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usafsam / mad_river_wf

SARS-CoV-2 analysis workflow, using Nextflow and bbtools
Apache License 2.0
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Feed combined consensus FASTA to pangolin and nextclade #5

Closed fanninpm closed 2 years ago

fanninpm commented 2 years ago

Currently, we are feeding individual FASTA files into pangolin and nextclade processes. It would be more efficient for these processes to receive the combined consensus FASTA file as input. Erin Young did something similar with the Cecret pipeline:

https://github.com/UPHL-BioNGS/Cecret/blob/5bb7d7b0a3a449e5b1ebacf5a242b4cbb118de58/Cecret.nf#L1209-L1301

friesac commented 2 years ago

Agreed, I would however continue to create the IVAR_CONSENSUS directory with the independent consensus fasta for each specimen in that directory.