From 331fe893ced6a1541ac3deea42c3334a578f7080 Mon Sep 17 00:00:00 2001 From: pdiakumis Date: Tue, 8 Oct 2024 11:47:09 +1100 Subject: [PATCH 1/2] update NEWS --- NEWS.md | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/NEWS.md b/NEWS.md index a144470..fcd845f 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,11 @@ +# dracarys 0.16.0 (2024-10-08) + +[0.15.0 - 0.16.0 diff](https://github.com/umccr/dracarys/compare/v0.15.0...v0.16.0) + +# dracarys 0.15.0 (2024-08-14) + +[0.14.0 - 0.15.0 diff](https://github.com/umccr/dracarys/compare/v0.14.0...v0.15.0) + # dracarys 0.14.0 (2024-05-13) [0.13.0 - 0.14.0 diff](https://github.com/umccr/dracarys/compare/v0.13.0...v0.14.0) From 1871b8b77446b32b7adba6f46a3d61ca0ff4c3d4 Mon Sep 17 00:00:00 2001 From: pdiakumis Date: Tue, 8 Oct 2024 15:47:16 +1100 Subject: [PATCH 2/2] update NEWS --- .Rbuildignore | 2 +- README.Rmd | 6 +- README.md | 59 ++++++++++------- conda/env/yaml/pkgdown.yaml | 2 + pkgdown/_pkgdown.yml | 8 +-- NEWS.md => vignettes/NEWS.Rmd | 116 +++++++++++++++++++++++++--------- 6 files changed, 131 insertions(+), 62 deletions(-) rename NEWS.md => vignettes/NEWS.Rmd (60%) diff --git a/.Rbuildignore b/.Rbuildignore index c5136c8..fcacee5 100644 --- 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 index 00476a7..e29b06a 100644 --- a/README.Rmd +++ b/README.Rmd @@ -36,15 +36,13 @@ require(dracarys) ## πŸ† 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]: - ## πŸ• Installation
@@ -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 index d712e46..21a5fd2 100644 --- a/README.md +++ b/README.md @@ -1,11 +1,11 @@ - [πŸ”₯ dracarys - UMCCR Workflow - Tidying](#-dracarys---umccr-workflow-tidying) - - [πŸ† Aim](#-aim) - - [πŸ• Installation](#-installation) - - [✨ Supported Workflows](#-supported-workflows) - - [πŸŒ€ CLI](#-cli) - - [πŸš• Running](#-running) + Tidying](#fire-dracarys---umccr-workflow-tidying) + - [πŸ† Aim](#trophy-aim) + - [πŸ• Installation](#pizza-installation) + - [✨ Supported Workflows](#sparkles-supported-workflows) + - [πŸŒ€ CLI](#cyclone-cli) + - [πŸš• Running](#taxi-running) @@ -22,9 +22,7 @@ install](https://anaconda.org/umccr/r-dracarys/badges/latest_release_date.svg)]( ## πŸ† 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 β€˜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. ## πŸ• Installation
+ + R @@ -43,8 +43,11 @@ remotes::install_github("umccr/dracarys@vX.X.X") # for vX.X.X Release/Tag ```
+
+ + Conda @@ -72,8 +75,11 @@ conda activate dracarys_env ```
+
+ + Docker @@ -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.
+ + R @@ -194,8 +203,11 @@ umccr_tidy(in_dir = in_dir, out_dir = out_dir, prefix = prefix) ```
+
+ + Mac/Linux @@ -210,8 +222,11 @@ dracarys.R tidy \ ```
+
+ + Docker diff --git a/conda/env/yaml/pkgdown.yaml b/conda/env/yaml/pkgdown.yaml index 79c706c..7d9aaa5 100644 --- 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 index 275ae6b..f535a7a 100644 --- 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 b/vignettes/NEWS.Rmd similarity index 60% rename from NEWS.md rename to vignettes/NEWS.Rmd index fcd845f..64e4cf7 100644 --- a/NEWS.md +++ b/vignettes/NEWS.Rmd @@ -1,42 +1,96 @@ -# dracarys 0.16.0 (2024-10-08) +--- +title: "News" +output: rmarkdown::html_document +--- -[0.15.0 - 0.16.0 diff](https://github.com/umccr/dracarys/compare/v0.15.0...v0.16.0) +```{r load_pkgs, echo=FALSE, message=FALSE, warning=FALSE} +require(htmltools, include.only = c("a")) +require(glue, include.only = "glue") +``` -# dracarys 0.15.0 (2024-08-14) -[0.14.0 - 0.15.0 diff](https://github.com/umccr/dracarys/compare/v0.14.0...v0.15.0) +```{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 0.14.0 (2024-05-13) +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}") + ) +} -[0.13.0 - 0.14.0 diff](https://github.com/umccr/dracarys/compare/v0.13.0...v0.14.0) +issue <- function(n) { + pr_or_issue(n, "issue") +} -# dracarys 0.13.0 (2024-03-15) +pr <- function(n) { + pr_or_issue(n, "pr") +} +``` -[0.12.0 - 0.13.0 diff](https://github.com/umccr/dracarys/compare/v0.12.0...v0.13.0) +## dracarys 0.16.0 (2024-10-08) -# dracarys 0.12.0 (2023-12-12) +Complete refactor of the dracarys R6 class system. +We now have a Wf super class which is the base for `Wf_*` subclasses. -[0.11.0 - 0.12.0 diff](https://github.com/umccr/dracarys/compare/v0.11.0...v0.12.0) +- 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 0.11.0 (2023-08-22) +- `r vdiff("0.16.0", "0.15.0")` -[0.10.0 - 0.11.0 diff](https://github.com/umccr/dracarys/compare/v0.10.0...v0.11.0) +## dracarys 0.15.0 (2024-08-14) -# dracarys 0.10.0 (2023-06-22) +- `r vdiff("0.15.0", "0.14.0")` -[0.9.0 - 0.10.0 diff](https://github.com/umccr/dracarys/compare/v0.9.0...v0.10.0) +## dracarys 0.14.0 (2024-05-13) -# dracarys 0.9.0 (2023-05-10) +- `r vdiff("0.14.0", "0.13.0")` -[0.8.0 - 0.9.0 diff](https://github.com/umccr/dracarys/compare/v0.8.0...v0.9.0) +## dracarys 0.13.0 (2024-03-15) -# dracarys 0.8.0 (2023-02-24) +- `r vdiff("0.13.0", "0.12.0")` -[0.7.0 - 0.8.0 diff](https://github.com/umccr/dracarys/compare/v0.7.0...v0.8.0) +## dracarys 0.12.0 (2023-12-12) -# dracarys 0.7.0 (2023-02-15) +- `r vdiff("0.12.0", "0.11.0")` -[0.6.0 - 0.7.0 diff](https://github.com/umccr/dracarys/compare/v0.6.0...v0.7.0) +## 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. @@ -60,9 +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`. @@ -94,37 +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.