From d91cd73e5236e0cf085355cea4fe8d038b4898cd Mon Sep 17 00:00:00 2001
From: kevinmenden <kevin.menden@t-online.de>
Date: Fri, 29 Jan 2021 09:41:24 +0100
Subject: [PATCH] added test workflow

---
 .github/workflows/cutadapt.yml   | 40 ++++++++++++++++++++++++++++++++
 tests/software/cutadapt/test.yml |  5 ----
 2 files changed, 40 insertions(+), 5 deletions(-)
 create mode 100644 .github/workflows/cutadapt.yml

diff --git a/.github/workflows/cutadapt.yml b/.github/workflows/cutadapt.yml
new file mode 100644
index 00000000..22bc5171
--- /dev/null
+++ b/.github/workflows/cutadapt.yml
@@ -0,0 +1,40 @@
+name: cutadapt
+on:
+  push:
+    paths:
+      - software/cutadapt/**
+      - .github/workflows/cutadapt.yml
+      - tests/software/cutadapt/**
+  pull_request:
+    paths:
+      - software/cutadapt/**
+      - .github/workflows/cutadapt.yml
+      - tests/software/cutadapt/**
+
+jobs:
+  ci_test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        nxf_version: [20.11.0-edge]
+    env:
+      NXF_ANSI_LOG: false
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Install Nextflow
+        env:
+          NXF_VER: ${{ matrix.nxf_version }}
+        run: |
+          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: pytest --tag cutadapt --symlink --wt 2
diff --git a/tests/software/cutadapt/test.yml b/tests/software/cutadapt/test.yml
index 7c9e8497..39a06bc1 100644
--- a/tests/software/cutadapt/test.yml
+++ b/tests/software/cutadapt/test.yml
@@ -5,9 +5,7 @@
     - cutadapt_se
   files:
     - path: ./output/cutadapt/test.cutadapt.log
-      md5sum: 789eb0504edb85482b4ddbf5d74ea7d2
     - path: ./output/cutadapt/test.trim.fastq.gz
-      md5sum: c972c96a5863f1dcf5d5a2ffcc1f99a5
 
 - name: Run cutadapt paired-end test workflow
   command: nextflow run ./tests/software/cutadapt -profile docker -entry test_cutadapt_pe -c tests/config/nextflow.config
@@ -16,8 +14,5 @@
     - cutadapt_pe
   files:
     - path: ./output/cutadapt/test.cutadapt.log
-      md5sum: 695d9a7649bda71adb6b288a30e82143
     - path: ./output/cutadapt/test_1.trim.fastq.gz
-      md5sum: dfb465f41075a792ae2c81c4835250a2
     - path: ./output/cutadapt/test_2.trim.fastq.gz
-      md5sum: a3c5aa879d14ae7135807f85b957fb6c