50 -05:00
parent 7f43f0282f
commit 96471746b9
Signed by: millironx
GPG key ID: 09335146883990B9
1 changed files with 59 additions and 1 deletions
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60
nextflow.config
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@ -61,7 +61,65 @@ try {
System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
}
singularity.enabled = true
profiles {
docker {
docker.enabled = true
docker.userEmulation = true
conda.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
conda.enabled = false
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
podman {
podman.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
shifter {
shifter.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
charliecloud {
charliecloud.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
apptainer.enabled = false
}
apptainer {
apptainer.enabled = true
apptainer.autoMounts = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
}
env {
R_PROFILE_USER = "/.Rprofile"