Run Pipeline Tests #14
Workflow file for this run
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name: Run Pipeline Tests | |
on: | |
workflow_dispatch | |
env: | |
NEXTFLOW_VERSION: 23.10.1 | |
NF_TEST_VERSION: 0.8.3 | |
jobs: | |
test_download: | |
name: Run ncbi_download test | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/[email protected] | |
- uses: actions/[email protected] | |
with: | |
java-version: '11' | |
distribution: 'adopt' | |
- run: rm -rf $GITHUB_WORKSPACE/* | |
- run: sudo bash; cd /opt; wget "https://github.com/nextflow-io/nextflow/releases/download/v${NEXTFLOW_VERSION}/nextflow"; chmod +x nextflow | |
- run: sudo bash; cd /opt; wget "https://github.com/askimed/nf-test/releases/download/v${NF_TEST_VERSION}/nf-test-${NF_TEST_VERSION}.tar.gz"; tar -xvf "nf-test-${NF_TEST_VERSION}.tar.gz"; chmod +x nf-test; rm "/opt/nf-test-${NF_TEST_VERSION}.tar.gz" | |
- run: echo "/opt" >> $GITHUB_PATH | |
- run: nf-test test tests/modules/download_ncbi.nf.test | |
test_gffread: | |
name: Run gffread test | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/[email protected] | |
- uses: actions/[email protected] | |
with: | |
java-version: '17' | |
distribution: 'adopt' | |
- run: rm -rf $GITHUB_WORKSPACE/* | |
- run: sudo bash; cd /opt; wget "https://github.com/nextflow-io/nextflow/releases/download/v${NEXTFLOW_VERSION}/nextflow"; chmod +x nextflow | |
- run: sudo bash; cd /opt; wget "https://github.com/askimed/nf-test/releases/download/v${NF_TEST_VERSION}/nf-test-${NF_TEST_VERSION}.tar.gz"; tar -xvf "nf-test-${NF_TEST_VERSION}.tar.gz"; chmod +x nf-test; rm "/opt/nf-test-${NF_TEST_VERSION}.tar.gz" | |
- run: echo "/opt" >> $GITHUB_PATH | |
- run: nf-test test tests/modules/gffread.nf.test | |
test_jcvi: | |
name: Run jcvi test | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/[email protected] | |
- uses: actions/[email protected] | |
with: | |
java-version: '17' | |
distribution: 'adopt' | |
- run: rm -rf $GITHUB_WORKSPACE/* | |
- run: sudo bash; cd /opt; wget "https://github.com/nextflow-io/nextflow/releases/download/v${NEXTFLOW_VERSION}/nextflow"; chmod +x nextflow | |
- run: sudo bash; cd /opt; wget "https://github.com/askimed/nf-test/releases/download/v${NF_TEST_VERSION}/nf-test-${NF_TEST_VERSION}.tar.gz"; tar -xvf "nf-test-${NF_TEST_VERSION}.tar.gz"; chmod +x nf-test; rm "/opt/nf-test-${NF_TEST_VERSION}.tar.gz" | |
- run: echo "/opt" >> $GITHUB_PATH | |
- run: nf-test test tests/modules/jcvi.nf.test | |
clean_finish: | |
name: Clean workspace after finish | |
needs: [test_download, test_gffread, test_jcvi] | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/[email protected] | |
- run: rm -rf $GITHUB_WORKSPACE/* |