From bacebdfb477821034b9893049406bc1a98f7a978 Mon Sep 17 00:00:00 2001
From: kevinmenden <kevin.menden@t-online.de>
Date: Fri, 29 Jan 2021 12:53:51 +0100
Subject: [PATCH] added pangolin workf

---
 .github/workflows/pangolin.yml  | 40 +++++++++++++++++++++++++++++++++
 tests/software/pangolin/main.nf |  2 +-
 2 files changed, 41 insertions(+), 1 deletion(-)
 create mode 100644 .github/workflows/pangolin.yml

diff --git a/.github/workflows/pangolin.yml b/.github/workflows/pangolin.yml
new file mode 100644
index 00000000..44d718f7
--- /dev/null
+++ b/.github/workflows/pangolin.yml
@@ -0,0 +1,40 @@
+name: pangolin
+on:
+  push:
+    paths:
+      - software/pangolin/**
+      - .github/workflows/pangolin.yml
+      - tests
+  pull_request:
+    paths:
+      - software/pangolin/**
+      - .github/workflows/pangolin.yml
+      - tests
+
+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 pangolin --symlink --wt 2
diff --git a/tests/software/pangolin/main.nf b/tests/software/pangolin/main.nf
index e987d069..455c1996 100644
--- a/tests/software/pangolin/main.nf
+++ b/tests/software/pangolin/main.nf
@@ -6,7 +6,7 @@ include { PANGOLIN } from '../../../software/pangolin/main.nf' addParams(options
 
 workflow test_pangolin {
     input = [ [ id:'test' ], // meta map
-              [ file("${launchDir}/../GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true) ] ]
+              [ file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true) ] ]
 
     PANGOLIN( input )
 }