Scalable, reproducible bioinformatics workflows using Nextflow & nf-core
Alexander Peltzer
ELIXIR Workshop on FAIR Computational Workflows
September 2, 2020
Dataflow Model
Domain-specific language
Executor abstraction
Tools
Guidelines
Pipelines
A community effort to collect a curated set of analysis pipelines built using Nextflow.
- 25 stable
- 15 in development
Github Actions: CI Testing
Linting
$ cd path/to/my_pipeline
$ nf-core lint .
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/tools version 1.10.dev0
INFO Testing pipeline: nf-core-testpipeline/
╭──────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ [!] 3 Test Warnings │
├──────────────────────────────────────────────────────────────────────────────────────────────────────────┤
│ https://nf-co.re/errors#5: GitHub Actions AWS full test should test full datasets: nf-core-testpipeline… │
│ https://nf-co.re/errors#8: Conda package is not latest available: bioconda::fastqc=0.11.8, 0.11.9 avail… │
│ https://nf-co.re/errors#8: Conda package is not latest available: bioconda::multiqc=1.7, 1.9 available │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭───────────────────────╮
│ LINT RESULTS SUMMARY │
├───────────────────────┤
│ [✔] 117 Tests Passed │
│ [!] 3 Test Warnings │
│ [✗] 0 Test Failed │
╰───────────────────────╯
JSON Schema
JSON Schema
JSON Schema
Nextflow Tower
AWS Megatests
FAIRification of nf-core
Dockstore (supported)
ro-crate (prototyping)
Evaluating
JSON Schema
ECCB2020 NXF + NF-Core
By Alexander Peltzer
ECCB2020 NXF + NF-Core
- 3,004