search

nhoffman / dada2-nf

A Nextflow pipeline for processing 16S rRNA sequences using dada2
0 stars 2 forks source link

Extend manifest.KEEP_COLS list or otherwise facilitate columns from input manifest propagation to output sample_info.csv #23

Closed dhoogest closed 3 years ago

dhoogest commented 3 years ago

https://github.com/nhoffman/dada2-nf/blob/79d9f75d852442012f72452845c939f3a4c5e332/bin/manifest.py#L26

We've got some additional/alternate column names in the NGS16S manifest that would be useful to preserve to limit downstream changes. Current manifest shape looks like this:

sampleid,batch,label,barcode_id,run_number,blast_database,desc,other,quant,paired_ntc

Seems like simplest approach would be to just extend the KEEP_COLS list to include these.