From 7bcecd13635dab6d24df4a66bbc15e6d58413443 Mon Sep 17 00:00:00 2001
From: Luca Cozzuto <lucacozzuto@gmail.com>
Date: Mon, 9 Sep 2024 19:53:29 +0200
Subject: [PATCH] adding workflows

---
 .github/workflows/build.yml | 58 +++++++++++++++++++++++++++++++++++++
 .github/workflows/docs.yml  | 24 +++++++++++++++
 2 files changed, 82 insertions(+)
 create mode 100644 .github/workflows/build.yml
 create mode 100644 .github/workflows/docs.yml

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
new file mode 100644
index 0000000..5a99934
--- /dev/null
+++ b/.github/workflows/build.yml
@@ -0,0 +1,58 @@
+name: mop3-CI
+# When this workflow is triggered
+on: 
+  push:
+    paths-ignore:
+      - 'docs/**'
+  pull_request:
+    paths-ignore:
+      - 'docs/**'
+
+jobs:
+  build:
+    name: mop3 ci
+    # This job runs on Linux
+    runs-on: ubuntu-20.04
+    timeout-minutes: 90
+    strategy:
+      fail-fast: false
+      matrix:
+        java_version: [11]
+
+    steps:
+      - name: Delete huge unnecessary tools folder
+        uses: jlumbroso/free-disk-space@main
+        with:
+         tool-cache: true
+        
+      - name: Environment
+        run: env | sort
+
+      - name: Checkout
+        uses: actions/checkout@v3
+        with:
+         token: ${{ github.token }}
+         repository: biocorecrg/master_of_pores
+         fetch-depth: 1
+         submodules: true
+
+      - name: Setup Java
+        uses: actions/setup-java@v2
+        with:
+         java-version: ${{ matrix.java_version }}
+         distribution: 'adopt'
+         architecture: x64
+        
+      - name: MOP3
+        run: |
+          curl -fsSL get.nextflow.io | bash
+          bash INSTALL.sh
+          cd mop_preprocess
+          ../nextflow run mop_preprocess.nf -params-file params.f5.yaml -with-docker -profile ci
+          cd ../mop_mod
+          ../nextflow run mop_mod.nf -params-file params.yaml -with-docker -profile ci
+          cd ../mop_tail
+           ../nextflow run mop_tail.nf -with-docker  -params-file params.yaml -profile ci
+
+        env:
+          NXF_ANSI_LOG: false
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
new file mode 100644
index 0000000..83fd1f0
--- /dev/null
+++ b/.github/workflows/docs.yml
@@ -0,0 +1,24 @@
+on: 
+  push:
+    paths:
+      - 'docs/**'
+  pull_request:
+    paths:
+      - 'docs/**'
+jobs:
+  build:
+    runs-on: ubuntu-20.04
+    steps:
+    - uses: actions/setup-python@v2
+    - uses: actions/checkout@master
+      with:
+        fetch-depth: 0 # otherwise, you will failed to push refs to dest repo
+    - name: Build and Commit
+      uses: sphinx-notes/pages@v2
+      with:
+        requirements_path: "docs/requirements.txt"
+    - name: Push changes
+      uses: ad-m/github-push-action@master
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        branch: gh-pages