From fee0707af1d3450780aa33f9d730f8f949fae10a Mon Sep 17 00:00:00 2001
From: kevinmenden <kevin.menden@t-online.de>
Date: Tue, 8 Dec 2020 14:19:34 +0100
Subject: [PATCH] added bowtie_align workflow test

---
 .github/workflows/bowtie_align.yml | 38 ++++++++++++++++++++++++++++++
 tests/software/bowtie/test.yml     |  2 +-
 2 files changed, 39 insertions(+), 1 deletion(-)
 create mode 100644 .github/workflows/bowtie_align.yml

diff --git a/.github/workflows/bowtie_align.yml b/.github/workflows/bowtie_align.yml
new file mode 100644
index 00000000..796b3389
--- /dev/null
+++ b/.github/workflows/bowtie_align.yml
@@ -0,0 +1,38 @@
+name: bowtie_align
+on:
+    push:
+        paths:
+            - software/bowtie/align/**
+            - software/bowtie/index/**
+            - .github/workflows/bowtie_align.yml
+            - tests/software/bowtie/**
+    pull_request:
+        paths:
+            - software/bowtie/align/**
+            - software/bowtie/index/**
+            - .github/workflows/bowtie_align.yml
+            - tests/software/bowtie/**
+
+jobs:
+    ci_test:
+        runs-on: ubuntu-latest
+        env:
+            NXF_ANSI_LOG: false
+        steps:
+            - 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: 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 bowtie_align --symlink --wt 2
diff --git a/tests/software/bowtie/test.yml b/tests/software/bowtie/test.yml
index 13b7b1fd..fb58b089 100644
--- a/tests/software/bowtie/test.yml
+++ b/tests/software/bowtie/test.yml
@@ -21,7 +21,7 @@
   command: nextflow run ./tests/software/bowtie -profile docker -entry test_bowtie_alignment_single_end -c tests/config/nextflow.config
   tags:
     - bowtie
-    - bwa_align
+    - bowtie_align
   files:
     - path: output/bowtie/NC_010473.index.1.ebwt
       md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c