diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 4e1e663..a62bdde 100644 --- 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 index da3939e..c7eba37 100644 --- 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 index 9d56ae4..b1aacbe 100644 --- a/docs/index.md +++ b/docs/index.md @@ -14,7 +14,7 @@ navigation: 1
-# ![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 index 7e1a126..fa82401 100644 --- 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 - + * **index_reference** index the reference file for Epinano diff --git a/docs/nanopreprocess.md b/docs/nanopreprocess.md index c310540..f90ce9d 100644 --- 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 - + | Process name | Description | | ------------- | ------------- | diff --git a/docs/nanotail.md b/docs/nanotail.md index d49f204..61fa708 100644 --- 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 - + 1. **check_reference** It verifies whether the reference is zipped and eventually unzip it 1. **tailfindr** it runs *tailfindr* tool in parallel.