Nextflow¶

nextflow/main.nf runs manifold-genetics pipeline as a Nextflow workflow, for Verily Workbench or any Nextflow executor.

nextflow run nextflow/main.nf -profile no_admixture \
    --fit_plink data/fit --project_plink data/project \
    --labels labels.csv --colormap colormap.json --outdir results/

Two profiles, one workflow:

full runs everything.
no_admixture passes --skip-admixture: no admixture step, plots or metrics.

Inputs are PLINK prefixes, labels and a colormap (or fit_/project_ versions of each), as for pipeline. Other options are in nextflow/nextflow.config; anything else goes through --extra_args. At biobank scale set --n_landmark 10000 --random_landmarking true.

Container¶

Runs use a container with the external tools built in, so nothing is downloaded during a run. It is published on Docker Hub for linux/amd64 as mattscicluna/manifold-genetics, tagged by branch (main), by commit (sha-<commit>), and by version (0.3.0, latest) once a release is tagged:

nextflow run nextflow/main.nf -profile no_admixture,docker \
    --container mattscicluna/manifold-genetics:sha-97ca2ba ...

Prefer a commit or release tag to a branch tag: a registry mirror can keep serving an old image under a branch name after it has moved. To build your own, docker build --platform linux/amd64 -t <registry>/manifold-genetics .

Add an execution profile to the workflow profile:

docker runs in the container locally (-profile no_admixture,docker).
google-batch runs on Google Batch, as on Verily Workbench (-profile no_admixture,google-batch), with --container set to an image the workspace can pull.
local uses the current environment.