From 6d857a2584dd32bd57b75aa332fa52a73af15994 Mon Sep 17 00:00:00 2001
From: Edmund Miller <edmund.a.miller@protonmail.com>
Date: Mon, 16 Nov 2020 09:37:22 -0600
Subject: [PATCH] ci(fastqc): Run pytest-workflow instead of workflow

This will check for the actual output files and their contents not just
whether the module runs or not.
---
 .github/workflows/fastqc.yml | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/fastqc.yml b/.github/workflows/fastqc.yml
index 45c2fbe4..352c7bb3 100644
--- a/.github/workflows/fastqc.yml
+++ b/.github/workflows/fastqc.yml
@@ -26,5 +26,12 @@ jobs:
         wget -qO- get.nextflow.io | bash
         sudo mv nextflow /usr/local/bin/
 
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: "3.x"
+    - name: Install dependencies
+      run: python -m pip install --upgrade pip pytest-workflow
+
     # Test the module
-    - run: nextflow run ./software/fastqc/test/ -profile docker
+    - run: pytest --tag fastqc --symlink