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UlthranUlthran
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Merge pull request #5 from sunbeam-labs/4-containerize-and-version
Containerize and version
2 parents 85e463b + 7510c0a commit 63ef925

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‎.github/workflows/conda_env_check.yml‎

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‎.github/workflows/docker.yml‎

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name: Push to DockerHub
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on:
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workflow_call:
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workflow_dispatch:
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jobs:
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build-and-push-to-dockerhub:
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name: Push Docker image to Docker Hub
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runs-on: ubuntu-latest
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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- name: Get sbx version
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shell: bash
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run: |
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SBX_VER=$(cat VERSION)
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echo "SBX_VER=$SBX_VER" >> $GITHUB_ENV
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- name: Log in to Docker Hub
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uses: docker/login-action@v3
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with:
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username: ${{ secrets.DOCKERHUB_USERNAME }}
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password: ${{ secrets.DOCKERHUB_TOKEN }}
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- name: Extract metadata (tags, labels) for Docker
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id: meta
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uses: docker/metadata-action@v5
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with:
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images: sunbeamlabs/sbx_assembly
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- name: Build and push Docker image for annotation
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uses: docker/build-push-action@v5
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with:
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context: .
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file: envs/sbx_annotation.Dockerfile
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push: true
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tags: sunbeamlabs/sbx_assembly:${{ env.SBX_VER }}-annotation
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labels: ${{ steps.meta.outputs.labels }}
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- name: Build and push Docker image for assembly
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uses: docker/build-push-action@v5
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with:
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context: .
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file: envs/sbx_assembly.Dockerfile
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push: true
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tags: sunbeamlabs/sbx_assembly:${{ env.SBX_VER }}-assembly
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labels: ${{ steps.meta.outputs.labels }}
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- name: Build and push Docker image for coverage
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uses: docker/build-push-action@v5
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with:
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context: .
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file: envs/sbx_coverage.Dockerfile
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push: true
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tags: sunbeamlabs/sbx_assembly:${{ env.SBX_VER }}-coverage
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labels: ${{ steps.meta.outputs.labels }}

‎.github/workflows/linter.yml‎

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‎.github/workflows/pr.yml‎

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name: Tests
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on:
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pull_request:
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branches:
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- main
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jobs:
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run-tests:
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uses: ./.github/workflows/tests.yml
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secrets: inherit
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‎.github/workflows/release.yml‎

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name: Release
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on:
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release:
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types: [published]
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workflow_dispatch:
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jobs:
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run-tests:
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uses: ./.github/workflows/tests.yml
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secrets: inherit
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check-version:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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- name: Get sbx version
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shell: bash
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run: |
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SBX_VER=$(cat VERSION)
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echo "SBX_VER=$SBX_VER" >> $GITHUB_ENV
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- id: get_version
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uses: battila7/get-version-action@v2
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- name: Check version
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shell: bash
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run: |
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RELEASE_VERSION=${{ steps.get_version.outputs.version-without-v }}
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echo "Release version: ${RELEASE_VERSION}"
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echo "Sbx version: ${{ env.SBX_VER }}"
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if [[ $RELEASE_VERSION == ${{ env.SBX_VER }} ]]; then
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echo "Versions match, continuing..."
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else
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echo "Versions don't match, exiting..."
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exit 1
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fi
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push-to-dockerhub:
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uses: ./.github/workflows/docker.yml
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secrets: inherit
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needs:
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- run-tests
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- check-version
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test-apptainer:
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name: Apptainer Test
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runs-on: ubuntu-latest
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needs: push-to-dockerhub
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steps:
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- name: Checkout Code
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uses: actions/checkout@v4
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- name: Set test env
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run: echo "SUNBEAM_TEST_PROFILE=apptainer" >> $GITHUB_ENV
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- uses: eWaterCycle/setup-apptainer@v2
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with:
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apptainer-version: 1.1.2
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- name: Test with Sunbeam
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uses: sunbeam-labs/sbx_test_action@v1
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with:
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test-directory: ".tests/e2e/"
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- name: Dump Logs
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shell: bash
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if: always()
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run: tail -n +1 logs/*
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- name: Dump Stats
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shell: bash
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if: always()
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run: cat stats/*

‎.github/workflows/tests.yml‎

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name: Tests
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on:
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pull_request:
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branches: [ master, main ]
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push:
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branches: [ master, main ]
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workflow_call:
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workflow_dispatch:
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schedule:
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- cron: "0 13 * * 1"
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jobs:
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jobs:
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lint:
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name: Lint Code
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runs-on: ubuntu-latest
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steps:
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- name: Checkout Code
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uses: actions/checkout@v4
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- uses: actions/setup-python@v5
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with:
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python-version: 3.12
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- name: Install Dependencies
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run: pip install black snakefmt
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- name: Run Linter
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run: |
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black --check .
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snakefmt --check *.smk
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test-unit:
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name: Run Extension Unit Tests
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runs-on: ubuntu-latest
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steps:
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- name: Checkout Code
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uses: actions/checkout@v4
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- uses: actions/setup-python@v5
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with:
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python-version: 3.12
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- name: Install Dependencies
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run: pip install pytest
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- name: Run Unit Tests
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run: true #pytest .tests/unit/
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# This'll require having a lib within scripts with internal tests
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test-e2e:
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name: Test Extension with Sunbeam
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runs-on: ubuntu-latest
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needs:
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- test-unit
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- lint
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steps:
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- name: Checkout Code
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uses: actions/checkout@v3
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uses: actions/checkout@v4
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- name: Test with Sunbeam
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uses: sunbeam-labs/sbx_test_action@v1
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- name: Dump Logs
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shell: bash
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if: always()
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run: tail -n +1 logs/*
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#- name: Dump Logs
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# shell: bash
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# if: always()
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# run: tail -n +1 logs/*
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- name: Dump Stats
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shell: bash
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if: always()
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run: cat stats/*
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#- name: Dump Stats
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# shell: bash
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# if: always()
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# run: cat stats/*

‎.gitignore‎

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__pycache__

‎.tests/test_megahit.sh‎

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‎README.md‎

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<!-- Begin badges -->
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[![Tests](https://github.com/sunbeam-labs/sbx_assembly/actions/workflows/tests.yml/badge.svg)](https://github.com/sunbeam-labs/sbx_assembly/actions/workflows/tests.yml)
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[![Super-Linter](https://github.com/sunbeam-labs/sbx_assembly/actions/workflows/linter.yml/badge.svg)](https://github.com/sunbeam-labs/sbx_assembly/actions/workflows/linter.yml)
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[![DockerHub](https://img.shields.io/docker/pulls/sunbeamlabs/sbx_assembly)](https://hub.docker.com/repository/docker/sunbeamlabs/sbx_assembly/)
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<!-- End badges -->
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A [Sunbeam](https://github.com/sunbeam-labs/sunbeam) extension for assembly of contigs using Megahit, gene annotation using Prodigal, and annotation using [Blast](https://blast.ncbi.nlm.nih.gov/Blast.cgi) and [Diamond](https://github.com/bbuchfink/diamond). It can also map reads to contigs and calculat per-base coverage using [Minimap2](https://github.com/lh3/minimap2) and [samtools](https://github.com/samtools/samtools).

‎VERSION‎

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0.0.0

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