nf-core / differentialabundance

Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
https://nf-co.re/differentialabundance
MIT License
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Provide a parameter to disable rmarkdown report creation in the differential abundance pipeline #275

Open shreya-sharma20 opened 1 month ago

shreya-sharma20 commented 1 month ago

Description of feature

When analyzing a large number of samples using the differential abundance pipeline, the markdown notebook compilation step fails due to memory issues.

For now, I have increased the memory for this process.

Feature Request: It'll be helpful if there is a parameter to disable this process if reports are not required.

dshechter commented 3 weeks ago

Additional suggestion to increase the RAM allocated for this process, e.g.

process {
    withName: 'NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:RMARKDOWNNOTEBOOK' {
        memory = 200.GB
    }
}

Could work with less than 200, just haven't tried it.