manually Add Vignette info from GalaxyCLI

Author: phoman14

.gitignore

@@ -1,8 +1,10 @@
-# For SCWorkflow dev
+.DS_Store
 .nfs*
-*.png
+#*.png
 Rcheck.txt
-*.pdf
+#*.pdf
 tests/testthat/otherData/
 .Rproj.user
-*.txt
+
+inst/doc
+inst/extdata/*

README.md

@@ -1,11 +1,28 @@
-# SCWorkflow
-Workflow Package for Analysis of Single Cell Data
+
+# **SCWorkflow**
+R package for Single Cell analysis
+
+[![Gitflow Action for R Package Development](https://github.com/NIDAP-Community/SCWorkflow/actions/workflows/gitflow-R-action.yml/badge.svg)](https://github.com/NIDAP-Community/SCWorkflow/actions/workflows/gitflow-R-action.yml) 
+[![Version](https://img.shields.io/github/v/release/nidap-community/scworkflow)](https://github.com/NIDAP-Community/SCWorkflow/releases/latest)
+[![Docker Image Version](https://img.shields.io/docker/v/nciccbr/scworkflow?label=docker)](https://hub.docker.com/r/nciccbr/scworkflow)
+
+
+[![](https://raw.githubusercontent.com/NIDAP-Community/SCWorkflow/GalaxyCLI/vignettes/SCWorkflow.png)](https://lucid.app/lucidchart/c7b852ad-72dc-4821-90d5-e45bed0c4199/view)
+
+
+<center>**Click Figure to Navigate Workflow**.</center>
+
+<br>
+<br>
 
 The Single Cell Workflow streamlines the analysis of multimodal Single Cell RNA-Seq data produced from 10x Genomics.  It can be run in a docker container, and for biologists, in user-friendly web-based interactive notebooks (NIDAP, Palantir Foundry). Much of it is based on the Seurat workflow in Bioconductor, and supports CITE-Seq data.  It incorporates a cell identification step (ModScore) that utilizes module scores obtained from Seurat and also includes Harmony for batch correction.
 
-Some of the steps in the workflow:
+<br>
+
+For further documentation see our detailed [Docs Website](https://nidap-community.github.io/SCWorkflow/)
 
-<img src="scWorkflow_image.png">
+<br>
+<br>
 
 
 Future Developments include addition of support for multiomics (TCR-Seq, ATAC-Seq) single cell data and integration with spatial transcriptomics data.

_pkgdown.yml

@@ -0,0 +1,70 @@
+url: https://nidap-community.github.io/SCWorkflow/
+template:
+  bootstrap: 5
+  bslib:
+    bootswatch: yeti
+    primary: "#296b7f"
+    secondary: "#7cc349"
+    base_font: {google: "Roboto"}
+    heading_font: {google: "Roboto"}
+    code_font: {google: "Roboto Mono"}
+    border-radius: 0
+    btn-border-radius: 3px
+    grid-gutter-width: 3rem
+    pkgdown-nav-height: 78px
+
+navbar:
+  structure:
+    left: [getting-started, articles, reference]
+    right: [search, github]
+  components:
+    getting-started:
+      text: Getting Started
+      href: articles/SCWorkflow-Usage.html
+  
+
+footer:
+  structure:
+    left: [developed_by]
+
+development:
+  mode: auto
+authors:
+  Kelly Sovacool:
+    href: "https://github.com/kelly-sovacool"
+  Philip Homan:
+    href: "https://github.com/phoman14"
+  Vishal Koparde:
+    href: "https://github.com/kopardev"
+  CCR Collaborative Bioinformatics Resource:
+    href: "https://github.com/CCBR"
+  footer:
+    roles: [cph, fnd]
+    text: "Created by the"
+
+articles:
+- title: Vignettes
+  navbar: ~
+  contents:
+  - SCWorkflow-Overview
+  - SCWorkflow-Annotations
+  - SCWorkflow-DEG
+  - SCWorkflow-Visualizations
+  - SCWorkflow-SubsetReclust
+ 
+- title: Developer
+  desc: Developer documentation
+  contents:
+  - SCWorkflow-Usage  
+  - cli
+  - README
+
+home:
+  sidebar:
+    structure: [links,citation, authors, license,  dev]
+  links:
+  - text: Browse code on GitHub
+    href: https://github.com/NIDAP-Community/SCWorkflow
+  strip_header: true
+
+

vignettes/.gitignore

@@ -0,0 +1,3 @@
+#*.html
+*.R
+*.Rds