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A Best-Practices community pipeline for WGS/WES
Maxime U Garcia ▸ @maxulysse
Seqera Labs ▸ Barcelona | Stockholm
2023-03-06@Genphyse
What is Sarek
A National Park in Northern Sweden.
- Long, deep, narrow valleys and wild, turbulent water
- A tortuous delta landscape
- Completely lacking in comfortable accommodations
- One of Sweden’s most inaccessible national parks
- There are no roads leading up to the national park
Explore strange new worlds
- Open-Source Nextflow Pipeline
- Community driven
- Workflow manager
- Data driven language
- Portable
- executable on multiple platforms
- Shareable and reproducible
- with containers or virtual environments
Data driven language
The execution graph depends on the input data,
and is calculated on the go.
In snakemake, it's the other way around.
The execution graph depends on the final target,
and is calculated before launch.
Portability
www.nextflow.io/docs/latest/executor.html
- Sun Grid Engine, SLURM, PBS/Torque…
- AWS, Azure, Google…
Reproducibility
Multiple flavors
Multiple modes
Reference genomes
- Currently using AWS iGenomes
- Considering refgenie
Preprocessing
Based on GATK Best Practices (GATK 4.3.0.0)
- Reads mapped to reference genome with
bwa mem - Duplicates marked with
picard MarkDuplicates - Recalibrate with
GATK BaseRecalibrator
Germline Variant Calling
- SNVs and small indels
- Deepvariant
- Freebayes
- HaplotypeCaller
- mpileup
- Strelka2
- Structural variants
- Manta
- TIDDIT
- CNVs
- CNVKIT
Somatic Variant Calling
- SNVs and small indels
- Freebayes
- Mutect2
- Strelka2
- Structural variants
- Manta
- TIDDIT
- Sample heterogeneity, ploidy and CNVs
- ASCAT
- CNVKIT
- Control-FREEC
- Microsatellite instability
- MSIsensorpro
Annotation
- Ensembl-VEP and SnpEff
- ClinVar, COSMIC, dbSNP, GENCODE, gnomAD, polyphen, sift, etc.
Reports
Sarek in Nextflow Tower
A community effort to collect a curated set of analysis pipelines built using Nextflow.
Community
Users
Developers
What does nf-core provide
- Pipelines: ready-made pipelines
- Docs : Guidelines, tutorials, videos
- Modules : single-tool wrappers
- Subworkflows : multi-tool wrappers
- Configs : shared infrastructure configs
- Test datasets : test data for
- Tools : linting, template + automation for
Pipeline requirements
nf-co.re/docs/contributing/adding_pipelines
- Nextflow based
- Common structure
- Stable release tags
- MIT license
- Software bundled for reproducibility
- Continuous Integration testing
- lagom
Training and other events
