From f1483acfb02af4aa90ccf9d538b5283f36c0039b Mon Sep 17 00:00:00 2001 From: Maxime Garcia Date: Fri, 11 Oct 2019 15:38:50 +0200 Subject: [PATCH] Worfklow (#45) * Add workflow figure * Include workflow figure in readme * Update CHANGELOG --- .github/markdownlint.yml | 3 +- CHANGELOG.md | 1 + README.md | 7 +- docs/images/sarek_workflow.png | Bin 0 -> 50856 bytes docs/images/sarek_workflow.svg | 3675 ++++++++++++++++++++++++++++++++ 5 files changed, 3683 insertions(+), 3 deletions(-) create mode 100644 docs/images/sarek_workflow.png create mode 100644 docs/images/sarek_workflow.svg diff --git a/.github/markdownlint.yml b/.github/markdownlint.yml index 8f97a170e..9a0066d6f 100644 --- a/.github/markdownlint.yml +++ b/.github/markdownlint.yml @@ -9,4 +9,5 @@ no-duplicate-header: siblings_only: true no-inline-html: allowed_elements: - - img \ No newline at end of file + - img + - p \ No newline at end of file diff --git a/CHANGELOG.md b/CHANGELOG.md index 436428b1c..e39a31024 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -17,6 +17,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. - [#41](https://github.com/nf-core/sarek/pull/41) - Update `qualimap` from `2.2.2b` to `2.2.2c` - [#41](https://github.com/nf-core/sarek/pull/41) - Update `tiddit` from `2.7.1` to `2.8.0` - [#41](https://github.com/nf-core/sarek/pull/41) - Update `vcfanno` from `0.3.1` to `0.3.2` +- [#45](https://github.com/nf-core/sarek/pull/45) - Include Workflow figure in `README.md` ### `Fixed` diff --git a/README.md b/README.md index 0de61ba17..d689576f1 100644 --- a/README.md +++ b/README.md @@ -15,10 +15,9 @@ [![Join us on Slack](https://img.shields.io/badge/slack-nfcore/sarek-blue.svg)](https://nfcore.slack.com/messages/CGFUX04HZ/) - ## Introduction - + Previously known as the Cancer Analysis Workflow (CAW), Sarek is a workflow designed to run analyses on whole genome or targeted sequencing data from regular samples or tumour / normal pairs and could include additional relapses. @@ -29,6 +28,10 @@ across multiple compute infrastructures in a very portable manner. Software dependencies are handled using [Conda](https://conda.io/), [Docker](https://www.docker.com) or [Singularity](https://www.sylabs.io/singularity/) - environment/container technologies that provide excellent reproducibility and ease of use. Thus making installation trivial and results highly reproducible. +

+ +

+ It's listed on the [Elixir - Tools and Data Services Registry](https://bio.tools/Sarek), [Dockstore](https://dockstore.org/workflows/github.com/nf-core/sarek) and [omicX - Bioinformatics tools](https://omictools.com/sarek-tool). ## Documentation diff --git a/docs/images/sarek_workflow.png b/docs/images/sarek_workflow.png new file mode 100644 index 0000000000000000000000000000000000000000..f7f019de0cd8cec8f39e17cfdc182eefb16a9160 GIT binary patch literal 50856 zcmb??Wl$YWu=c?{K!UpjcX!v|?he7--GaLYcL*f7y9WvG?(TMQ{r3H;?!WuPj1JBg zSr`0xAP@=Yo4AOYXZBf+ho_qQ^P`XlWhb^MLMQa^;NW}`#E8H^7&J94S9Ivbd;Mvc z(Pt=q%}{-$vKBQM@vqcn)G8PWjGg4_)}N)Bk_BD-1G0}Zz9tWT-Sf@0$lc5JxoAC{ z=mc*(bX@vu6cs2@6SS0@X2oSjHjA_)U5S`FtT$0TS7`-J&-#^*AMvk4gckBnm)ouC zawK!Y$-juRv0(jWAskZ*9szrLwLu|DP+U=?LE;3322wkS@e*F1%JVl}|BXaCD7>UC z2#AsqMxaA=o_$b+#YTKS4#E0?)>rIwdo~p+9Q{ zH*yzSrn<6agW7nX)T9evXunaep(DTRRh$o*uAUesXQ1N&Jw&@f zA)%fhk_u;8YrQ5Q8UeH9Zx(ff4jaSr5rDCzk~qjN!k+mJ)DV$_rh}8esK2Jmlw&n3 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Strelka2• Manta• ASCAT, Control-FREECsnpEff, VEPsnpEff, VEPAnnotation + + +Reports + + +2.5 \ No newline at end of file