v0.5

viral_refbased_assembly now accepts reference FASTA, GFF, and Primer BED. Syntax has been cleaned, and Bedtools step removed.

v0.4.5

Fix array input for sc2 batch upload

v0.4.4

Pangolin hardcode input tag: "staphb/pangolin:2.2.1-pangolearn-2021-02-06"

• optional input string for user to modify

v0.4.3

Revert to most recent stable Pangolin tag: staphb/pangolin:2.1.10-pangolearn-2021-02-01

v0.4.2

Fix issue with input params

v0.4.1

• Fix SC2 batch submission imputs
• Add noramlise (int) input to clear labs workflow; default changed to 20000

v0.4

Updates to clearlabs_refbased_assembly:

• added vadr task & ncbi subission tasks

Created sc2_batch_submission workflow

v0.3.3

Enable genomics_cluster_analysis workflow to be run on Terra

Grab appropriate pre-primertrimmed bam for qc metrics for ClearLabs workflows

v0.3.2

Adding cluster analysis workflow to dockstore.yml

v0.3.1

Update task_taxonID.wdl

• Explicitly define nextclade output encoding (etf-8)

Update Clear Labs workflows to include Kraken2 human-read screening