v1.4.0-waphl edits to Nextclade task

ThieaCoV_Illumina_PE updated to handle Nextclade version 3.3.1

v1.3.0-waphl

theiacov_illumina_pe has been updated to include flagging of sequences by VADR under the same conditions used by Genbank for flagging manual curation.

Original TheiaProk updates and WAPHL QC checker

This release contains updates Theiagen's public_health_bioinformatics repository in addition to a WAPHL QC checker output for the theiaprok_illumina_pe_waphl workflow.

Adding function to output Nextclade Lineages to Terra

1.2.1-waphl

Update task_nextclade.wdl

RECAPP can use pre-generated clades or clusters

Users can assign the declared_cluster variable to use any Array[String] (or column of data in a Terra.bio table) to determine how RECAPP splits up data for more in-depth analysis

Null values in epi output is now represented with the string "NULL"

Edit at request of ww epis for ease of use in R

Adding Functionality to Freyja Pipeline for Biobot Data

v1.0.0-beta

Update task_waphl_utils.wdl