nhoffman / dada2-nf

A Nextflow pipeline for processing 16S rRNA sequences using dada2
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'downsample' argument in params does not downsample reads from barcodecop onward #44

Closed dhoogest closed 2 years ago

dhoogest commented 2 years ago

Desired behavior is to specify a numeric value (or None) to indicate the downsampling threshold per sample, then to have filtering/denoising steps performed on the downsampled reads. In order to keep conditional logic simple in this pipeline it might be useful to modify barcodecop to handle None input for --head instead of attempting to extend arguments based on the presence of a param here.

Needs some discussion prior to addressing.

dhoogest commented 2 years ago

/cc @nhoffman @crosenth @mwohl - followup issue from our discussion today.

dhoogest commented 2 years ago

See related https://github.com/nhoffman/dada2-nf/issues/27

dhoogest commented 2 years ago

See option for introducing barcodcop argument (without changes to barcodecop itself) with https://github.com/nhoffman/dada2-nf/pull/45