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JIANHONG OU 2022-06-03 14:38:59 -04:00
parent 22f65eedc7
commit 3cd3d2dad3
1 changed files with 42 additions and 42 deletions
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.github/workflows/ci.yml vendored
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@ -73,51 +73,51 @@ jobs:
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.parameters }} nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.parameters }}
motus: motus:
name: Test mOTUs with workflow parameters name: Test mOTUs with workflow parameters
if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/taxprofiler') }} if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/taxprofiler') }}
runs-on: ubuntu-latest runs-on: ubuntu-latest
env: env:
NXF_VER: ${{ matrix.nxf_ver }} NXF_VER: ${{ matrix.nxf_ver }}
NXF_ANSI_LOG: false NXF_ANSI_LOG: false
strategy: strategy:
matrix: matrix:
# Nextflow versions # Nextflow versions
include: include:
# Test pipeline minimum Nextflow version # Test pipeline minimum Nextflow version
- NXF_VER: "21.10.3" - NXF_VER: "21.10.3"
NXF_EDGE: "" NXF_EDGE: ""
# Test latest edge release of Nextflow # Test latest edge release of Nextflow
- NXF_VER: "" - NXF_VER: ""
NXF_EDGE: "1" NXF_EDGE: "1"
steps: steps:
- name: Check out pipeline code - name: Check out pipeline code
uses: actions/checkout@v2 uses: actions/checkout@v2
- name: Install Nextflow - name: Install Nextflow
env: env:
NXF_VER: ${{ matrix.NXF_VER }} NXF_VER: ${{ matrix.NXF_VER }}
# Uncomment only if the edge release is more recent than the latest stable release # Uncomment only if the edge release is more recent than the latest stable release
# See https://github.com/nextflow-io/nextflow/issues/2467 # See https://github.com/nextflow-io/nextflow/issues/2467
# NXF_EDGE: ${{ matrix.NXF_EDGE }} # NXF_EDGE: ${{ matrix.NXF_EDGE }}
run: | run: |
wget -qO- get.nextflow.io | bash wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/ sudo mv nextflow /usr/local/bin/
- name: Show current locale - name: Show current locale
run: locale run: locale
- name: Set UTF-8 enabled locale - name: Set UTF-8 enabled locale
run: | run: |
sudo locale-gen en_US.UTF-8 sudo locale-gen en_US.UTF-8
sudo update-locale LANG=en_US.UTF-8 sudo update-locale LANG=en_US.UTF-8
- name: Prepare the database - name: Prepare the database
run: | run: |
wget https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py wget https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py
python downloadDB.py python downloadDB.py > download_db_log.txt
echo 'tool,db_name,db_params,db_path\nmotus,db_mOTU,,db_mOTU' > 'database_motus.csv' echo 'tool,db_name,db_params,db_path\nmotus,db_mOTU,,db_mOTU' > 'database_motus.csv'
- name: Run pipeline with test data - name: Run pipeline with test data
run: | run: |
nextflow run ${GITHUB_WORKSPACE} -profile test_motus,docker --outdir ./results --databases ./database_motus.csv nextflow run ${GITHUB_WORKSPACE} -profile test_motus,docker --outdir ./results --databases ./database_motus.csv