Changes in v0.15.0

• docs: add readme documenting usage of catalog_build package (#664) @hunterckx (#699)

🚀 Features

• feat: add new measles workflow @d-callan (#735)
• feat: add annotation workflow category and workflows @d-callan (#707)
• feat: format table numbers with a comma (#719) @frano-m (#720)
• feat: sort organism details assembly list by is_ref then accession number (#721) @frano-m (#722)
• feat: update column isref to display a chip (#716) @frano-m (#717)
• feat: update filters group filters, filter by range, with search (#714) @frano-m (#715)
• feat: pre filter read run popup depending on the workflow type (#706) @frano-m (#708)
• feat: add ungrouped column filters to read run (#700) @frano-m (#701)
• feat: show all read runs for organisms with less than 200 read runs (#696) @frano-m (#698)

🐛 Bug Fixes

• fix: remove unused launchStep.tsx and step.ts (#670) @mvdbeek (#672)

🧰 Maintenance

• chore: update findable-ui to latest v42.0.1 (#693) @frano-m (#695)

Full Changelog: v0.14.0...v0.15.0

Changes in v0.14.0

🚀 Features

• feat: update covid priority pathogen ranking @d-callan (#684)
• feat: warnings for failed automagical gtf files @d-callan (#683)
• feat: remove workflow stepper feature flag @d-callan (#676)
• feat: add display label for xeno refgene @d-callan (#678)
• feat: add hgPhyloPlace link for measles @d-callan (#674)
• feat: configure active workflows with stepper inputs @mvdbeek (#662)
• feat: add all input parameters to workflows.yml (#653) @mvdbeek (#660)
• feat: fill in collection_type in type guide (#658) @mvdbeek (#661)

🐛 Bug Fixes

• fix: fix GTF stepper for human accession (#679) @mvdbeek (#681)
• fix: add error handling to stepper steps @mvdbeek (#680)
• fix: don't run eslint on anything that's in .gitignore @mvdbeek (#671)
• fix: make assemblies more stable @d-callan (#644)
• fix: allow priority pathogen page scrolling @dannon (#657)

🧰 Maintenance

• chore: update findable-ui to latest version v38.2.0 (#668) @frano-m (#669)
• chore: release tooling tweaks and doc updates @dannon (#656)

Full Changelog: v0.13.0...v0.14.0

Changes in v0.13.0

🚀 Features

• feat: add IWC linkage from workflows @dannon (#599)
• feat: add serotype and isolate info for assemblies @d-callan (#642)
• feat: restore hero background on home, about and roadmap pages (#636) @frano-m (#646)
• feat: revert roadmap typography to match brc design mocks (#637) @frano-m (#645)
• feat: link pathogen detail pages priority tag to the organism list filtered by the prioirty (#630) @frano-m (#641)
• feat: draft new user facing roadmap (#558) @d-callan (#589)
• feat: add priority pathogen @frano-m (#622)
• feat: add priority pathogen level and name to organisms and assemblies (#606) @hunterckx (#613)
• feat: implement outbreak detail page (#507) @frano-m (#612)
• feat: add responsive view to priority pathogens view (#610) @frano-m (#611)
• feat: implement outbreaks page (#506) @frano-m (#605)
• feat: workflow stepper 'upload your own data' button is disabled (#575) @frano-m (#604)
• feat: add brc-wide calendar @dannon (#639)

🐛 Bug Fixes

• fix: clean up priority pathogen display names @d-callan (#633)
• fix: only one of two paired fastq listed in workflow stepper (#578) @frano-m (#603)
• fix: set dbkey when sending reference fasta or dbkey (#634) @mvdbeek (#638)
• fix: publication workflow changes to use PRs instead of pushing to branch directly on tag/publish @dannon (#600)
• fix: sunburst display issues in firefox @dannon (#598)

🧰 Maintenance

• chore: update findable-ui to latest v38.1.1 (#635) @frano-m (#640)
• chore: update findable-ui to latest 37.1.0 (#601) @frano-m (#602)
• refactor: refactor prioritypathogenview to prioritypathogensview (#607) @frano-m (#608)

Full Changelog: v0.12.0...v0.13.0

Changes in v0.12.0

• chore: remove required GitHub issue linking from PR title validation @dannon (#587)
• fix: typos in the about and roadmap pages @dannon (#584)

🚀 Features

• feat: add bv-brc viruses @d-callan (#553)

Full Changelog: v0.11.0...v0.12.0

Changes in v0.11.0

🚀 Features

• feat: move schemas and iwc workflows script to python package (#540) @hunterckx (#552)
• feat: generate taxa tree from assemblies and display accurate assembly count in sunburst (#522) @hunterckx (#550)
• feat: add paired collection parameter to haploid variant calling workflow (#562) @hunterckx (#563)
• feat: include hashes in paired collections sent to galaxy (#470) @hunterckx (#538)
• feat: update sunburst colors (#482) @d-callan (#549)
• feat: improve schema descriptions (#375) @d-callan (#541)
• feat: add basic hgPhyloPlace links to outbreaks schema (#528) @d-callan (#542)
• feat: adding niaid biodefense bacteria (#384) @d-callan (#486)
• feat: highlight prototype pathogen viral families in outbreaks tab (#525) @d-callan (#536)
• feat: update data catalog to support filtering on outbreak taxa (#495) @d-callan (#501)
• feat: allow multiple accessions to be specified when getting data from ena (#513) @hunterckx (#526)
• feat: create paired-end workflow configuration step (#456) @frano-m (#497)
• feat: add outbreaks.json (#484) @hunterckx (#490)
• feat: add support for multiple pairs in SANGER_READ_RUN value (#473) @hunterckx (#487)
• feat: visibility and navigation improvements for hierarchical viz (#289) @dannon (#485)
• feat: homepage sunburst display of available data (#289) @dannon (#396)
• feat: add Release Drafter configuration and publish release workflow (#478) @dannon (#448)
• feat: return collection for SANGER_READ_RUN workflow parameter variable (#468) @hunterckx (#469)
• feat: adding niaid biodefense viruses (#383) @d-callan (#387)
• feat: update settings for common name in organisms list and add to assemblies list (#465) @hunterckx (#467)
• feat: add common name column and filter to organisms list (#463) @hunterckx (#464)
• feat: add outbreak schema and initial outbreaks (#450) @d-callan (#462)
• feat: add species common names to data catalog (#451) @d-callan (#458)
• feat: add stub of SANGER_READ_RUN workflow parameter variable (#459) @hunterckx (#460)

🐛 Bug Fixes

• fix: make consistent navigation behavior between sunburst and side panel (#557) @d-callan (#567)
• fix: counts in sunburst side panel represent assemblies (#564) @d-callan (#566)
• fix: refreshing on organisms or assemblies page hangs on dev (#561) @frano-m (#565)
• fix: remove count from sunburst tooltip/link for clarity #481 #545 #522 @dannon (#546)
• fix: filter labels incorrect for taxonomic level (#544) @frano-m (#548)
• fix: fix back button behaviour from assemblies back to sunburst on homepage (#521) @frano-m (#543)
• fix: fix sunburst links to assemblies page (#520) @frano-m (#534)
• fix: outbreak titles should be explicit (#494) @d-callan (#498)
• fix: adjust color application at root node of hierarchy (#289) @dannon (#479)
• fix: use generic title for hierarchy viewer list nav (#289) @dannon (#480)

🧰 Maintenance

• chore: update findable-ui to latest version v28.0.0 (#491) @frano-m (#492)
• chore: adjust release-drafter configuration for better display (#478) @dannon (#477)
• chore: automate data catalog building (#397) @mvdbeek (#410)
• style: apply consistent python formatting, import sorting -- automate w/ ruff #393 @dannon (#392)

Full Changelog: v0.10.0...v0.11.0

0.10.0 (2025-04-02)

Features

• add check for ploidy to the assemblies qc report (#366) (#441) (b421c04)
• add launch galaxy button to workflow stepper (#437) (#443) (a94c7b6)
• add loading ui to gtf step and stepper when launching galaxy (#446) (#447) (b762e84)
• adding organism specific workflows (#357) (#412) (a63f0fb)
• create configure inputs title and breadcrumbs (#427) (#428) (577d897)
• create workflow configuration main column with two placeholder steps (#433) (#434) (96930a2)
• create workflow configuration side column (#431) (#432) (5d9d111)
• fetch gtf file types for the gtf step (#435) (#436) (fd20496)
• introduce workflow configuration page (#422) (#426) (6ed9eac)
• optionally hide 'coming soon' for empty workflow categories (#442) (#449) (62ba68b)
• update assembly page title and side column for selecting a workflow (#444) (#445) (2e69b61)

Bug Fixes

• add error handling to ucsc files request (#438) (#439) (744644a)

Chores

• update findable-ui to latest version v24.0.0 (#429) (#430) (bc51e93)

Content

• update cards on main page to add webinar YouTube link (#454) (#455) (0269348)

Code Refactoring

• refactor dynamic route from data/[...params] to data/[params]/index (#424) (#425) (8bc5d20)

0.9.0 (2025-03-24)

Features

• landing page organism viz - data (#289) (#290) (6817ece)

Bug Fixes

• don't run deploy jobs on forks (#408) (#409) (17f317c)
• github action syntax needs single quotes, resolves deploys (d142b04)
• github action syntax needs single quotes, resolves deploys (#417) (#416) (d142b04)
• handle NCBI rate limit (df84da0)
• handle NCBI rate limit (#407) (#406) (df84da0)
• include ncbiGene.gtf.gz file if there's no refSeq gtf (#414) (#413) (89799d4)

Chores

• use requests session to reuse tcp connection (#397) (#405) (dacdbb2)

0.8.0 (2025-03-20)

Features

• add realm to taxonomic lineage filters (#389) (#390) (0d96267)
• allow limiting workflows by taxonomy id (#356) (#369) (364876f)
• build catalog and add qc report (#344) (#364) (a3a70ca)
• remove retired ncbi superkingdom rank and add domain (#385) (#386) (a7af98a)
• update workflows from IWC manifest and set assembly-specific parameters (#351, #339) (#342) (f5720a8)

Bug Fixes

• avoid assembly duplication due to duplicate taxonomy ids and add checks for duplicate entity ids (#367) (#368) (e625081)
• use correct variant calling landing body even when gene model url is absent (#347) (#365) (038d76e)

Chores

• add .venv to prettier ignore list (28981f7)
• add .venv to prettier ignore list (#373) (#374) (28981f7)
• remove issue number check from commit message validation (bba7273)
• Remove issue number check from husky (#363) (#372) (bba7273)
• rename genomes.json to assemblies.json (#343) (#360) (bebcfb2)
• replace HTML scraping with API calls (#346) (#378) (6b6c3c0)
• update findable-ui to latest v22.0.0 (#391) (#395) (8ee5a6a)

Content

• explain 'free' compute at tacc (#237) (#370) (39bab23)
• remove cards from the carousel/card deck (#403) (#404) (9f4f70e)

Continuous Integration

• add github action and workflow to check pr title for commit message format (#377) (#380) (b128499)
• fix linkml checks so that they exit with failure if the check fails for any file (#341) (#376) (a450ea5)

0.7.0 (2025-03-03)

Features

• add back all assemblies (#323) (#340) (6bff3c8)
• add filters for taxonomic levels to organisms list (#301) (#306) (665a20a)
• add taxonomic levels to assembly list (#312) (#316) (06bdb3c)
• added additional workflows (#322) (#335) (8cab2ad)
• allow organisms to have multiple ploidies separately matched with workflows (#334) (#338) (7ce865a)

Styles

• fix prettierignoring of catalog files (#317) (#318) (9c97653)

0.6.0 (2025-02-18)

Features

• add instructions section to home page (#278) (#303) (173f3b1)
• add linkml schemas for data source files (#269, #270) (#283) (b208c53)
• create catalog build python package (#251) (#258) (c31cf6e)
• derive workflows from yaml files (#260) (#265) (0b42fd7)
• fetch raw/primary data information from sra (#295) (5ded790)
• move assembly species from breadcrumbs to subtitle (#276) (#280) (aedfc32)
• only show workflows with compatible ploidies (#297) (#299) (9e2e04c)
• support multiple analysis methods per category (#279) (#296) (57d55db)
• update workflow card for "Launch Galaxy" button (#300) (#302) (1004775)

Chores

• delete unused build-genomes-files.py (#267) (#274) (4032561)

Content

• update main page (#243) (#259) (bbdee9f)

Documentation

• add instructions for building the catalog and adding assemblies (#266) (#268) (56110b9)

Code Refactoring

• remove unused workflows from catalog (#272) (#273) (9d37334)
• reorganize catalog folders (#271) (#281) (b9e3a38)