Releases | Open Source Science

taxodactyl - v1.2.0

Bug fixes:

Omit verbose logging from throttle
P5 allow no tasks when there are unknown taxa (resolves #130)
Change example report to one with proper phylo tree
Fix ordering of BOLD results in container runtime (resolves #131)

New features - bold_database_name parameter added, default COX1_SPECIES_PUBLIC

Full Changelog: https://github.com/qcif/daff-biosecurity-wf2/compare/v1.1.0...v1.2.0 Full Changelog: https://github.com/qcif/taxodactyl/compare/v1.1.0...v1.2.0

- Python
Published by mantczakaus 8 months ago

Main changes

Name of the workflow and repository changed to taxodactyl User documentation: https://qcif.github.io/daff-biosecurity-wf2/understanding-the-analysis.html Sample from candidate hits when too many hits for phylogeny; new parameter phylogeny_max_hits_per_species (see parameter documentation and understanding the analysis guide)

New features

Report TOI table display identity as percent - it used to be shown as a decimal like 0.9 Handle no BLAST hits returned in report - it used to look weird if there were no BLAST hits

Bug fixes

Replace FLAGS.NA with FLAGS.ERROR where appropriate (don't say there was no p5 result because of family+ rank when it was actually because of an error) Catch error reading flags.csv level Fix occurrence map text position Fix p5 rendering logic to handle zero records and NA country properly - hides the bar charts when zero records and hides section 5.3 when country is NA Fix attributeerror in report p5 template rendering Fix typo calculating hsp.identity - previously it was always 100% but fortunately this was only used for rendering the BLAST alignment

Full Changelog for taxodactyl: https://github.com/qcif/taxodactyl/compare/v1.0.0...v1.1.0 Full Changelog for daff-biosecurity-wf2: https://github.com/qcif/daff-biosecurity-wf2/compare/release1.0.0...release1.1

- Python
Published by mantczakaus 8 months ago

taxodactyl - v1.0.0

Initial production release https://github.com/qcif/daff-biosecurity-wf2/releases/tag/v1.0.0 1. NCBI/BLAST workflow meets MVP but has some issues around workflow format and handling of taxonomic synonyms 2. BOLD workflow is not yet functional due to restrictive BOLD API rate limits Full Changelog: https://github.com/qcif/daff-biosecurity-wf2/compare/v0.2.6...v1.0.0 Pull the docker image: neoformit/daff-taxonomic-assignment:v1.0.0

Nextflow changes: - Additional parameters & metadata columns added - Updated documentation - Workflow name changed Full Changelog: https://github.com/qcif/taxapus/compare/v0.2.6...v1.0.0

- Python
Published by mantczakaus 8 months ago

taxodactyl - v0.2.6

uses daff-taxonomic-assignment v0.2.6; last pre-release

Full Changelog: https://github.com/qcif/nf-daff-biosecurity-wf2/compare/v0.2.4-patch...v0.2.6

- Python
Published by mantczakaus 9 months ago