Rp3 add support for adapter files in bbduk, update ci test

theiagen / public_health_viral_genomics

Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, especially SARS-CoV-2

https://public-health-viral-genomics-theiagen.readthedocs.io/

GNU Affero General Public License v3.0

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Rp3 add support for adapter files in bbduk, update ci test #186

Closed kapsakcj closed 1 year ago

kapsakcj commented 1 year ago

Setting as a draft for now while we test in Terra. Wanted to start this PR so I can further update CI hashes. They likely have changed since Robert's initial PR #185 .

This PR adds a few more changes to PR185 , allowing for the user to optional provide a FASTA file for adapters and phix which will be used by bbduk for trimming/removal in theiacov_illumina_pe and theiacov_illumina_se workflows

This will address issue #184