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cellprofiler-nf docker needed #1

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tcrombie opened this issue May 17, 2022 · 0 comments
Open

cellprofiler-nf docker needed #1

tcrombie opened this issue May 17, 2022 · 0 comments
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enhancement New feature or request

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@tcrombie
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We should make a docker image specific to cellprofiler-nf. At the moment we are using the NemaScan docker file which is bloated with software not required for this workflow. See, nextflow.config for call to NemaScan docker:

process {
    container = 'andersenlab/nemascan:20220407173056db3227' // still need to make cp docker img

    withLabel: cellpro {
        container = 'cellprofiler/cellprofiler:4.2.1'
        memory = { 8.GB * task.attempt } // 8.GB working for all dauerProtocol3
        time = { 30.min * task.attempt }

        errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
        maxRetries = 3
    }
}
@tcrombie tcrombie added the enhancement New feature or request label May 17, 2022
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