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added bowtie_align workflow test

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This commit is contained in:
kevinmenden 2020-12-08 14:19:34 +01:00
parent 73530e8df7
commit fee0707af1
2 changed files with 39 additions and 1 deletions
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38
.github/workflows/bowtie_align.yml vendored Normal file
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@ -0,0 +1,38 @@
name: bowtie_align
on:
push:
paths:
- software/bowtie/align/**
- software/bowtie/index/**
- .github/workflows/bowtie_align.yml
- tests/software/bowtie/**
pull_request:
paths:
- software/bowtie/align/**
- software/bowtie/index/**
- .github/workflows/bowtie_align.yml
- tests/software/bowtie/**
jobs:
ci_test:
runs-on: ubuntu-latest
env:
NXF_ANSI_LOG: false
steps:
- uses: actions/checkout@v2
- name: Install Nextflow
run: |
export NXF_VER="20.07.1"
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 bowtie_align --symlink --wt 2

2
tests/software/bowtie/test.yml
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@ -21,7 +21,7 @@
command: nextflow run ./tests/software/bowtie -profile docker -entry test_bowtie_alignment_single_end -c tests/config/nextflow.config
tags:
- bowtie
- bwa_align
- bowtie_align
files:
- path: output/bowtie/NC_010473.index.1.ebwt
md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c