upgrade docs for 1.0

biocorecrg · Dec 3, 2024 · 6d1107d · 6d1107d
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diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -11,25 +11,26 @@ jobs:
   build:
     runs-on: ubuntu-22.04
     steps:
-    - id: deployment
-      uses: sphinx-notes/pages@v3
-      with:
-        publish: false
-    - uses: peaceiris/actions-gh-pages@v4
-      with:
-        github_token: ${{ secrets.GITHUB_TOKEN }}
-        destination_dir: ${{ github.ref_name }}
-        publish_dir: ${{ steps.deployment.outputs.artifact }}
     - uses: actions/checkout@v4
       with:
-        ref: ${{ github.event.repository.default_branch }}
+        ref: ${{ github.ref }}
+        path: ${{ github.ref_name }}
     - uses: actions/checkout@v4
       with:
         ref: gh-pages
         path: gh-pages
+    - name: Prepare Ruby and Jekyll
+      uses: ruby/setup-ruby@v1
+      with:
+        ruby-version: '3.3'
+    - name: Build deps and website
+      run: |
+        cd ${{ github.ref_name }}/docs/ \
+        && bundle install && bundle exec jekyll build
     - name: Copy file
       run: |
-        cp ./assets/docs/index.html ./gh-pages/
+        mkdir -p ./gh-pages/${{ github.ref_name }}/ \
+        && cp -pr ${{ github.ref_name }}/docs/_site/* ./gh-pages/${{ github.ref_name }}/
     - name: Deploy to GitHub Pages
       uses: peaceiris/actions-gh-pages@v4
       with:

diff --git a/docs/_config.yml b/docs/_config.yml
@@ -1,6 +1,7 @@
 title: Master of Pores
 description: Nextflow pipeline for analysis of Nanopore data from direct RNA sequencing.
-url: "https://biocorecrg.github.io/master_of_pores/" 
+url: "https://biocorecrg.github.io"
+baseurl: "/master_of_pores/MOP1.0"
 
 # Build settings
 markdown: kramdown

diff --git a/docs/index.md b/docs/index.md
@@ -14,7 +14,7 @@ navigation: 1
 
 <br/>
 
-# ![Direct RNA nanopore analysis pipeline](https://raw.githubusercontent.com/biocorecrg/master_of_pores/master/docs/logo_master.jpg) 
+# ![Direct RNA nanopore analysis pipeline](https://raw.githubusercontent.com/biocorecrg/master_of_pores/v1.0/docs/logo_master.jpg) 
 
 # Nanopore analysis pipeline
 Nextflow pipeline for analysis of Nanopore data from direct RNA sequencing. This is a joint project between [CRG bioinformatics core](https://biocore.crg.eu/) and [Epitranscriptomics and RNA Dynamics research group](https://www.crg.eu/en/programmes-groups/novoa-lab).  

diff --git a/docs/nanomod.md b/docs/nanomod.md
@@ -9,7 +9,7 @@ This module allows to predict the loci with RNA modifications starting from data
 
 ## Workflow
 
-<img src="https://raw.githubusercontent.com/biocorecrg/master_of_pores/master/docs/dag_mod_2.png" width="600" align="middle">
+<img src="https://raw.githubusercontent.com/biocorecrg/master_of_pores/v1.0/docs/dag_mod_2.png" width="600" align="middle">
 
 
 * **index_reference** index the reference file for Epinano

diff --git a/docs/nanopreprocess.md b/docs/nanopreprocess.md
@@ -11,7 +11,7 @@ This module takes as input the raw fast5 reads and produces a number of outputs
 
 ## Workflow
 
-<img src="https://raw.githubusercontent.com/biocorecrg/master_of_pores/master/docs/dag_graph3.png" width="600" align="middle">
+<img src="https://raw.githubusercontent.com/biocorecrg/master_of_pores/v1.0/docs/dag_graph3.png" width="600" align="middle">
 
 | Process name  | Description |
 | ------------- | ------------- |

diff --git a/docs/nanotail.md b/docs/nanotail.md
@@ -9,7 +9,7 @@ This module allows to estimates polyA sizes by using two different methods (nano
 
 # Workflow
 
-<img src="https://raw.githubusercontent.com/biocorecrg/master_of_pores/master/docs/dag_nanotail.png" width="600" align="middle">
+<img src="https://raw.githubusercontent.com/biocorecrg/master_of_pores/v1.0/docs/dag_nanotail.png" width="600" align="middle">
 
  1. **check_reference** It verifies whether the reference is zipped and eventually unzip it
  1. **tailfindr** it runs *tailfindr* tool in parallel.