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Make container/conda profiles more strict #866

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Merged
ewels merged 5 commits into from
Mar 10, 2021
Merged

Make container/conda profiles more strict #866

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8563567
Make container/conda profiles more strict
jfy133 Feb 26, 2021
3bc66a5
Update nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextfl…
ewels Feb 26, 2021
fc4c17b
Merge branch 'master' into container-profile-strictness
ewels Mar 9, 2021
ec8f8d7
Added new container configs
jfy133 Mar 10, 2021
0de7c18
Merge branch 'dev' into container-profile-strictness
ewels Mar 10, 2021
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31 changes: 29 additions & 2 deletions nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config
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Original file line number Diff line number Diff line change
Expand Up @@ -58,27 +58,54 @@ try {
}

profiles {
conda { process.conda = "$projectDir/environment.yml" }
conda {
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud = false
process.conda = "$projectDir/environment.yml"
}
debug { process.beforeScript = 'echo $HOSTNAME' }
docker {
docker.enabled = true
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
// Avoid this error:
// WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
// Testing this in nf-core after discussion here https://github.com/nf-core/tools/pull/351
// once this is established and works well, nextflow might implement this behavior as new default.
docker.runOptions = '-u \$(id -u):\$(id -g)'
}
singularity {
docker.enabled = false
singularity.enabled = true
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
singularity.autoMounts = true
}
podman {
singularity.enabled = false
docker.enabled = false
podman.enabled = true
shifter.enabled = false
charliecloud = false
}
shifter {
singularity.enabled = false
docker.enabled = false
podman.enabled = false
shifter.enabled = true
charliecloud.enabled = false
}
charliecloud {
charliecloud {
singularity.enabled = false
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = true
}
test { includeConfig 'conf/test.config' }
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