From 86219a586bdadb82471007f5827f198d32eacb11 Mon Sep 17 00:00:00 2001
From: Edmund Miller <edmund.a.miller@protonmail.com>
Date: Tue, 24 Nov 2020 20:57:13 -0600
Subject: [PATCH] ci(trimgalore): Use pytest-workflow

---
 .github/workflows/software/trimgalore.yml | 22 ++++++++++++++--------
 1 file changed, 14 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/software/trimgalore.yml b/.github/workflows/software/trimgalore.yml
index 689a0fa0..16081569 100644
--- a/.github/workflows/software/trimgalore.yml
+++ b/.github/workflows/software/trimgalore.yml
@@ -17,14 +17,20 @@ jobs:
     env:
       NXF_ANSI_LOG: false
     steps:
+      - uses: actions/checkout@v2
 
-    - uses: actions/checkout@v2
+      - name: Install Nextflow
+        run: |
+          export NXF_VER="20.07.1"
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
 
-    - name: Install Nextflow
-      run: |
-        export NXF_VER="20.07.1"
-        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/trimgalore/test/ -profile docker
+      # Test the module
+      - run: pytest --tag trimgalore --symlink --wt 2