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Bioinformatics session

A two-day workshop for bioinformaticians and molecular biologists with focus on the TSO500 pipeline in InPreD

https://inpred.github.io/24-03_bioinfo_ws/

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Overview

1. Setup
2. Development & Collaboration
3. Nextflow
4. tso500_nxf_workflow
5. Python

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1. Setup

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1.1. Create a GitHub account

• go to https://github.com/ and click on Sign up

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1.1. Create a GitHub account

• enter your email

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1.1. Create a GitHub account

• set a password

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1.1 Create a GitHub account

• choose a username

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1.1 Create a GitHub account

• choose email preferences

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1.1 Create a GitHub account

• solve the puzzle

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1.1 Create a GitHub account

• create your account

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1.1 Create a GitHub account

• find the activation code in the email you received

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1.1 Create a GitHub account

• select the desired options

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1.1 Create a GitHub account

• choose the free plan

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1.2. Be added to InPreD organisation at GitHub

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1.3. Resources

• Getting started with your GitHub account

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2. Development & Collaboration

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2.1. Short git introduction

• distributed version control system
• tracks history of changes commited by different contributors
• every developer has full copy of project and its history

2.1.1 git config

git config --global user.name <your name>
git config --global user.email <your email>

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2.1.2. Basic git commands

git init: initialises new git repository

git clone <repository url>: creates local copy of remote repository

git add <file/s>: stage new or changed files (anything that should be committed to the repository)

git commit -m "feat: my new feature": commit changes to the repository

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2.1.2.1. commit message conventions

<type>[optional scope]: <description>

• feat: new feature
• fix: patching bug
• refactor: code change that neither is neither feat nor fix
• build: build system related changes
• perf: improving performance

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2.1.2.1. commit message conventions

<type>[optional scope]: <description>

• chore: code unrelated changes, e.g. dependencies
• style: code change that does not change meaning
• test: changes to tests
• docs: adding/updating documentation
• ci: continuous integration, e.g. github actions

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2.1.2. Basic git commands

git status: overview over untracked, modified and staged changes

git branch: show local branches

git merge: merge branches

git pull: load changes from remote counterpart

git push: upload changes to remote counterpart

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2.2. Branching model: simplied Gitflow workflow

• start with two branches to record project history: main and develop
• each new feature resides in its own branch (feature branch)
• feature branch is generally created off latest develop commit
• upon feature completion, feature branch is merged into develop

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2.2. Branching model: simplied Gitflow workflow

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2.3. GitHub Actions

• continuous integration (CI) and continuous deployment (CD)
• building, testing and deploying directly from GitHub
• set up by adding yaml instructions to .github/workflows

name: GitHub Actions Demo
on: [push]
jobs:
  Explore-GitHub-Actions:
    runs-on: ubuntu-latest
    steps:
      - run: echo "Hello world!"

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2.3. GitHub Actions

name: Docker Build
on:
  push:
    branches:
      - main
      - develop
    tags:
      - '*.*.*'

jobs:
  test:
    name: Run unit tests
    runs-on: ubuntu-latest
    steps:
      -
        name: Check out the repo
        uses: actions/checkout@v4
      -
        name: Unit testing
        uses: fylein/python-pytest-github-action@v2
        with:
          args: pip3 install -r requirements.txt && pytest
  ...

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2.3. GitHub Actions

...
  build:
    name: Build Image
    runs-on: ubuntu-latest
    needs: test
    steps:
      -
        name: Check out the repo
        uses: actions/checkout@v4
      -
        name: Lint Dockerfile
        uses: hadolint/[email protected]
      -
        name: Docker Meta
        id: meta
        uses: docker/metadata-action@v5
        with:
          images: |
            inpred/local_app_prepper
          tags: |
            latest
            type=semver,pattern={{version}}
            type=semver,pattern={{major}}.{{minor}}
            type=semver,pattern={{major}}
      -
        name: Login to Dockerhub
        uses: docker/login-action@v3
        with:
          username: ${{ secrets.DOCKERHUB_USERNAME }}
          password: ${{ secrets.DOCKERHUB_TOKEN }}
      -
        name: Build and push image to Docker Hub
        uses: docker/build-push-action@v5
        with:
          push: true
          tags: ${{ steps.meta.outputs.tags }}
          labels: ${{ steps.meta.outputs.labels }}

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2.3. GitHub Actions

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2.3. GitHub Actions

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2.3. GitHub Actions

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2.4. GitHub workflow

• go to issues and create a New issue

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2.4. GitHub workflow

• give the issue a descriptive title and a description and Submit new issue

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2.4. GitHub workflow

• if you decide to work on the issue (own repository), Create a branch via the issue

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2.4. GitHub workflow

• Change branch source to develop and Create branch

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2.4. GitHub workflow

• load the new branch to your local repository, check it out and start working
• push your changes back to the remote

$ git pull
$ git checkout 4-new-fancy-feature
$ git add README.md
$ git commit -m "docs: updating docs"
$ git push

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2.4. GitHub workflow

• for repositories you don't have access to, create a fork

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2.4. GitHub workflow

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2.4. GitHub workflow

• once you have a fork, git clone your forked repository
• create a new branch and work on that
• git push your changes back to the forked remote

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2.4. GitHub workflow

• when you are done, go to pull requests and create a New pull request

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2.4. GitHub workflow

• choose develop as base and your new feature branch (same repo or forked) for compare

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2.4. GitHub workflow

• assign yourself, add at least one reviewer (cog icon), provide some context and Create pull request

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2.4. GitHub workflow

• if you still want to work on the pull request, you can Convert to draft to let the reviewers know that it is not done yet
• otherwise you can just wait for them to review your changes

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2.4. GitHub workflow

• as a reviewer, make your you check your email notifications to see if there is pull requests waiting for you
• open the pull request and start the review in the Files changed tab

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2.4. GitHub workflow

• you can leave comments and suggestions in the code by hovering over the line with the changes and clicking on +

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2.4. GitHub workflow

• you can type your comment

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2.4. GitHub workflow

• or you leave a suggestion, ideally you click Start a review to initialise the reviewing process

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2.4. GitHub workflow

• when you are done with reviewing, Finish your review

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2.4. GitHub workflow

• again, leave a comment if you like, and choose if you just want to Comment, Approve or Request changes

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2.4. GitHub workflow

• you can add a general comment to the pull request under Conversation

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2.4. GitHub workflow

• after the reviewer left their comments and suggestions, you can address them one by one by replying or applying the suggested changes
• whenever a certain comment/suggestion is handled (discussion comes to conclusion, suggestion was applied), you can resolve it

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2.4. GitHub workflow

• as soon as the reviewers gave you an approval, you can finally Merge pull request

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2.4.1 Hands-on pull request

• go to https://github.com/InPreD/24-03_bioinfo_ws/
• create fork to your own account
• open an issue "test pull request" or similar and create a branch
• go to the branch and add a markdown file with your first name and favorite emoji to the participants folder, ideally the file is named <your first name>.md
• open a pull request in the original repository and add someone else in the group to review your pull request
• review someone else's pull request, give feedback and approve if correct

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2.5. Release

• releases should be from main branch
• good practice is to open a pull request for develop into main when you are done with the desired features

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2.5. Release

• whenever you are ready for a new release, create a new release

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2.5. Release

• add a title and a description for your release and Choose a tag

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2.5. Release

• ideally, you choose a tag according to semantic versioning

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2.5.1. Semantic versioning

• version tag should be MAJOR.MINOR.PATCH
• you increment one of the three depending on the change
  • MAJOR: version when you make incompatible API changes
  • MINOR: version when you add functionality in a backward compatible manner
  • PATCH: version when you make backward compatible bug fixes

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2.5. Release

• when you are satisfied with your release, Publish release

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2.6. Licensing

• let's discuss

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2.7. Resources

• About Git
• Gitflow workflow
• GitHub Actions
• Semantic versioning
• Licensing

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3. Nextflow

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3.1. Short introduction

• workflow manager that enables scalable and reproducible scientific workflows using software containers
• an extension of groovy which is object-oriented programming language for the Java platform
• can be used with an array of executors, such as SLURM, k8s, AWS, Azure, Google Cloud and many more
• nf-core: project/community that develops framework for nextflow including guidelines, tools, modules, subworkflows, pipelines and test data

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3.2. Requirements

• POSIX compatible system (e.g. Linux, Os X)
• Bash
• Java ≥ 11 / ≤ 21
• Docker/Singularity

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3.3. Installation

$ curl -s https://get.nextflow.io | bash
$ chmod +x nextflow

or

$ wget -O nextflow https://github.com/nextflow-io/nextflow/releases/download/v23.10.1/nextflow-23.10.1-all

or via browser at https://github.com/nextflow-io/nextflow/releases

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3.4. Best pratice: nf-core template

workflow_repo
├── LICENSE
├── README.md
├── assets
│   ├── mock.genome.fasta
│   ├── samplesheet.csv
│   └── schema_input.json
├── bin
│   └── script.py
├── conf
│   ├── base.config
│   ├── modules.config
│   └── test_stub.config
├── lib
│   ├── NfcoreSchema.groovy
│   ├── NfcoreTemplate.groovy
│   ├── WorkflowMain.groovy
│   └── nfcore_external_java_deps.jar
├── main.nf
├── modules
│   ├── local
│   │   ├── module_1.nf
│   │   └── module_2.nf
│   └── nf-core
│       ├── module_1
│       │   └── arg_1
│       │       ├── main.nf
│       │       └── meta.yml
│       └── custom
│           └── dumpsoftwareversions
│               ├── main.nf
│               ├── meta.yml
│               └── templates
│                   └── dumpsoftwareversions.py
├── modules.json
├── nextflow.config
├── nextflow_schema.json
└── workflows
    └── main.nf

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3.6 Resources

• nextflow.io
• nf-co.re
• nf-core github

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4. tso500_nxf_workflow

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4.1. Status update

• modified nf-core template (removed unnecessary functionality, config and metadata files)
• added devcontainer to have controlled environment (dind and sind available)
• stubbing data available
• containing three modules so far (localapp_prepper, LocalApp, dumpsoftwareversions)
• using nf-validation plugin

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4.2. Overview

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4.3. Demonstration

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4.4. Outlook

• samplesheet_generator
• tsoppi (requires some restructuring)
• PRONTO
• include configuration files for each node
• Documentation

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4.5. Resources

• repository
• local_app_prepper
• samplesheet_generator

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5. Python project

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5.1. Repository structure

• consistency/standard
• keep main script short and sweet - functionality in modules

#!/usr/local/bin/python

from my_module import main

if __name__ == "__main__":
    main()

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5.1. Repository structure

• module folder should contain __init__.py
• keep functions short and try to refactor big functions
• leave descriptive comments in code
• use libraries to make your life easier
  • pandas: csv/tsv files
  • click or argparse: define cli input flags
• introduce proper exception handling
• logging with log levels

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5.1.1. Unit testing

• pytest for testing
• include unit tests for functions, preferable table-driven

def addition(x, y):
  return x+y

import pytest

@pytest.mark.parametrize("x, y, z", [(1, 1, 2), (1, -1, 0)])
def test_eval(x, y, z):
    assert addition(x, y) == z

$ pytest

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5.1. Repository structure

• include test data for unit testing if necessary
• create container image from project, preferably docker
• include all necessary dependencies in requirements.txt (locked versions)
• add GitHub actions for testing, linting, building, etc.
• preferable include a devcontainer definition
• README.md and other docs

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5.1. Repository structure

/repo
|-- .devcontainer
|   `-- devcontainer.json
|-- .github
|   `-- workflows
|       `-- main.yml
|-- .gitignore
|-- Dockerfile
|-- docs
|-- LICENSE
|-- README.md
|-- my_tool.py
|-- my_module
|   |-- __init__.py
|   |-- my_module.py
|   `-- tests
|       |-- __init__.py
|       `-- my_module_test.py
|-- requirements.txt
`-- test

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5.2. Resources

• pandas
• click
• argparse
• exception handling
• logging
• pytest unittesting
• inpred dockerhub
• devcontainers