fix layout and links, no_render

systemPipeR · Apr 5, 2024 · 5791cb3 · 5791cb3
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diff --git a/blogdown/md5sum.txt b/blogdown/md5sum.txt
@@ -57,7 +57,7 @@
 "content/en/sp/spt/systemPipeTools.Rmd" "a264c32e1c6988991c662dd723bfbba6"
 "content/en/sp/SPT/systemPipeTools.Rmd" "cd15da1552273645e0df5d0b5a033a8b"
 "content/en/spr_wf/_index.Rmarkdown" "ac58ef0bfc62be3c929021c3171f1bfa"
-"content/en/spr_wf/installWF.Rmarkdown" "24ee302827ec5721b33b61347adb2873"
+"content/en/spr_wf/installWF.Rmarkdown" "04301542d939ef9073c16596df722855"
 "content/en/spr_wf/newWF.Rmarkdown" "19b8bdf42bb9e8a8b09eb47cb7a1d836"
 "content/en/spr/SPRinstall.Rmarkdown" "92f686d202914627265e24f9ac894633"
 "content/en/spr/systempiper_vignette/systemPipeR.Rmarkdown" "b8b11bf9f425f19e08f09f6194351c91"

diff --git a/config.toml b/config.toml
@@ -417,49 +417,11 @@ enable = false
     url = "/spr_wf"
     parent = "Workflows"
     weight = 1
-  [[menu.main]]
-    name = "Templates"
-    url = "/spr_wf/templates"
-    parent = "Workflows"
-    weight = 1
-    [[menu.main]]
-      name = "RNA-Seq"
-      url = "/spr_wf/templates/rnaseq"
-      parent = "Workflows"
-      weight = 2
-    [menu.main.params]
-      level = 2
-    [[menu.main]]
-      name = "VAR-Seq"
-      url = "/spr_wf/templates/varseq"
-      parent = "Workflows"
-      weight = 3
-    [menu.main.params]
-      level = 2
-    [[menu.main]]
-      name = "ChIP-Seq"
-      url = "/spr_wf/templates/chipseq"
-      parent = "Workflows"
-      weight = 4
-    [menu.main.params]
-      level = 2
-    [[menu.main]]
-      name = "RIBO-Seq"
-      url = "/spr_wf/templates/chipseq"
-      parent = "Workflows"
-      weight = 5
-    [menu.main.params]
-      level = 2
   [[menu.main]]
     name = "How to install Workflow"
     url = "/spr_wf/installwf/"
     parent = "Workflows"
     weight = 6
-  [[menu.main]]
-    name = "Rules to create Workflow"
-    url = "/spr_wf/newwf"
-    parent = "Workflows"
-    weight = 7
 ## Training
 [[menu.main]]
   name = "Outreach"

diff --git a/content/en/_index.html b/content/en/_index.html
@@ -19,7 +19,7 @@
   loadLogo("images/sp_org_links.svg")
 </script>
 
-<br> </br>
+<!-- <br> </br> -->
 <div class="mx-auto">
 	<a class="btn btn-lg btn-primary mr-3 mb-4" href="{{< relref "/about/" >}}">
 		Learn More <i class="fas fa-arrow-alt-circle-right ml-2"></i>

diff --git a/content/en/spr_wf/_index.md b/content/en/spr_wf/_index.md
@@ -39,23 +39,23 @@ systemPipeRdata::genWorkflowEnv("")
 
 
 
-| WorkFlow |  Description  | Version | GitHub | 
-|:-----------------------:|:-----------------------:|:----------------:|:--------------------:|
-| [SPchipseq](https://systempiper.github.io/SPchipseq/articles/SPchipseq.html) | ChIP-Seq Workflow Template | ![Stable](https://img.shields.io/badge/lifecycle-stable-green.svg) | <a href="https://github.com/systemPipeR/SPchipseq"> <img src="https://raw.githubusercontent.com/systemPipeR/systemPipeR/gh-pages/images/GitHub-Mark-120px-plus.png" align="center" style="width:20px;" /> | 
-| [SPriboseq](https://systempiper.github.io/SPriboseq/articles/SPriboseq.html) | RIBO-Seq Workflow Template | ![Stable](https://img.shields.io/badge/lifecycle-stable-green.svg) | <a href="https://github.com/systemPipeR/SPriboseq"> <img src="https://raw.githubusercontent.com/systemPipeR/systemPipeR/gh-pages/images/GitHub-Mark-120px-plus.png" align="center" style="width:20px;" /> | 
-| [SPrnaseq](https://systempiper.github.io/SPrnaseq/articles/SPrnaseq.html) | RNA-Seq Workflow Template | ![Stable](https://img.shields.io/badge/lifecycle-stable-green.svg) | <a href="https://github.com/systemPipeR/SPrnaseq"> <img src="https://raw.githubusercontent.com/systemPipeR/systemPipeR/gh-pages/images/GitHub-Mark-120px-plus.png" align="center" style="width:20px;" /> | 
-| [SPvarseq](https://systempiper.github.io/SPvarseq/articles/SPvarseq.html) | VAR-Seq Workflow Template | ![Stable](https://img.shields.io/badge/lifecycle-stable-green.svg) | <a href="https://github.com/systemPipeR/SPvarseq"> <img src="https://raw.githubusercontent.com/systemPipeR/systemPipeR/gh-pages/images/GitHub-Mark-120px-plus.png" align="center" style="width:20px;" /> | 
-| [SPscrnaseq](https://github.com/systemPipeR/SPscrnaseq) | Single-Cell RNA-Seq Workflow Template | ![Stable](https://img.shields.io/badge/lifecycle-stable-green.svg) | <a href="https://github.com/systemPipeR/SPscrnaseq"> <img src="https://raw.githubusercontent.com/systemPipeR/systemPipeR/gh-pages/images/GitHub-Mark-120px-plus.png" align="center" style="width:20px;" /> |
-| [SPblast](https://github.com/systemPipeR/SPblast) | BLAST Workflow Template | ![Stable](https://img.shields.io/badge/lifecycle-stable-green.svg) | <a href="https://github.com/systemPipeR/SPblast"> <img src="https://raw.githubusercontent.com/systemPipeR/systemPipeR/gh-pages/images/GitHub-Mark-120px-plus.png" align="center" style="width:20px;" /> | 
-| [SPcheminfo](https://github.com/systemPipeR/SPcheminfo) | Basic drug discovery workflow | ![Stable](https://img.shields.io/badge/lifecycle-stable-green.svg) | <a href="https://github.com/systemPipeR/SPcheminfo"> <img src="https://raw.githubusercontent.com/systemPipeR/systemPipeR/gh-pages/images/GitHub-Mark-120px-plus.png" align="center" style="width:20px;" /> | 
-| [SPmethylseq](https://github.com/systemPipeR/SPmethylseq) | Methyl-Seq Workflow Template | ![Experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg) | <a href="https://github.com/systemPipeR/SPmethylseq"> <img src="https://raw.githubusercontent.com/systemPipeR/systemPipeR/gh-pages/images/GitHub-Mark-120px-plus.png" align="center" style="width:20px;" /> | 
-| [SPdenovo](https://github.com/systemPipeR/SPdenovo) | De novo transcriptome assembly Workflow Template | ![Experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg) | <a href="https://github.com/systemPipeR/SPdenovo"> <img src="https://raw.githubusercontent.com/systemPipeR/systemPipeR/gh-pages/images/GitHub-Mark-120px-plus.png" align="center" style="width:20px;" /> | 
-| [SPclipseq](https://github.com/systemPipeR/SPclipseq) | CLIP-Seq Workflow Template | ![Experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg) | <a href="https://github.com/systemPipeR/SPclipseq"> <img src="https://raw.githubusercontent.com/systemPipeR/systemPipeR/gh-pages/images/GitHub-Mark-120px-plus.png" align="center" style="width:20px;" /> | 
-| [SPmetatrans](https://github.com/systemPipeR/SPmetatrans) | Metatranscriptomic Sequencing Workflow Template | ![Experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg) | <a href="https://github.com/systemPipeR/SPmetatrans"> <img src="https://raw.githubusercontent.com/systemPipeR/systemPipeR/gh-pages/images/GitHub-Mark-120px-plus.png" align="center" style="width:20px;" /> | 
-| [SPatacseq](https://github.com/systemPipeR/SPatacseq) | ATAC-Seq Workflow Template | ![Experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg) | <a href="https://github.com/systemPipeR/SPatacseq"> <img src="https://raw.githubusercontent.com/systemPipeR/systemPipeR/gh-pages/images/GitHub-Mark-120px-plus.png" align="center" style="width:20px;" /> | 
-| [SPpolyriboseq](https://github.com/systemPipeR/SPpolyriboseq) | Polyribosomal RNA-Seq Workflow Template | ![Experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg) | <a href="https://github.com/systemPipeR/SPpolyriboseq"> <img src="https://raw.githubusercontent.com/systemPipeR/systemPipeR/gh-pages/images/GitHub-Mark-120px-plus.png" align="center" style="width:20px;" /> | 
-| [SPhic](https://github.com/systemPipeR/SPhic) | Hi-C Workflow Template | ![Experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg) | <a href="https://github.com/systemPipeR/SPhic"> <img src="https://raw.githubusercontent.com/systemPipeR/systemPipeR/gh-pages/images/GitHub-Mark-120px-plus.png" align="center" style="width:20px;" /> | 
-| [SPmirnaseq](https://github.com/systemPipeR/SPmirnaseq) | MicroRNA-Seq Workflow Template | ![Experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg) | <a href="https://github.com/systemPipeR/SPmirnaseq"> <img src="https://raw.githubusercontent.com/systemPipeR/systemPipeR/gh-pages/images/GitHub-Mark-120px-plus.png" align="center" style="width:20px;" /> | 
+|   WorkFlow    |                   Description                    |                                     Status                                      |                                                                                                              Link                                                                                                              |
+| :-----------: | :----------------------------------------------: | :-----------------------------------------------------------------------------: | :----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: |
+|   SPchipseq   |            ChIP-Seq Workflow Template            |       ![Stable](https://img.shields.io/badge/lifecycle-stable-green.svg)        | <a href="https://www.bioconductor.org/packages/release/data/experiment/vignettes/systemPipeRdata/inst/doc/systemPipeChIPseq.html" target="_blank"> <img src="bioconductor_logo_rgb.png" align="center" style="width:100px;" /> |
+|   SPriboseq   |            RIBO-Seq Workflow Template            |       ![Stable](https://img.shields.io/badge/lifecycle-stable-green.svg)        | <a href="https://www.bioconductor.org/packages/release/data/experiment/vignettes/systemPipeRdata/inst/doc/systemPipeRIBOseq.html" target="_blank"> <img src="bioconductor_logo_rgb.png" align="center" style="width:100px;" /> |
+|   SPrnaseq    |            RNA-Seq Workflow Template             |       ![Stable](https://img.shields.io/badge/lifecycle-stable-green.svg)        | <a href="https://www.bioconductor.org/packages/release/data/experiment/vignettes/systemPipeRdata/inst/doc/systemPipeRNAseq.html" target="_blank"> <img src="bioconductor_logo_rgb.png" align="center" style="width:100px;" />  |
+|   SPvarseq    |            VAR-Seq Workflow Template             |       ![Stable](https://img.shields.io/badge/lifecycle-stable-green.svg)        | <a href="https://www.bioconductor.org/packages/release/data/experiment/vignettes/systemPipeRdata/inst/doc/systemPipeVARseq.html" target="_blank"> <img src="bioconductor_logo_rgb.png" align="center" style="width:100px;" />  |
+|  SPscrnaseq   |      Single-Cell RNA-Seq Workflow Template       |       ![Stable](https://img.shields.io/badge/lifecycle-stable-green.svg)        |      <a href="https://www.bioconductor.org/packages/release/data/experiment/vignettes/systemPipeRdata/inst/doc/SPscrna.html" target="_blank"> <img src="bioconductor_logo_rgb.png" align="center" style="width:100px;" />      |
+|    SPblast    |             BLAST Workflow Template              |       ![Stable](https://img.shields.io/badge/lifecycle-stable-green.svg)        |      <a href="https://www.bioconductor.org/packages/release/data/experiment/vignettes/systemPipeRdata/inst/doc/SPblast.html" target="_blank"> <img src="bioconductor_logo_rgb.png" align="center" style="width:100px;" />      |
+|  SPcheminfo   |          Basic drug discovery workflow           |       ![Stable](https://img.shields.io/badge/lifecycle-stable-green.svg)        |    <a href="https://www.bioconductor.org/packages/release/data/experiment/vignettes/systemPipeRdata/inst/doc/SPcheminfo.html" target="_blank"> <img src="bioconductor_logo_rgb.png" align="center" style="width:100px;" />     |
+|  SPmethylseq  |           Methyl-Seq Workflow Template           | ![Experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg) |  <a href="https://github.com/systemPipeR/SPmethylseq" target="_blank"> <img src="https://raw.githubusercontent.com/systemPipeR/systemPipeR/gh-pages/images/GitHub-Mark-120px-plus.png" align="center" style="width:20px;" />   |
+|   SPdenovo    | De novo transcriptome assembly Workflow Template | ![Experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg) |    <a href="https://github.com/systemPipeR/SPdenovo" target="_blank"> <img src="https://raw.githubusercontent.com/systemPipeR/systemPipeR/gh-pages/images/GitHub-Mark-120px-plus.png" align="center" style="width:20px;" />    |
+|   SPclipseq   |            CLIP-Seq Workflow Template            | ![Experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg) |   <a href="https://github.com/systemPipeR/SPclipseq" target="_blank"> <img src="https://raw.githubusercontent.com/systemPipeR/systemPipeR/gh-pages/images/GitHub-Mark-120px-plus.png" align="center" style="width:20px;" />    |
+|  SPmetatrans  | Metatranscriptomic Sequencing Workflow Template  | ![Experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg) |  <a href="https://github.com/systemPipeR/SPmetatrans" target="_blank"> <img src="https://raw.githubusercontent.com/systemPipeR/systemPipeR/gh-pages/images/GitHub-Mark-120px-plus.png" align="center" style="width:20px;" />   |
+|   SPatacseq   |            ATAC-Seq Workflow Template            | ![Experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg) |   <a href="https://github.com/systemPipeR/SPatacseq" target="_blank"> <img src="https://raw.githubusercontent.com/systemPipeR/systemPipeR/gh-pages/images/GitHub-Mark-120px-plus.png" align="center" style="width:20px;" />    |
+| SPpolyriboseq |     Polyribosomal RNA-Seq Workflow Template      | ![Experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg) | <a href="https://github.com/systemPipeR/SPpolyriboseq" target="_blank"> <img src="https://raw.githubusercontent.com/systemPipeR/systemPipeR/gh-pages/images/GitHub-Mark-120px-plus.png" align="center" style="width:20px;" />  |
+|     SPhic     |              Hi-C Workflow Template              | ![Experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg) |     <a href="https://github.com/systemPipeR/SPhic" target="_blank"> <img src="https://raw.githubusercontent.com/systemPipeR/systemPipeR/gh-pages/images/GitHub-Mark-120px-plus.png" align="center" style="width:20px;" />      |
+|  SPmirnaseq   |          MicroRNA-Seq Workflow Template          | ![Experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg) |   <a href="https://github.com/systemPipeR/SPmirnaseq" target="_blank"> <img src="https://raw.githubusercontent.com/systemPipeR/systemPipeR/gh-pages/images/GitHub-Mark-120px-plus.png" align="center" style="width:20px;" />   |
 
 
 

diff --git a/content/en/spr_wf/bioconductor_logo_rgb.png b/content/en/spr_wf/bioconductor_logo_rgb.png
diff --git a/content/en/spr_wf/installWF.Rmarkdown b/content/en/spr_wf/installWF.Rmarkdown
@@ -23,7 +23,7 @@ suppressPackageStartupMessages({
 })
 ```
 
-## Starting with pre-configured workflow templates
+## Starting with pre-configured stable workflow templates
 
 To test workflows quickly or design new ones from existing templates, users can
 generate with a single command workflow instances fully populated with sample data 
@@ -53,26 +53,26 @@ A collection of workflow templates are available, and it is possible to browse t
 current availability, as follows:
 
 ```{r eval=TRUE, tidy=FALSE}
-availableWF(github = TRUE)
+availableWF()
 ```
 
-This function returns the list of workflow templates available within the package 
-and [systemPipeR Project Organization](https://github.com/systemPipeR) on GitHub. Each one 
-listed template can be created as described above. 
 
-The workflow template choose from Github will be installed as an R package, and 
-also it creates an environment with all the settings and files to run the demo analysis.
+In addition, one can check experimental workflows available in the Github 
+Organization [systemPipeR](https://github.com/systemPipeR) as follows:
 
-```{r eval=FALSE, tidy=FALSE}
-genWorkenvir(workflow="systemPipeR/SPrnaseq", mydirname="NULL")
-setwd("systemPipeVARseq")
+```{r eval=TRUE, tidy=FALSE}
+availableWF(github = TRUE)
 ```
 
-Besides, it is possible to choose different versions of the workflow template, 
-defined through other branches on the GitHub Repository. By default, the _`master`_ 
-branch is selected, however, it is possible to define a different branch with the _`ref`_ argument. 
+Installation of experimental workflows can done by `git clone` the repository.
+```bash
+git clone <URL FROM THE TABLE ABOVE>
+cd <REPO_NAME>
+```
 
+After the installation, start the SPR project as others.
 ```{r eval=FALSE, tidy=FALSE}
-genWorkenvir(workflow="systemPipeR/SPrnaseq", ref = "singleMachine")
-setwd("systemPipeRNAseq")
+library(systemPipeR)
+sal <- SPRproject()
+sal <- importWF(sal, file_path = "workflow_name.Rmd")
 ```