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Update clusterOptions #154

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cflerin opened this issue Mar 5, 2020 · 0 comments · Fixed by #224
Closed

Update clusterOptions #154

cflerin opened this issue Mar 5, 2020 · 0 comments · Fixed by #224
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enhancement New feature or request

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@cflerin
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cflerin commented Mar 5, 2020

The current use of clusterOptions is specific to the VSC and won't work with other HPC systems:

clusterOptions "-l nodes=1:ppn=2 -l walltime=1:00:00 -A ${params.global.qsubaccount}"

An improvement would be to specify the resource usage per process using the built-in directives, and have a VSC profile that sets cluster-specific settings.

process example {
    cpus 4
    memory 10.GB
    disk '2 GB'
    queue 'bigmem'
    time '1h'
    ...
}

Even better, we could set these dynamically based on the number of cells and genes (https://www.nextflow.io/docs/latest/process.html#dynamic-directives)

@cflerin cflerin added the enhancement New feature or request label Mar 5, 2020
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