added pangolin workf

This commit is contained in:
kevinmenden 2021-01-29 12:53:51 +01:00
parent 44df90a795
commit bacebdfb47
2 changed files with 41 additions and 1 deletions

40
.github/workflows/pangolin.yml vendored Normal file
View file

@ -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

View file

@ -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 )
}