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Gibbons-Lab / medi

Metagenomic Estimation of Dietary Intake and Content.
Apache License 2.0
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process merge seems missing in build_kraken.nf #1

Closed cschu closed 9 months ago

cschu commented 9 months ago

Hi, the build_kraken workflow references a process/workflow named merge

workflow {
    [...]
    self_classify(library.out, build_kraken_db)
    merge(classify.out.collect(), build_kraken_db)
    build_bracken(merge.out) | add_food_info
}

However, this identifier is not defined anywhere. As the build_bracken command operates on merge.out, I also don't assume that this is supposed to be the Channel.merge operator.

Thanks, Christian

cdiener commented 9 months ago

My bad, I was reverting a recent change that tried to parallelize the BRACKEN preclassification but it turned out to be too heavy on RAM. Should be fixed now.

cschu commented 9 months ago

Cool, thanks. I also assume that the classify.out.collect() should actually be self_classify.out.collect() ?

nvm - misread the code