From b52ab454c71cca940485e2fe429bf60c8972a9f6 Mon Sep 17 00:00:00 2001
From: skchronicles <kuhnsa3@gmail.com>
Date: Wed, 16 Mar 2022 17:24:54 -0400
Subject: [PATCH] Adding ci workflows to build docs and run tests

---
 .github/workflows/docs.yml  | 18 ++++++++++++++++++
 .github/workflows/main.yaml | 30 ++++++++++++++++++++++++++++++
 2 files changed, 48 insertions(+)
 create mode 100644 .github/workflows/docs.yml
 create mode 100644 .github/workflows/main.yaml

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
new file mode 100644
index 0000000..f0c554b
--- /dev/null
+++ b/.github/workflows/docs.yml
@@ -0,0 +1,18 @@
+name: docs
+on:
+  workflow_dispatch:
+  push:
+    paths:
+      - 'docs/**'
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        with:
+          python-version: 3.9
+      - run: pip install --upgrade pip
+      - run: pip install -r docs/requirements.txt
+      - run: mkdocs gh-deploy --force
diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml
new file mode 100644
index 0000000..7d66e2a
--- /dev/null
+++ b/.github/workflows/main.yaml
@@ -0,0 +1,30 @@
+name: tests
+
+on:
+  push:
+    branches:
+      - master
+      - main
+  pull_request:
+    branches_ignore: []
+
+jobs:
+  Dry_Run_and_Lint:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - uses: docker://snakemake/snakemake:v5.24.2
+    - name: Dry Run with test data
+      run: |
+        docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \
+        /opt2/metavirs run --input \
+        /opt2/.tests/WT_S1.R1.fastq.gz /opt2/.tests/WT_S1.R2.fastq.gz \
+        /opt2/.tests/WT_S2_R1.fastq.gz /opt2/.tests/WT_S2_R2.fastq.gz \
+        /opt2/.tests/WT_S3_1.fastq.gz /opt2/.tests/WT_S3_2.fastq.gz \
+        /opt2/.tests/WT_S4_R1.001.fastq.gz /opt2/.tests/WT_S4_R2.001.fastq.gz \
+        --output /opt2/output --mode local --dry-run
+    - name: Lint Workflow
+      continue-on-error: true
+      run: |
+        docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 snakemake --lint -s /opt2/output/workflow/Snakefile -d /opt2/output || \
+        echo 'There may have been a few warnings or errors. Please read through the log to determine if its harmless.'