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"standard" and "slurm" profiles are referenced twice #192

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chasemc opened this issue Oct 18, 2021 · 0 comments · Fixed by #195
Closed

"standard" and "slurm" profiles are referenced twice #192

chasemc opened this issue Oct 18, 2021 · 0 comments · Fixed by #195
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nextflow Nextflow related issues/code

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@chasemc
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chasemc commented Oct 18, 2021

I'm honestly not sure if this results in an additive profile or if the second overwrites the first?
currently in coffee shop because no internet, will have to test later or @WiscEvan if you have a minute.

Autometa/nextflow.config

Lines 132 to 173 in f372b82

profiles {
standard {
// https://www.nextflow.io/docs/latest/executor.html#local
// simple profile that runs all processess locally
process.executor = "local"
}
slurm {
// https://www.nextflow.io/docs/latest/executor.html#slurm
// simple profile for running jobs on slurm
process.executor = "slurm"
// queue is the slurm partition to use.
// Set SLURM partition with queue directive.
process.queue = "queue"
}
}
profiles {
debug { process.beforeScript = 'echo $HOSTNAME' }
standard {
docker.enabled = true
docker.userEmulation = true
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
slurm {
docker.enabled = true
docker.userEmulation = true
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}

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