v1.4.3-dev

What's Changed

• New env/cli param --temp_root by @neoformit in #174
• Link to NCBI BLAST in report table(s) by @neoformit in #175
• Strip Cloudgene config from repo by @neoformit in #181
• Candidates table shows taxonomy by @neoformit in #189
• Rework phylogeny sequence selection algorithm by @neoformit in #188
• 4 test scenarios written in nf-test with snapshots added
• blast.xml file can be used as input (not tested thoroughly & missing validation)

New Contributors

• @mantczakaus made their first contribution in #182

Bug fixes

• Error: "No sequences matched for alignment. Check sequence ID format compatibility between candidates and queries."
• taxa_of_interest, host, country shouldn't be a mandatory columns
• FastME fails for some PREDICTED RefSeq records
• Omit distribution map for Family+ level targets
• Fix cache unit tests in github workflow by @neoformit in #177

Full Changelog: v1.3.3...v1.4.3-dev

Pull the docker image: neoformit/taxodactyl:v1.4.3-dev

v1.3.3

This fixes a critical bug where a race condition on the cache SQLite3 database causes an infinite hang in the EVALUATE_DATABASE_COVERAGE process.

Implement file lock interface to cache db

Observe env var CACHE_DISABLED=1

Full Changelog: v1.3.0...v1.3.3
Pull the docker image: neoformit/taxodactyl:v1.3.3

v1.3.0

What's Changed

Big changes

• Cloudgene deployment by @neoformit in #146
• Update CLI args by @neoformit in #153
• Major overhaul of report layout
• Cached API responses for faster run time (default 1 week cache timeout)
• More merging of Python scripts repo into Taxodactyl repo

Smaller changes

• JSON flag files by @neoformit in #140
• Update analysis docs
• Describe tree colour-coding
• Update analysis docs
• Revoke redundant PHYLOGENY_MIN_HIT_IDENTITY param
• Add figure documenting systematic sampling of hits
• Fix img url
• Display count of all filtered hits, not just candidate hits in candid…
• Add integration test case c15
• Bump version
• Fix PMI DB cov button max flag
• Positive species ID requires flag 4A
• Fix flag extra text default value
• Move tests into scripts dir
• Refactor aux files into scripts dir
• Update gitignore
• JSON flag files
• Touch up "no locus" report dialog
• Fix up styling of blast result table for clarity
• Refactor p4 report section into modal in candidates table
• Move phylogenetic tree to modal in candidates report section
• Major refactor of report overview components
• Display minimum reported hit identity in report
• Prevent splitting sample ID by period
• Cache Entrez/GBIF API requests

Full Changelog: v1.2.0...v1.3.0

Pull the docker image: neoformit/taxodactyl:v1.3.0

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: qcif/daff-biosecurity-wf2@v1.1.0...v1.2.0
Full Changelog: v1.1.0...v1.2.0

v1.1.0

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: v1.0.0...v1.1.0
Full Changelog for daff-biosecurity-wf2: qcif/daff-biosecurity-wf2@release_1.0.0...release_1.1

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: qcif/daff-biosecurity-wf2@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: v0.2.6...v1.0.0

v0.2.6

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

Full Changelog: v0.2.4-patch...v0.2.6

v0.2.4-patch

Uses https://github.com/qcif/daff-biosecurity-wf2/releases/tag/v0.2.4-patch

Full Changelog: v0.2.4...v0.2.4-patch

v0.2.4

Uses daff-taxonomic-assignment/v0.2.4 (GitHub relese)

Issues fixed

• 2 43 Segmentation fault (core dumped) fastme
• 6 MSA: Change <sample_id> to QUERY
• 10 Megablast should be used instead of blastn

Full Changelog: v0.2.3...v0.2.4

v0.2.3

neoformit/daff-taxonomic-assignment:v0.2.3

Full Changelog: v0.2.2...v0.2.3