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NEWS

Source: vignettes/NEWS.qmd

v0.1.0 (2026-07-28)

Major refactor. GitHub org migrated from umccr to tidywf. All 19 tool configs consolidated from dual raw.yaml + tidy.yaml files into a single schema.yaml per tool, with parsing simplified across the board (pr189). The nemo API was updated (nemofy/diro → run/output_dir, pr200). DVC switched to per-file tracking backed by a public Cloudflare R2 remote (pr190, pr203). Docker images now build for both linux/amd64 and linux/arm64 (pr198). GHA refactored to use reusable workflows from tidywf/actions (pr181).

Changes

  • GitHub org: umccr → tidywf (URLs, remotes, labels, conda recipe)
  • Schema: all tools migrated from raw.yaml + tidy.yaml to a single schema.yaml; initially introduced as LinkML (pr174) then simplified; old config files removed; parsing simplified across all tools (pr189); simplified version/qc handling (pr205); renamed txt ftypes to tsv, added equal-keyvalue ftype (pr206)
  • Flagstats: removed standalone class — covered by Bamtools
  • Bamtools: dropped histogram parser; gene-coverage split into genecvggenes + genecvgcvg tables via tidy_genecvg_split() (pr210); handle summary + wgsmetrics subtables
  • Cobalt: handle sample + buckets subtables
  • Alignments: dropped histogram rows from markdup parser
  • Linx: fixed germline file handling (pr189); added v1.25 test data; germline vs somatic outputs now get symmetric _germline / _somatic prefixes via the refine_files hook (also tags the somatic side, scoped to parsers that actually have a germline counterpart); relies on nemo running the hook before disambiguation (pr208)
  • Purple: germline vs somatic outputs now get symmetric _germline / _somatic prefixes via the refine_files hook (pr208)
  • Sage: added v3.4.4 test data; germline vs somatic outputs (separated by a germline/ / somatic/ subfolder rather than by basename) now get _germline / _somatic prefixes via refine_files, keyed off the parent folder, with the variant also injected into bname so repeat runs are numbered independently per variant (logic in the refine_by_variant_folder() helper); the gene-coverage file (.sage.gene.coverage.tsv) is now parsed by Sage’s own genecvg table rather than the bamtools schema, so it is tidied as sage_genecvg and picks up the germline/somatic tagging, with the genes/cvg split shared with Bamtools via tidy_genecvg_split() (pr208, pr210)
  • Cuppa: handle v1.4 sampleId column (fixes iss172); use csv ftype for datacsv; add plotter functions (pr173); predsum tidy schema fix (pr179, iss178)
  • DVC: switch from directory-level to per-file .dvc tracking, backed by public Cloudflare R2 (pr190, pr203); dvc_download_file() / dvc_download_all() download helpers subsequently moved to nemo (pr204)
  • Wigits: re-add Esvee; use metapkg; WIGITS_TOOLS changed from character vector to named list of R6 classes (pr191)
  • Vignettes: add quickstart, structure, schema_table, cicd, devnotes; refactor uml; remove schemas_raw + schemas_tidy; consolidate installation fragments (pr193); add Output Naming vignette extending nemo’s shared template with the Linx/Purple/Sage special cases (pr208); add Panache format vignettes (pr207)
  • GHA: use reusable workflows for conda/docker/pkgdown (pr181); add version-bumping workflow (pr183, pr185); fix permissions (pr182); refactor deploy workflow (pr175, pr176); add multi-arch Docker support (pr198)
  • Move shiny and website to separate repos (pr171)
  • Pre-commit: replace lorenzwalthert/precommit with posit-dev/air-pre-commit (air-format); add CLAUDE.md + new-tool skill (pr180)

nemo API changes (pr200)

  • nemofy() / diro → run() / output_dir (two-step: first wrangle/out_dir, then run/output_dir)
  • out_dir → output_dir; pfix_include → prefix_include; output column input_pfix → input_prefix; CLI flag --out_dir → --output_dir
  • Config/Tool renames: raw_schemas_all → schemas_raw; tidy_schemas_all → schemas_tidy; get_tidy_schema → get_schema_tidy; get_raw_schema → get_schema_raw
  • All subclasses declare cloneable = FALSE
  • .parse_file*()/.tidy_file() public dot methods moved to private in nemo
  • self$get_schema_*() shortcuts removed from Tool; use self$config$get_schema_*() directly
  • Linx/Purple: germline/somatic prefix logic moved to initialize() (later reworked into the refine_files hook, pr208)

Contributors

v0.0.7 (2026-02-09)

  • cuppa: handle rna predsum (pr170, iss169)
  • s3sync: add isofox + alignments md.metrics

v0.0.6 (2026-02-04)

v0.0.5 (2025-09-07)

Major refactor, moving core functionality to nemo

  • move Config, Tool, Workflow classes to nemo
  • move utils to nemo
  • CLI: use nemo wrapper
  • use conda env for pkgdown

v0.0.4 (2025-08-19)

Major documentation update - see pr138 for details.

  • test data update
  • full README re-write
  • pkgdown vignette re-org
  • add vignettes for raw/tidy schemas, uml diagram
  • add pkgdown/extra.scss for CSS customisation
  • add logo

v0.0.3 (2025-08-04)

Fixed bug where normalizePath was getting called with NULL output directory in the db format case (pr133).

v0.0.2 (2025-07-14)

Mostly Shiny, Conda, Docker, pkgdown and GitHub Actions support.

  • Add GitHub Actions for deployment of the following (pr130, iss9):
    • Conda: add recipe and rattler-builder (pr124, iss4)
    • Docker: add Dockerfile (pr130)
    • Shiny: add summary app (pr122)
    • CLI: Add listing and tidy include/exclude support (pr116)
    • Add pkgdown support (pr125, iss37)
    • Add DVC support with some purple test data (pr126, iss59)
  • Optimise file listing (pr131, iss127)
    • Remove File class

v0.0.1 (2025-06-19)

Initial release of tidywigits.