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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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84
.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 }}
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
env:
NXF_VER: ${{ matrix.nxf_ver }}
NXF_ANSI_LOG: false
strategy:
matrix:
# Nextflow versions
include:
# Test pipeline minimum Nextflow version
- NXF_VER: "21.10.3"
NXF_EDGE: ""
# Test latest edge release of Nextflow
- NXF_VER: ""
NXF_EDGE: "1"
name: Test mOTUs with workflow parameters
if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/taxprofiler') }}
runs-on: ubuntu-latest
env:
NXF_VER: ${{ matrix.nxf_ver }}
NXF_ANSI_LOG: false
strategy:
matrix:
# Nextflow versions
include:
# Test pipeline minimum Nextflow version
- NXF_VER: "21.10.3"
NXF_EDGE: ""
# Test latest edge release of Nextflow
- NXF_VER: ""
NXF_EDGE: "1"
steps:
- name: Check out pipeline code
uses: actions/checkout@v2
steps:
- name: Check out pipeline code
uses: actions/checkout@v2
- name: Install Nextflow
env:
NXF_VER: ${{ matrix.NXF_VER }}
# Uncomment only if the edge release is more recent than the latest stable release
# See https://github.com/nextflow-io/nextflow/issues/2467
# NXF_EDGE: ${{ matrix.NXF_EDGE }}
run: |
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Install Nextflow
env:
NXF_VER: ${{ matrix.NXF_VER }}
# Uncomment only if the edge release is more recent than the latest stable release
# See https://github.com/nextflow-io/nextflow/issues/2467
# NXF_EDGE: ${{ matrix.NXF_EDGE }}
run: |
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Show current locale
run: locale
- 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: 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
echo 'tool,db_name,db_params,db_path\nmotus,db_mOTU,,db_mOTU' > 'database_motus.csv'
- 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\nmotus,db_mOTU,,db_mOTU' > 'database_motus.csv'
- name: Run pipeline with test data
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test_motus,docker --outdir ./results --databases ./database_motus.csv
- name: Run pipeline with test data
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test_motus,docker --outdir ./results --databases ./database_motus.csv