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Add humann3 DNA rules #20

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rroutsong opened this issue Jul 9, 2024 · 0 comments
Open

Add humann3 DNA rules #20

rroutsong opened this issue Jul 9, 2024 · 0 comments
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enhancement New feature or request

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@rroutsong
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rroutsong commented Jul 9, 2024

Generate taxonomic profile from DNA inputs to skip translated nucleotide search for RNA classification

Normalize RNA reads to DNA copy number

Rule should wrap this execution signature:

humann --threads 16 \
        --input ${PR} \
        --input-format fastq \
        --output-basename ${SAMPLE} \
        --output ${OUTPUT} 

Without --remove-tmp will generate a "buglist.tsv" which then needs to inform the humann3 RNA rule.

This is two-fold:

  1. it appropriately creates a taxonomic profile at the gene level instead of the transcript level
  2. skips the translated nucleotide search that can take an extended amount of time in RNA
@rroutsong rroutsong added the enhancement New feature or request label Jul 9, 2024
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