Merge pull request #140 from umccr/docs_update

NEWS v0.16.0
umccr · Oct 8, 2024 · f7022c9 · f7022c9
2 parents 00e82fe + 1871b8b
commit f7022c9
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -5,7 +5,7 @@
 ^TODO\.md$
 ^\.DS_Store$
 ^\.Rproj\.user$
-^\.bumpversion\.cfg$
+^\.bumpversion\.toml$
 ^\.dockerignore$
 ^\.dvc$
 ^\.dvcignore$

diff --git a/README.Rmd b/README.Rmd
@@ -36,15 +36,13 @@ require(dracarys)
 
 ## 🏆 Aim
 
-Given a [ICA GDS][ica-gds], AWS S3 or local directory with results from a UMCCR workflow,
+Given a directory with results from a DRAGEN/UMCCR workflow,
 {dracarys} will grab files of interest and transform them into 'tidier'
 structures for output into TSV/Parquet/RDS format for downstream ingestion
 into a database/data lake.
 See supported [workflows](#supported-workflows), [running](#running) examples,
 and [CLI](#cli) options in the sections below.
 
-[ica-gds]: <https://developer.illumina.com/illumina-connected-analytics>
-
 ## 🍕 Installation
 
 <details>
@@ -98,7 +96,7 @@ docker pull --platform linux/amd64 ghcr.io/umccr/dracarys:X.X.X
 ## ✨ Supported Workflows
 
 
-{dracarys} supports most outputs from the following UMCCR workflows:
+{dracarys} supports most outputs from the following DRAGEN/UMCCR workflows:
 
 | Workflow   | Description |
 |------------|-------------|

diff --git a/README.md b/README.md
@@ -1,11 +1,11 @@
 
 - [🔥 dracarys - UMCCR Workflow
-  Tidying](#-dracarys---umccr-workflow-tidying)
-  - [🏆 Aim](#-aim)
-  - [🍕 Installation](#-installation)
-  - [✨ Supported Workflows](#-supported-workflows)
-  - [🌀 CLI](#-cli)
-  - [🚕 Running](#-running)
+  Tidying](#fire-dracarys---umccr-workflow-tidying)
+  - [🏆 Aim](#trophy-aim)
+  - [🍕 Installation](#pizza-installation)
+  - [✨ Supported Workflows](#sparkles-supported-workflows)
+  - [🌀 CLI](#cyclone-cli)
+  - [🚕 Running](#taxi-running)
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
@@ -22,9 +22,7 @@ install](https://anaconda.org/umccr/r-dracarys/badges/latest_release_date.svg)](
 
 ## 🏆 Aim
 
-Given a [ICA
-GDS](https://developer.illumina.com/illumina-connected-analytics), AWS
-S3 or local directory with results from a UMCCR workflow, {dracarys}
+Given a directory with results from a DRAGEN/UMCCR workflow, {dracarys}
 will grab files of interest and transform them into ‘tidier’ structures
 for output into TSV/Parquet/RDS format for downstream ingestion into a
 database/data lake. See supported [workflows](#supported-workflows),
@@ -34,7 +32,9 @@ below.
 ## 🍕 Installation
 
 <details>
+
 <summary>
+
 R
 </summary>
 
@@ -43,8 +43,11 @@ remotes::install_github("umccr/[email protected]") # for vX.X.X Release/Tag
 ```
 
 </details>
+
 <details>
+
 <summary>
+
 Conda
 </summary>
 
@@ -72,8 +75,11 @@ conda activate dracarys_env
 ```
 
 </details>
+
 <details>
+
 <summary>
+
 Docker
 </summary>
 
@@ -87,20 +93,21 @@ docker pull --platform linux/amd64 ghcr.io/umccr/dracarys:X.X.X
 
 ## ✨ Supported Workflows
 
-{dracarys} supports most outputs from the following UMCCR workflows:
+{dracarys} supports most outputs from the following DRAGEN/UMCCR
+workflows:
 
-| Workflow             | Description                                                                                                                                    |
-|----------------------|------------------------------------------------------------------------------------------------------------------------------------------------|
-| bcl_convert          | [BCLConvert](https://emea.support.illumina.com/sequencing/sequencing_software/bcl-convert.html) workflow                                       |
+| Workflow | Description |
+|----|----|
+| bcl_convert | [BCLConvert](https://emea.support.illumina.com/sequencing/sequencing_software/bcl-convert.html) workflow |
 | tso_ctdna_tumor_only | [ctDNA TSO500](https://support-docs.illumina.com/SW/DRAGEN_TSO500_ctDNA_v2.1/Content/SW/TSO500/WorkflowDiagram_appT500ctDNAlocal.htm) workflow |
-| wgs_alignment_qc     | [DRAGEN DNA](https://support-docs.illumina.com/SW/DRAGEN_v40/Content/SW/DRAGEN/GPipelineIntro_fDG.htm) (alignment) workflow                    |
-| wts_alignment_qc     | [DRAGEN RNA](https://support-docs.illumina.com/SW/DRAGEN_v40/Content/SW/DRAGEN/GPipelineIntro_fDG.htm) (alignment) workflow                    |
-| wts_tumor_only       | [DRAGEN RNA](https://support-docs.illumina.com/SW/DRAGEN_v40/Content/SW/DRAGEN/GPipelineIntro_fDG.htm) workflow                                |
-| wgs_tumor_normal     | [DRAGEN Tumor/Normal](https://support-docs.illumina.com/SW/DRAGEN_v40/Content/SW/DRAGEN/GPipelineIntro_fDG.htm) workflow                       |
-| umccrise             | [umccrise](https://github.com/umccr/umccrise) workflow                                                                                         |
-| rnasum               | [RNAsum](https://github.com/umccr/RNAsum) workflow                                                                                             |
-| sash                 | [sash](https://github.com/scwatts/sash) workflow                                                                                               |
-| oncoanalyser         | [oncoanalyser](https://github.com/nf-core/oncoanalyser) workflow                                                                               |
+| wgs_alignment_qc | [DRAGEN DNA](https://support-docs.illumina.com/SW/DRAGEN_v40/Content/SW/DRAGEN/GPipelineIntro_fDG.htm) (alignment) workflow |
+| wts_alignment_qc | [DRAGEN RNA](https://support-docs.illumina.com/SW/DRAGEN_v40/Content/SW/DRAGEN/GPipelineIntro_fDG.htm) (alignment) workflow |
+| wts_tumor_only | [DRAGEN RNA](https://support-docs.illumina.com/SW/DRAGEN_v40/Content/SW/DRAGEN/GPipelineIntro_fDG.htm) workflow |
+| wgs_tumor_normal | [DRAGEN Tumor/Normal](https://support-docs.illumina.com/SW/DRAGEN_v40/Content/SW/DRAGEN/GPipelineIntro_fDG.htm) workflow |
+| umccrise | [umccrise](https://github.com/umccr/umccrise) workflow |
+| rnasum | [RNAsum](https://github.com/umccr/RNAsum) workflow |
+| sash | [sash](https://github.com/scwatts/sash) workflow |
+| oncoanalyser | [oncoanalyser](https://github.com/nf-core/oncoanalyser) workflow |
 
 See which output files from these workflows are supported in [Supported
 Files](https://umccr.github.io/dracarys/articles/files.html).
@@ -123,7 +130,7 @@ export PATH="${dracarys_cli}:${PATH}"
 ```
 
     dracarys.R --version
-    dracarys.R 0.14.0
+    dracarys.R 0.16.0
 
     #-----------------------------------#
     dracarys.R --help
@@ -181,7 +188,9 @@ parquet, or both. To get just a list of supported files within the
 specified input directory, use the `-n (--dryrun)` option.
 
 <details>
+
 <summary>
+
 R
 </summary>
 
@@ -194,8 +203,11 @@ umccr_tidy(in_dir = in_dir, out_dir = out_dir, prefix = prefix)
 ```
 
 </details>
+
 <details>
+
 <summary>
+
 Mac/Linux
 </summary>
 
@@ -210,8 +222,11 @@ dracarys.R tidy \
 ```
 
 </details>
+
 <details>
+
 <summary>
+
 Docker
 </summary>
 

diff --git a/conda/env/yaml/pkgdown.yaml b/conda/env/yaml/pkgdown.yaml
@@ -6,6 +6,8 @@ dependencies:
   - r-dracarys
   - r-devtools
   - r-dt
+  - r-glue
+  - r-htmltools
   - r-kableextra
   - r-patchwork
   - r-pkgdown

diff --git a/pkgdown/_pkgdown.yml b/pkgdown/_pkgdown.yml
@@ -12,7 +12,7 @@ authors:
     href: https://github.com/victorskl
 navbar:
   structure:
-    left: [home, articles]
+    left: [home, articles, news]
     right: [reference, search, github]
   components:
     home:
@@ -27,6 +27,6 @@ navbar:
         href: articles/developers.html
       - text: Files
         href: articles/files.html
-
-news:
-  one_page: true
+    news:
+      text: NEWS
+      href: articles/NEWS.html
diff --git a/NEWS.md → vignettes/NEWS.Rmd b/NEWS.md → vignettes/NEWS.Rmd
@@ -1,34 +1,96 @@
-# dracarys 0.14.0 (2024-05-13)
+---
+title: "News"
+output: rmarkdown::html_document
+---
 
-[0.13.0 - 0.14.0 diff](https://github.com/umccr/dracarys/compare/v0.13.0...v0.14.0)
+```{r load_pkgs, echo=FALSE, message=FALSE, warning=FALSE}
+require(htmltools, include.only = c("a"))
+require(glue, include.only = "glue")
+```
 
-# dracarys 0.13.0 (2024-03-15)
 
-[0.12.0 - 0.13.0 diff](https://github.com/umccr/dracarys/compare/v0.12.0...v0.13.0)
+```{r echo=FALSE}
+repo <- "https://github.com/umccr/dracarys"
+vdiff <- function(new, old) {
+  stopifnot(utils::compareVersion(new, old) == 1)
+  htmltools::a(
+    href = glue::glue("{repo}/compare/v{old}...v{new}"),
+    glue::glue("v{new} - v{old} diff")
+  )
+}
 
-# dracarys 0.12.0 (2023-12-12)
+pr_or_issue <- function(n, type) {
+  stopifnot(is.numeric(n), n > 0, type %in% c("issue", "pr"))
+  type2 <- ifelse(type == "pr", "pull", "issue")
+  htmltools::a(
+    href = glue::glue("{repo}/{type2}/{n}"),
+    glue::glue("{type}{n}")
+  )
+}
 
-[0.11.0 - 0.12.0 diff](https://github.com/umccr/dracarys/compare/v0.11.0...v0.12.0)
+issue <- function(n) {
+  pr_or_issue(n, "issue")
+}
 
-# dracarys 0.11.0 (2023-08-22)
+pr <- function(n) {
+  pr_or_issue(n, "pr")
+}
+```
 
-[0.10.0 - 0.11.0 diff](https://github.com/umccr/dracarys/compare/v0.10.0...v0.11.0)
+## dracarys 0.16.0 (2024-10-08)
 
-# dracarys 0.10.0 (2023-06-22)
+Complete refactor of the dracarys R6 class system.
+We now have a Wf super class which is the base for `Wf_*` subclasses.
 
-[0.9.0 - 0.10.0 diff](https://github.com/umccr/dracarys/compare/v0.9.0...v0.10.0)
+- cttsov2: initial support (`r pr(135)`)
+- cttsov1: major refactor (`r pr(133)`)
+- umccrise: major refactor, summary report (`r pr(127)`)
+- switch to bump-my-version for bumping (`r pr(139)`)
+- Sash support (`r pr(129)`)
+  - add summary report
+- MultiQC: add Sash support (`r pr(137)`)
+- docker: use multi-stage build (`r pr(122)`)
+- BCL Convert: support 4.2.7 (`r pr(124)`)
+- refactor filesystem management
+  - better support for S3
 
-# dracarys 0.9.0 (2023-05-10)
+- `r vdiff("0.16.0", "0.15.0")`
 
-[0.8.0 - 0.9.0 diff](https://github.com/umccr/dracarys/compare/v0.8.0...v0.9.0)
+## dracarys 0.15.0 (2024-08-14)
 
-# dracarys 0.8.0 (2023-02-24)
+- `r vdiff("0.15.0", "0.14.0")`
 
-[0.7.0 - 0.8.0 diff](https://github.com/umccr/dracarys/compare/v0.7.0...v0.8.0)
+## dracarys 0.14.0 (2024-05-13)
 
-# dracarys 0.7.0 (2023-02-15)
+- `r vdiff("0.14.0", "0.13.0")`
 
-[0.6.0 - 0.7.0 diff](https://github.com/umccr/dracarys/compare/v0.6.0...v0.7.0)
+## dracarys 0.13.0 (2024-03-15)
+
+- `r vdiff("0.13.0", "0.12.0")`
+
+## dracarys 0.12.0 (2023-12-12)
+
+- `r vdiff("0.12.0", "0.11.0")`
+
+## dracarys 0.11.0 (2023-08-22)
+
+- `r vdiff("0.11.0", "0.10.0")`
+
+## dracarys 0.10.0 (2023-06-22)
+
+- `r vdiff("0.10.0", "0.9.0")`
+
+## dracarys 0.9.0 (2023-05-10)
+
+- `r vdiff("0.9.0", "0.8.0")`
+
+## dracarys 0.8.0 (2023-02-24)
+
+- `r vdiff("0.8.0", "0.7.0")`
+
+## dracarys 0.7.0 (2023-02-15)
+
+- `r vdiff("0.7.0", "0.6.0")`
 
 Mostly added use cases based on requests from the curation team related to
 umccrise (CHORD, HRDetect, QC summary), PCGR, and MultiQC.
@@ -52,9 +114,9 @@ umccrise (CHORD, HRDetect, QC summary), PCGR, and MultiQC.
   - GH Actions: use "miniforge-variant: Mambaforge"
     (see [this issue](https://github.com/conda-incubator/setup-miniconda/issues/274)).
 
-# dracarys 0.6.0 (2023-01-09)
+## dracarys 0.6.0 (2023-01-09)
 
-[0.5.0 - 0.6.0 diff](https://github.com/umccr/dracarys/compare/v0.5.0...v0.6.0)
+- `r vdiff("0.6.0", "0.5.0")`
 
 - :wrench: GH Actions:
   - replace `::set-output`.
@@ -86,37 +148,37 @@ umccrise (CHORD, HRDetect, QC summary), PCGR, and MultiQC.
   - 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 0.5.0 (2022-09-28)
 
-[0.4.0 - 0.5.0 diff](https://github.com/umccr/dracarys/compare/v0.4.0...v0.5.0)
+- `r vdiff("0.5.0", "0.4.0")`
 
 - MultiQC: update column mappings ([pr15](https://github.com/umccr/dracarys/pull/15), [pr16](https://github.com/umccr/dracarys/pull/16)).
   - move map to separate TSV
 - CLI: add option for output format (tsv, parquet, or both) ([pr18](https://github.com/umccr/dracarys/pull/18)).
 - new contributors: [@victorskl](https://github.com/victorskl)
 
-# dracarys 0.4.0 (2022-09-12)
+## dracarys 0.4.0 (2022-09-12)
 
-[0.3.0 - 0.4.0 diff](https://github.com/umccr/dracarys/compare/v0.3.0...v0.4.0)
+- `r vdiff("0.4.0", "0.3.0")`
 
 - :star: support for DRAGEN TSO500 ctdna output ([pr14](https://github.com/umccr/dracarys/pull/14)).
   - also add Quarto HTML report template
 
-# dracarys 0.3.0 (2022-08-28)
+## dracarys 0.3.0 (2022-08-28)
 
-[0.2.0 - 0.3.0 diff](https://github.com/umccr/dracarys/compare/v0.2.0...v0.3.0)
+- `r vdiff("0.3.0", "0.2.0")`
 
 - :star: MultiQC: support for DRAGEN ctdna output ([pr13](https://github.com/umccr/dracarys/pull/13)).
 
-# dracarys 0.2.0 (2022-07-23)
+## dracarys 0.2.0 (2022-07-23)
 
-[0.1.0 - 0.2.0 diff](https://github.com/umccr/dracarys/compare/v0.1.0...v0.2.0)
+- `r vdiff("0.2.0", "0.1.0")`
 
 - Add `MULTIQC_COLUMNS` tibble that maps the raw metric name to a cleaner name
   ([pr12](https://github.com/umccr/dracarys/pull/12)).
 - Support for more MultiQC JSONs (from bcbio-wts and bcbio-wgs).
 
-# dracarys 0.1.0 (2022-07-11)
+## dracarys 0.1.0 (2022-07-11)
 
 - Initial release of dracarys.
 - Support for [MultiQC](https://github.com/ewels/MultiQC) JSON tidying.