CLI reference

The current top-level CLI emphasizes two active flows:

  • package a local CLI Nextflow run as a portable archive, and

  • import a previously built archive.

Package a CLI Nextflow run

Subcommand:

epi4you nextflow-run

List candidate runs:

epi4you nextflow-run --nxf_work /data/nextflow_runs --list

Bundle one run:

epi4you nextflow-run \
    --nxf_work /data/nextflow_runs \
    --runid clever_ampere \
    --twome /tmp/clever_ampere.2me.tar

Relevant options:

--nxf_work

Path to the directory containing the historical Nextflow run context.

--nxf_bin

Optional explicit path to the nextflow executable. If omitted, epi4you falls back to which nextflow.

--list

Lists successful runs parsed from nextflow log.

--runid

The Nextflow run_name to package.

--twome

Destination path for the generated .2me archive.

--force

Allows overwriting an existing destination archive.

Import an archive

Subcommand:

epi4you import

Import example:

epi4you import --twome /tmp/clever_ampere.2me.tar

Relevant options:

--twome

Path to the archive being imported.

--force

Reserved for higher-level overwrite semantics in the import flow.

Notes on older capabilities

The repository still contains code for a broader asset-management vision:

  • workflow packaging,

  • Docker/container capture,

  • database operations, and

  • legacy Desktop-oriented archive flows.

Those areas help explain the structure of the codebase and manifest model, even though the current top-level CLI is centered on nextflow-run and import.