News • dracarys

:star: Added :
- R functions:
  - umccr_tidy: workhorse that handles the tidying and method dispatch.
  - gds_file_presignedurl
- R6 classes:
  - PcgrJsonFile
  - PcgrTiersFile
  - UmChordTsvFile
  - UmHrdetectTsvFile
  - UmQcSumFile
  - UmSigsSnvFile
  - MultiqcFile
:wrench:
- Updated README with unified dracarys tidy CLI.
- Added a fun column to FILE_REGEX for handling method dispatch.
- GH Actions: Remove linux/arm64 from docker since conda pkgs don’t generally have ARM64 equivalents.
- GH Actions: use “miniforge-variant: Mambaforge” (see this issue).

dracarys 0.6.0 (2023-01-09)

v0.6.0 - v0.5.0 diff
:wrench: GH Actions:
- replace ::set-output.
- add linux/arm64 support.
:wrench: R core:
- replace select .data with quotes.
- bump Roxygen 7.2.1 -> 7.2.2
- add {fs}, {httr}, {jose}, {sessioninfo} dependencies.
- import %||% from {rlang} to specify fallback values in NULL cases.
:sparkles: pkgdown: change theme to simplex.
:whale: Docker:
- bump mambaforge: 4.12.0-2 -> 22.9.0-2
- bump conda-lock: 1.0.5 -> 1.3.0
:computer: CLI:
- add support for tidying outputs from the UMCCR TSO500 ctDNA workflow, and for generating a HTML file with tidy results from the same workflow.
:star: Added R functions:
- tso_tidy for tidying outputs from the UMCCR TSO500 ctDNA workflow.
- tso_rmd for generating a HTML file with tidy results from the above workflow.
- dr_gds_download for downloading dracarys-related files from GDS.
- gds_files_list for listing files on GDS via the API.
- gds_file_download and gds_file_download_api for downloading files from GDS via the ica binary and API (via presigned URLs), respectively.
- ica_token_validate for validating the ICA access token is valid and has not expired.
:x: Removed R functions:
- TsoCombinedVariantOutputFile: these files were deemed to have less info compared to other output files.
- dracarys_tidy_multiqc: renamed to dracarys_multiqc.
- mkdir: use fs::create_dir instead.
- Remove {tibble}, {readr} and {ggplot} multi-imports for R6, since we can get away with just importing a single function in one of the R6 classes.

dracarys 0.5.0 (2022-09-28)

v0.5.0 - v0.4.0 diff
MultiQC: update column mappings (pr15, pr16).
- move map to separate TSV
CLI: add option for output format (tsv, parquet, or both) (pr18).
new contributors: @victorskl

dracarys 0.4.0 (2022-09-12)

v0.4.0 - v0.3.0 diff
:star: support for DRAGEN TSO500 ctdna output (pr14).
- also add Quarto HTML report template

dracarys 0.3.0 (2022-08-28)

v0.3.0 - v0.2.0 diff
:star: MultiQC: support for DRAGEN ctdna output (pr13).

dracarys 0.2.0 (2022-07-23)

v0.2.0 - v0.1.0 diff
Add MULTIQC_COLUMNS tibble that maps the raw metric name to a cleaner name (pr12).
Support for more MultiQC JSONs (from bcbio-wts and bcbio-wgs).

dracarys 0.1.0 (2022-07-11)

Initial release of dracarys.
Support for MultiQC JSON tidying.
Add conda, conda-lock, Docker support (pr11).
CLI support for dracarys.R tidy.
- Initially supporting just MultiQC json input (from dragen-alignment, dragen-transcriptome, dragen-tumor-normal, dragen-umccrise, and bcbio-umccrise).