Skip to content

Run Pipeline Tests

Run Pipeline Tests #16

Workflow file for this run

name: Run Pipeline Tests
on:
workflow_dispatch
env:
NEXTFLOW_VERSION: 23.10.1
NF_TEST_VERSION: 0.8.4
AWS_CLI_VERSION: 2.15.19
AWS_ACCESS_KEY_ID: ${{ secrets.AWS_PUBLIC_KEY }}
AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_KEY }}
AWS_DEFAULT_REGION: 'us-east-1'
jobs:
build:
runs-on: ubuntu-latest
steps:
- name: Clean workspace before start
run: rm -rf $GITHUB_WORKSPACE/*
- uses: actions/[email protected]
- name: Set up JDK 17.0.9+0
uses: actions/[email protected]
with:
java-version: '17.0.9+9'
distribution: 'adopt'
- name: Install nextflow
run: sudo bash; cd /opt; wget "https://github.com/nextflow-io/nextflow/releases/download/v${NEXTFLOW_VERSION}/nextflow"; chmod +x nextflow;
- name: Install nf-test
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"
- name: Install aws cli
run: curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64-${AWS_CLI_VERSION}.zip" -o "awscliv2.zip"; unzip awscliv2.zip; sudo ./aws/install --update
- name: Add software to path
run: echo "/opt" >> $GITHUB_PATH;
- name: Run r processing test
run: nf-test test tests/modules/local/r_processing.nf.test
- name: Run dereplication test
run: nf-test test tests/modules/local/vsearch_derep.nf.test
- name: Run fastq filter test
run: nf-test test tests/modules/local/vsearch_fastq_filter.nf.test
- name: Run cutadapt test
run: nf-test test tests/modules/nf-core/cutadapt/main.nf.test
- name: Run pear test
run: nf-test test tests/modules/nf-core/pear/main.nf.test
- name: Run sintax test
run: nf-test test tests/modules/nf-core/vsearch/sintax/main.nf.test
- name: Clean workspace after finish
run: rm -rf $GITHUB_WORKSPACE/*