From e9e795633dbd91e356eaa6ba9e75ee350e2e186b Mon Sep 17 00:00:00 2001
From: kevinmenden <kevin.menden@t-online.de>
Date: Mon, 1 Feb 2021 14:02:06 +0100
Subject: [PATCH] added fastp tests

---
 .github/workflows/fastp.yml   | 40 +++++++++++++++++++++++++++++++++++
 tests/software/fastp/main.nf  | 30 ++++++++++++++++++++++++++
 tests/software/fastp/test.yml | 27 +++++++++++++++++++++++
 3 files changed, 97 insertions(+)
 create mode 100644 .github/workflows/fastp.yml
 create mode 100644 tests/software/fastp/main.nf
 create mode 100644 tests/software/fastp/test.yml

diff --git a/.github/workflows/fastp.yml b/.github/workflows/fastp.yml
new file mode 100644
index 00000000..90ad15ef
--- /dev/null
+++ b/.github/workflows/fastp.yml
@@ -0,0 +1,40 @@
+name: fastp
+on:
+  push:
+    paths:
+      - software/fastp/**
+      - .github/workflows/fastp.yml
+      - tests
+  pull_request:
+    paths:
+      - software/fastp/**
+      - .github/workflows/fastp.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: ${{ matrix.nxf_version }}
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.x"
+      - name: Install dependencies
+        run: python -m pip install --upgrade pip pytest-workflow
+
+      # Test the module
+      - run: pytest --tag fastp --symlink --wt 2
diff --git a/tests/software/fastp/main.nf b/tests/software/fastp/main.nf
new file mode 100644
index 00000000..000fcdd8
--- /dev/null
+++ b/tests/software/fastp/main.nf
@@ -0,0 +1,30 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { FASTP } from '../../../software/fastp/main.nf'  addParams( options: [:] )
+
+/*
+ * Test with single-end data
+ */
+workflow test_fastp_se {
+    def input = []
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file("${launchDir}/tests/data/fastq/rna/test_single_end.fastq.gz", checkIfExists: true) ] ]
+
+    FASTP( input )
+}
+
+/*
+ * Test with paired-end data
+ */
+
+workflow test_fastp_pe {
+    def input = []
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
+                file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ]
+
+    FASTP( input )
+}
+
diff --git a/tests/software/fastp/test.yml b/tests/software/fastp/test.yml
new file mode 100644
index 00000000..56cbcaa7
--- /dev/null
+++ b/tests/software/fastp/test.yml
@@ -0,0 +1,27 @@
+- name: fastp_se
+  command: nextflow run ./tests/software/fastp -profile docker -entry test_fastp_se -c ./tests/config/nextflow.config
+  tags:
+    - fastp
+    - fastp_se
+  files:
+    - path: ./output/fastp/test.fastp.json
+      md5sum: b81d53bfa5c1553bed89f6475edcf437
+    - path: ./output/fastp/test.trim.fastq.gz
+      md5sum: 2f5516df477b123e3f78adb67effa3bc
+    - path: ./output/fastp/test.fastp.log
+    - path: ./output/fastp/test.fastp.html
+
+- name: fastp_pe
+  command: nextflow run ./tests/software/fastp -profile docker -entry test_fastp_pe -c ./tests/config/nextflow.config
+  tags:
+    - fastp
+    - fastp_pe
+  files:
+    - path: ./output/fastp/test.fastp.html
+    - path: ./output/fastp/test.fastp.json
+      md5sum: 40db7fcbed478b0a96a1c5c1bb5f737b
+    - path: ./output/fastp/test.fastp.log
+    - path: ./output/fastp/test_1.trim.fastq.gz
+      md5sum: c8844c05194b50ae368e6825e997aa7f
+    - path: ./output/fastp/test_2.trim.fastq.gz
+      md5sum: 9238b07bb1609e939be7c8889b72c209