added pangolin workf

.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

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 )
 }