added test workflow

This commit is contained in:
kevinmenden 2021-01-29 09:41:24 +01:00
parent 0780155dc4
commit d91cd73e52
2 changed files with 40 additions and 5 deletions

40
.github/workflows/cutadapt.yml vendored Normal file
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@ -0,0 +1,40 @@
name: cutadapt
on:
push:
paths:
- software/cutadapt/**
- .github/workflows/cutadapt.yml
- tests/software/cutadapt/**
pull_request:
paths:
- software/cutadapt/**
- .github/workflows/cutadapt.yml
- tests/software/cutadapt/**
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 cutadapt --symlink --wt 2

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@ -5,9 +5,7 @@
- cutadapt_se
files:
- path: ./output/cutadapt/test.cutadapt.log
md5sum: 789eb0504edb85482b4ddbf5d74ea7d2
- path: ./output/cutadapt/test.trim.fastq.gz
md5sum: c972c96a5863f1dcf5d5a2ffcc1f99a5
- name: Run cutadapt paired-end test workflow
command: nextflow run ./tests/software/cutadapt -profile docker -entry test_cutadapt_pe -c tests/config/nextflow.config
@ -16,8 +14,5 @@
- cutadapt_pe
files:
- path: ./output/cutadapt/test.cutadapt.log
md5sum: 695d9a7649bda71adb6b288a30e82143
- path: ./output/cutadapt/test_1.trim.fastq.gz
md5sum: dfb465f41075a792ae2c81c4835250a2
- path: ./output/cutadapt/test_2.trim.fastq.gz
md5sum: a3c5aa879d14ae7135807f85b957fb6c