Merge pull request #42 from rki-mf1/feature_sample_sheet #50
Workflow file for this run
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name: tests | |
on: | |
push: | |
branches: [ "main", "dev", "ci" ] | |
pull_request: | |
branches: [ "main", "dev" ] | |
# designed as in: https://github.com/marketplace/actions/setup-miniconda | |
jobs: | |
build: | |
name: build nf env | |
runs-on: "ubuntu-latest" | |
defaults: | |
run: | |
shell: bash -el {0} | |
steps: | |
- uses: actions/checkout@v4 | |
- uses: conda-incubator/setup-miniconda@v3 | |
with: | |
miniconda-version: "latest" | |
activate-environment: nextflow | |
environment-file: env/conda_nxf.yml | |
channels: conda-forge,bioconda,defaults | |
channel-priority: true | |
auto-activate-base: false | |
- name: Test conda installation | |
run: | | |
conda info | |
conda list | |
conda config --show-sources | |
conda config --show | |
- name: Test nextflow installation | |
run: | | |
nextflow -version | |
run-hap: | |
name: Run hap.nf | |
needs: build | |
runs-on: "ubuntu-latest" | |
defaults: | |
run: | |
shell: bash -el {0} | |
steps: | |
- uses: actions/checkout@v4 | |
- uses: conda-incubator/setup-miniconda@v3 | |
with: | |
miniconda-version: "latest" | |
activate-environment: nextflow | |
environment-file: env/conda_nxf.yml | |
channels: conda-forge,bioconda,defaults | |
channel-priority: true | |
auto-activate-base: false | |
- name : Download reference | |
run: | | |
wget https://www.ebi.ac.uk/ena/browser/api/fasta/MN908947.3 | |
sed 's/>ENA|MN908947|MN908947.3 Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome./>MN908947.3/g' MN908947.3 > MN908947.3.fasta | |
mkdir -p reference/Sars-Cov-2/Wuhan-Hu-1/ | |
mv MN908947.3.fasta reference/Sars-Cov-2/Wuhan-Hu-1/ | |
- name: Test haplotype simulation | |
run: | | |
nextflow run hap.nf -profile local,conda | |
run-eval: | |
name: Run eval.nf | |
needs: build | |
runs-on: "ubuntu-latest" | |
defaults: | |
run: | |
shell: bash -el {0} | |
steps: | |
- uses: actions/checkout@v4 | |
- uses: conda-incubator/setup-miniconda@v3 | |
with: | |
miniconda-version: "latest" | |
activate-environment: nextflow | |
environment-file: env/conda_nxf.yml | |
channels: conda-forge,bioconda,defaults | |
channel-priority: true | |
auto-activate-base: false | |
- name : Download reference | |
run: | | |
wget https://www.ebi.ac.uk/ena/browser/api/fasta/MN908947.3 | |
sed 's/>ENA|MN908947|MN908947.3 Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome./>MN908947.3/g' MN908947.3 > MN908947.3.fasta | |
mkdir -p reference/Sars-Cov-2/Wuhan-Hu-1/ | |
mv MN908947.3.fasta reference/Sars-Cov-2/Wuhan-Hu-1/ | |
- name: Test callset evaluation | |
run: | | |
nextflow run eval.nf -profile local,conda --callsets_dir aux/ci_data/ | |