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Run Pipeline Tests

Run Pipeline Tests #12

Workflow file for this run

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: '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: /opt/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: /opt/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: /opt/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/*