Nextflow Summit 2024

📅 October 28 - November 1, 2024 🇪🇸Barcelona, Spain

👩 Eirini Liampa

🤵 Xuyang Yuan

2024-11-20

Conference Agenda

• Day 1 (Mon): Hackathon day 1 + Quiz@Hard Rock Cafè
• Day 2 (Tue): Hackathon day 2
• Day 3 (Wed): Hackathon day 3 + Summit Day 1
• Day 4 (Thu): Summit Day 2 + Halloween Party
• Day 5 (Fri): Summit Day 3

          

Nextflow Hackathon

Project: GA4GH Quality Control of Whole Genome Sequencing metrics and reference implementations

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(Standardized QC Metrics, Definition And Implementation)

e.g. coverage

• Many Available Tools
  • samtools, picard, sambamba, indexcov, mosdepth
• Each Tool Gives Different Results
  • All chromosomes or autosomes only❓
  • N bases masked❓
  • Duplicates excluded❓
  • Soft-clipped bases included❓
  • Base quality filtering❓ threshold❓
  • Mapping quality filtering❓ threshold❓

implementations: c-BIG/NPM-sample-qc
implementations: xuyangyuio/ousamg-sample-qc

          

Nextflow LSP

Editor support: vscode emacs neovim

Supported language features:

• code navigation (outline, go to definition, find references)
  
• completion
  
• diagnostics (errors, warnings)
  
• formatting
  
• hover hints
  
• rename
  
• DAG preview for workflows

 
 

Nextflow is widely used

Community is growing quickly

 
 

Metagenomics analyzes DNA from all organisms in a sample.

This talk covers nf-core pipelines for profiling, assembly, and functional screening in metagenomics.

It introduces the meta-omics group and plans for better pipeline integration.

 
 

Ensuring the correctness and reliability of large and complex pipelines is challenging

nf-test, testing framework, modular, test individual process blocks, workflow patterns, and entire pipelines

DSL2-like syntax, snapshot testing, testing only changed modules, CI support, plugin system (new)

Seqera Platform demo

Gitpod demo