Switch from SeqyClean to Trimmomatic/bbduk

StaPH-B / titan

Public health bioinformatics repository for WDL workflows to analyze viral genomes.

GNU Affero General Public License v3.0

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Closed jvhagey closed 3 years ago

jvhagey commented 3 years ago

[x] Remove seqyclean task from wf_read_QC_trim.wdl
[x] Implement changes @kevinlibuit has made with Theiagen's workflow mentioned, by creating a new task that contains Trimmomatic and bbduk steps.
[x] Add code to call these tasks in wf_read_QC_trim.wdl

k-florek commented 3 years ago

I've addressed this points in Pull Request #12 please let me know if I have missed anything.