Nextflow Summit 2024

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

👩 Eirini Liampa

🤵 Xuyang Yuan

2024-11-20

Conference Agenda

Day 1 (Mon): Hackathon/Training day 1 + Social Event
Day 2 (Tue): Hackathon/Training day 2
Day 3 (Wed): Hackathon/Training day 3 + Summit Day 1
Day 4 (Thu): Summit Day 2 + Halloween Party
Day 5 (Fri): Summit Day 3

HACKATHON

Nextflow Hackathon

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

Motivation & Mandate
Standardized QC Metrics, Definition And Implementation

Many available tools ( e.g. coverage)
- samtools, picard, sambamba, indexcov, mosdepth
Different tools give different results depending on defaults settings and options ( e.g. coverage)
- All chromosomes or autosomes only❓
- N bases masked❓
- Duplicates excluded❓
- Soft-clipped bases included❓
- Base quality filtering❓
  - If yes, what’s the cutoff to throw away bases❓
- Mapping quality filtering❓
  - If yes, whta’s the cutoff to throw away reads❓

Implementation:

National Precision Medicine programme in Singapore (NPM)
- c-BIG/NPM-sample-qc
- Tools
  - CollectMultipleMetrics
  - CollectVariantCallingMetrics
  - CollectWgsMetrics
  - bcftools
  - samtools
  - verifyBamID2 (DNA contamination estimation from sequence reads using ancestry-agnostic method)
- GRCh38
- Test run ✅
OUSAMG
- xuyangyuio/ousamg-sample-qc
- GRCh37
- Mosdepth

SUMMIT

GENERAL TALKS ABOUT NEXTFLOW, BIOINFORMATICS, INDUSTRY ETC.

Nextflow is widely used

Community is growing quickly

REGULATION

EXPERIENCE SHARING IN A VARIETY OF FIELDS

Australian BioCommons

Metagenomics analyzes DNA from all organisms in a sample.

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

meta-omics group and plans for better pipeline integration.

Genie: Genomics England’s pipeline orchestration platform

Successor of Bertha for 100K genomes project, not adaptable, no industry standard, e.g. Nextflow, not scalable, not cloud compatible
Genie does all above
For 100K new born genomes project
Pipelines run automatically and continuously

AWS Lambda Function AWS Eventbridge AWS Step Function

The SARS-CoV-2 pandemic drove the development of CLIMB-COVID, a platform enabling collaboration on over 3.5 million genome sequences for pandemic research and response in the UK. Building on this, CLIMB-TRE now offers a broader infrastructure for pathogen genome surveillance, integrating data from multiple sources with quality control and analysis capabilities. This session explores its technical design, focusing on Nextflow workflows and cloud-based user analysis.

Porting somatic variant calling pipelines (SNVs, Small INDELs, SVs, allele-specific somatic copy number aberrations (sCNAs)) of National Center for Tumor Diseases (NCT) and the German Cancer Research Center (DKFZ) to Nextflow to achiev FAIR compliance.