Nextflow Summit 2024

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

đź‘© Eirini Liampa
🤵 Xuyang Yuan

2024-11-13

Conference Agenda

  • Day 1 (Mon): Hackathon day 1 + Social event
  • 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
(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 onlyâť“
    • N bases maskedâť“
    • Duplicates excludedâť“
    • Soft-clipped bases includedâť“
    • Base quality filteringâť“ thresholdâť“
    • Mapping quality filteringâť“ thresholdâť“

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

Seqera Platform demo

Gitpod demo