From 77da5008c78f6a838216abf9e0eaebf858374ea6 Mon Sep 17 00:00:00 2001
From: SimonDMurray <simondonaldmurray@gmail.com>
Date: Mon, 18 Mar 2024 15:02:44 +0000
Subject: [PATCH] added first version of nf-test actions

---
 .github/workflows/test-pipeline.yml | 59 +++++++++++++++++++++++++++++
 1 file changed, 59 insertions(+)
 create mode 100644 .github/workflows/test-pipeline.yml

diff --git a/.github/workflows/test-pipeline.yml b/.github/workflows/test-pipeline.yml
new file mode 100644
index 0000000..017358d
--- /dev/null
+++ b/.github/workflows/test-pipeline.yml
@@ -0,0 +1,59 @@
+name: Run Pipeline Tests
+
+on:
+  workflow_dispatch
+
+env:
+  NEXTFLOW_VERSION: 23.10.1
+  NF_TEST_VERSION: 0.8.4
+
+jobs:
+
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Clean workspace before start
+      run: rm -rf $GITHUB_WORKSPACE/*
+
+    - uses: actions/checkout@v4.1.1
+
+    - name: Set up JDK 11
+      uses: actions/setup-java@v4.0.0
+      with:
+        java-version: '11'
+        distribution: 'adopt'
+
+    - name: Install nextflow
+      run: sudo bash; cd /opt; wget "https://github.com/nextflow-io/nextflow/releases/download/v${NEXTFLOW_VERSION}/nextflow"; chmod +x nextflow;
+
+    - name: Install nf-test
+      run: sudo bash; cd /opt; wget "https://github.com/askimed/nf-test/releases/download/v${NF_TEST_VERSION}/nf-test-${NF_TEST_VERSION}.tar.gz"; tar -xvf "nf-test-${NF_TEST_VERSION}.tar.gz"; chmod +x nf-test; rm "/opt/nf-test-${NF_TEST_VERSION}.tar.gz"
+
+    - name: Add software to path
+      run: echo "/opt" >> $GITHUB_PATH;
+
+    - name: Run bash processing test
+      run: nf-test test tests/modules/local/processing.nf.test
+
+    - name: Run r processing test
+      run: nf-test test tests/modules/local/r_processing.nf.test
+
+    - name: Run dereplication test
+      run: nf-test test tests/modules/local/vsearch_derep.nf.test
+
+    - name: Run fastq filter test
+      run: nf-test test tests/modules/local/vsearch_fastq_filter.nf.test
+
+    - name: Run cutadapt test
+      run: nf-test test tests/modules/nf-core/cutadapt/main.nf.test
+
+    - name: Run pear test
+      run: nf-test test tests/modules/nf-core/pear/main.nf.test
+
+    - name: Run sintax test
+      run: nf-test test tests/modules/nf-core/vsearch/sintax/main.nf.test
+
+    - name: Clean workspace after finish
+      run: rm -rf $GITHUB_WORKSPACE/*