From 901ae48e95c359aef75ca885438ce004915ac27f Mon Sep 17 00:00:00 2001 From: GitHub Actions Date: Tue, 8 Oct 2024 04:58:57 +0000 Subject: [PATCH] Built site for dracarys@0.16.0: 93ae318 - see https://umccr.github.io/dracarys/ --- 404.html | 5 +- CODE_OF_CONDUCT.html | 5 +- LICENSE-text.html | 5 +- LICENSE.html | 5 +- articles/NEWS.html | 376 ++++++++++++++++++ articles/developers.html | 37 +- articles/files.html | 309 +++++++------- articles/flames.html | 5 +- articles/index.html | 7 +- authors.html | 9 +- index.html | 27 +- news/index.html | 211 ---------- pkgdown.js | 8 + pkgdown.yml | 7 +- reference/BcftoolsStatsFile.html | 5 +- reference/BclconvertReports.html | 258 +++++++++++- reference/BclconvertReports375.html | 308 ++++++++++++++ reference/FastqcMetricsFile.html | 5 +- reference/File.html | 5 +- reference/FragmentLengthHistFile-1.png | Bin 122899 -> 122858 bytes reference/FragmentLengthHistFile.html | 5 +- reference/MappingMetricsFile.html | 5 +- reference/MultiqcFile.html | 8 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reference/gds_list_files_filter_relevant.html | 138 +++++++ reference/gds_volumes_list.html | 5 +- reference/grep_file.html | 88 ++++ reference/ica_token_validate.html | 5 +- reference/index.html | 251 +++++++----- reference/local_list_files_dir.html | 95 +++++ .../local_list_files_filter_relevant.html | 104 +++++ reference/match_regex.html | 5 +- reference/multiqc_column_map_append.html | 5 +- reference/multiqc_date_fmt.html | 5 +- reference/multiqc_parse_bargraph_plot.html | 5 +- reference/multiqc_parse_gen.html | 5 +- reference/multiqc_parse_plots.html | 5 +- reference/multiqc_parse_raw.html | 5 +- reference/multiqc_parse_raw_interop.html | 5 +- reference/multiqc_parse_xyline_plot.html | 5 +- .../multiqc_parse_xyline_plot_contig_cvg.html | 5 +- reference/multiqc_tidy_json.html | 5 +- reference/rdf2tab.html | 5 +- reference/read.File.html | 5 +- reference/read.html | 5 +- reference/s3_file_presignedurl.html | 102 +++++ reference/s3_list_files_dir.html | 99 +++++ ...tml => 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b/404.html index 6be7897..295eb21 100644 --- a/404.html +++ b/404.html @@ -20,7 +20,7 @@ dracarys - 0.15.0 + 0.16.0 + + + + + +
+ + + + +
+
+ +

News

+ + + Source: vignettes/NEWS.Rmd +
NEWS.Rmd
+
+ + + +
+

dracarys 0.16.0 (2024-10-08) +

+

Complete refactor of the dracarys R6 class system. We now have a Wf +super class which is the base for Wf_* subclasses.

+
    +
  • cttsov2: initial support +(pr135)
    • +
  • cttsov1: major refactor +(pr133)
    • +
  • umccrise: major refactor, summary report +(pr127)
    • +
  • switch to bump-my-version for bumping +(pr139)
    • +
  • Sash support +(pr129) +
      +
    • add summary report
      • +
    +
    • +
  • MultiQC: add Sash support +(pr137)
    • +
  • docker: use multi-stage build +(pr122)
    • +
  • BCL Convert: support 4.2.7 +(pr124)
    • +
  • refactor filesystem management +
      +
    • better support for S3
      • +
    +
    • +
  • v0.16.0 - v0.15.0 diff
    • +
+
+
+

dracarys 0.15.0 (2024-08-14) +

+ +
+
+

dracarys 0.14.0 (2024-05-13) +

+ +
+
+

dracarys 0.13.0 (2024-03-15) +

+ +
+
+

dracarys 0.12.0 (2023-12-12) +

+ +
+
+

dracarys 0.11.0 (2023-08-22) +

+ +
+
+

dracarys 0.10.0 (2023-06-22) +

+ +
+
+

dracarys 0.9.0 (2023-05-10) +

+ +
+
+

dracarys 0.8.0 (2023-02-24) +

+ +
+
+

dracarys 0.7.0 (2023-02-15) +

+ +

Mostly added use cases based on requests from the curation team +related to umccrise (CHORD, HRDetect, QC summary), PCGR, and +MultiQC.

+
    +
  • :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) +

+ +
+
+

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) +

+ +
+
+

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).
      • +
    +
    • +
+
+
+
+ + + + +
+ + + + + + + diff --git a/articles/developers.html b/articles/developers.html index 4097a68..4f3159a 100644 --- a/articles/developers.html +++ b/articles/developers.html @@ -20,7 +20,7 @@ dracarys - 0.15.0 + 0.16.0