mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-29 19:19:55 +00:00
101 lines
3.3 KiB
YAML
101 lines
3.3 KiB
YAML
name: nf-core CI
|
|
# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
|
|
on:
|
|
push:
|
|
branches:
|
|
- dev
|
|
pull_request:
|
|
release:
|
|
types: [published]
|
|
|
|
env:
|
|
NXF_ANSI_LOG: false
|
|
|
|
jobs:
|
|
test:
|
|
name: Run pipeline with test data
|
|
# Only run on push if this is the nf-core dev branch (merged PRs)
|
|
if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/taxprofiler') }}"
|
|
runs-on: ubuntu-latest
|
|
strategy:
|
|
matrix:
|
|
NXF_VER:
|
|
- "21.10.3"
|
|
- "latest-everything"
|
|
parameters:
|
|
- "--perform_longread_qc false"
|
|
- "--perform_shortread_qc false"
|
|
- "--shortread_qc_tool fastp"
|
|
- "--shortread_qc_tool fastp --shortread_qc_mergepairs --shortread_qc_excludeunmerged"
|
|
- "--shortread_qc_tool fastp --shortread_qc_mergepairs"
|
|
- "--shortread_qc_tool adapterremoval"
|
|
- "--shortread_qc_tool adapterremoval --shortread_qc_mergepairs --shortread_qc_excludeunmerged"
|
|
- "--shortread_qc_tool adapterremoval --shortread_qc_mergepairs"
|
|
- "--shortread_complexityfilter_tool bbduk"
|
|
- "--shortread_complexityfilter_tool prinseqplusplus"
|
|
- "--perform_runmerging"
|
|
- "--perform_runmerging --shortread_qc_mergepairs"
|
|
- "--shortread_complexityfilter false --perform_shortread_hostremoval"
|
|
|
|
steps:
|
|
- name: Check out pipeline code
|
|
uses: actions/checkout@v2
|
|
|
|
- name: Install Nextflow
|
|
uses: nf-core/setup-nextflow@v1
|
|
with:
|
|
version: "${{ matrix.NXF_VER }}"
|
|
|
|
- name: Show current locale
|
|
run: locale
|
|
|
|
- name: Set UTF-8 enabled locale
|
|
run: |
|
|
sudo locale-gen en_US.UTF-8
|
|
sudo update-locale LANG=en_US.UTF-8
|
|
|
|
- name: Run pipeline with test data
|
|
uses: Wandalen/wretry.action@v1.0.11
|
|
with:
|
|
command: nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.parameters }}
|
|
attempt_limit: 3
|
|
|
|
motus:
|
|
name: Test mOTUs with workflow parameters
|
|
if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/taxprofiler') }}
|
|
runs-on: ubuntu-latest
|
|
strategy:
|
|
matrix:
|
|
NXF_VER:
|
|
- "21.10.3"
|
|
- "latest-everything"
|
|
|
|
steps:
|
|
- name: Check out pipeline code
|
|
uses: actions/checkout@v2
|
|
|
|
- name: Install Nextflow
|
|
uses: nf-core/setup-nextflow@v1
|
|
with:
|
|
version: "${{ matrix.NXF_VER }}"
|
|
|
|
- name: Show current locale
|
|
run: locale
|
|
|
|
- name: Set UTF-8 enabled locale
|
|
run: |
|
|
sudo locale-gen en_US.UTF-8
|
|
sudo update-locale LANG=en_US.UTF-8
|
|
|
|
- name: Prepare the database
|
|
run: |
|
|
wget https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py
|
|
python downloadDB.py > download_db_log.txt
|
|
echo 'tool,db_name,db_params,db_path' > 'database_motus.csv'
|
|
echo 'motus,db_mOTU,,db_mOTU' >> 'database_motus.csv'
|
|
|
|
- name: Run pipeline with test data
|
|
uses: Wandalen/wretry.action@v1.0.11
|
|
with:
|
|
command: nextflow run ${GITHUB_WORKSPACE} -profile test_motus,docker --outdir ./results --databases ./database_motus.csv
|
|
attempt_limit: 3
|