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Run Pipeline Tests

Run Pipeline Tests #26

Workflow file for this run

name: Run Pipeline Tests
on:
workflow_dispatch
env:
NEXTFLOW_VERSION: 23.10.1
NF_TEST_VERSION: 0.8.3
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 $GITHUB_WORKSPACE/*
- uses: actions/[email protected]
- name: Set up JDK 11
uses: actions/[email protected]
with:
java-version: '11'
distribution: 'adopt'
- name: Install nextflow
run: sudo bash; cd /opt; wget "https://github.com/nextflow-io/nextflow/releases/download/v${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 ncbi_download test
run: nf-test test tests/modules/download_ncbi.nf.test
- name: Run gffread test
run: nf-test test tests/modules/gffread.nf.test
- name: Run longest test
run: nf-test test tests/modules/longest.nf.test
- name: Run jcvi test
run: nf-test test tests/modules/jcvi.nf.test
- name: Download synteny module test cds files
run: aws s3 cp s3://synteny-test-data/data/synteny_input/Drosophila_santomea.cds data/synteny_input/Drosophila_santomea.cds; aws s3 cp s3://synteny-test-data/data/synteny_input/Drosophila_simulans.cds data/synteny_input/Drosophila_simulans.cds
- name: Run synteny test
run: nf-test test tests/modules/synteny.nf.test
- name: Run chromopaint test
run: nf-test test tests/modules/chromo.nf.test
- name: Run score test
run: nf-test test tests/modules/score.nf.test
- name: Run score_tree test
run: nf-test test tests/modules/score_tree.nf.test
- name: Run go test
run: nf-test test tests/modules/go.nf.test
- name: Run go summarise test
run: nf-test test tests/modules/go_summarise.nf.test
- name: Clean workspace after finish
run: rm -rf $GITHUB_WORKSPACE/*