nf-lamin plugin

A Nextflow plugin that integrates LaminDB data provenance into Nextflow workflows.

Installation

To install a development build of the plugin, run the following command:

make install

To uninstall the plugin, run the following command:

make uninstall

Usage

To use the plugin in a Nextflow workflow, create a Nextflow config nextflow.config that specifies which LaminDB instance to use and an API key:

plugins {
  id 'nf-lamin'
}

lamin {
  instance = "laminlabs/lamindata"
  api_key = secrets.LAMIN_API_KEY
}

Tip

You can fetch your Lamin API key from your Lamin Hub account settings.

Example with nf-core/scrnaseq workflow:

nextflow run nf-core/scrnaseq \
  -latest -resume \
  -r 2.7.1 \
  -profile docker \
  --input https://github.com/nf-core/test-datasets/raw/scrnaseq/samplesheet-2-0.csv \
  --fasta https://github.com/nf-core/test-datasets/raw/scrnaseq/reference/GRCm38.p6.genome.chr19.fa \
  --gtf https://github.com/nf-core/test-datasets/raw/scrnaseq/reference/gencode.vM19.annotation.chr19.gtf \
  --protocol 10XV2 \
  --skip_emptydrops \
  --outdir output/scrnaseq

Example with Viash Hub workflow:

nextflow run https://packages.viash-hub.com/vsh/toolbox.git \
  -revision v0.1.0 \
  -main-script target/nextflow/bgzip/main.nf \
  -profile docker \
  -latest \
  --input https://github.com/nf-core/test-datasets/raw/scrnaseq/samplesheet-2-0.csv \
  --output output.gz \
  --publish_dir gs://di-temporary/scratch/temp-nf-lamin

Nextflow 24.10.6 is available - Please consider updating your version to it
N E X T F L O W  ~  version 24.10.5
Pulling vsh/toolbox ...
Launching `https://packages.viash-hub.com/vsh/toolbox` [modest_gautier] DSL2 - revision: 09c015bdf2 [v0.1.0]
Connected to Lamin instance: laminlabs/lamindata
[8b/6a2386] Submitted process > bgzip:processWf:bgzip_process (run)
[26/5cbfdd] Submitted process > bgzip:publishStatesSimpleWf:publishStatesProc (run)

Note

Replace the --publish_dir with a valid path to a cloud bucket for this example to work.

Logs produced by lamin:

DEBUG nextflow.lamin.LaminObserver - onFlowCreate triggered!
DEBUG nextflow.lamin.api.LaminHub - Fetching access token...
DEBUG nextflow.lamin.api.LaminHub - Access token refreshed successfully.
INFO  nextflow.lamin.LaminObserver - Connected to Lamin instance: laminlabs/lamindata
DEBUG nextflow.lamin.LaminObserver - Fetch or create Transform object:
  transform = ln.Transform(
    key="https://packages.viash-hub.com/vsh/toolbox:target/nextflow/bgzip/main.nf",
    version="v0.1.0",
    source_code='''{"repository":"https://packages.viash-hub.com/vsh/toolbox","main-script":"target/nextflow/bgzip/main.nf","commit-id":"09c015bdf233c4911f469219ebf46b0c51faa734","revision":"v0.1.0"}''',
    type="pipeline",
    reference="https://packages.viash-hub.com/vsh/toolbox",
    reference_type="url",
    description="bgzip: Block compression/decompression utility"
).save()

DEBUG nextflow.lamin.LaminObserver - Create Run object:
  transform = ln.Transform.get("abcdef123456")
  run = ln.Run(
    transform=transform,
    name="modest_gautier",
    created_at="2025-05-01T15:50:53.158377805+02:00",
    started_at="2025-05-01T15:50:53.158377805+02:00",
    reference="https://cloud.seqera.io/...",
    reference_type="url",
    project=...
    created_by=...
).save()

DEBUG nextflow.lamin.LaminObserver - onFlowComplete triggered!
DEBUG nextflow.lamin.LaminObserver - Finalise Run object:
  run = ln.Run.get("abcdef123456")
  run.finished_at = "2025-05-01T15:51:03.312545607+02:00"

Contributing

See CONTRIBUTING.md for more information about contributing to this repository.