Local Docker Run

Local Docker Run#

Use the distributed Docker image for workstation or single-server execution. Keep study-specific parameters in a small project config and mount data, outputs, anatomy, and the FreeSurfer license separately.

Example#

The command below runs the full MEG branch with existing FreeSurfer/DeepPrep anatomy. Event, covariance, coregistration, and source settings must already be defined for the dataset. For a first dataset check, use --steps meg_ica and omit the anatomy mounts instead.

docker run --rm -it \
  -v /data/study/meg:/input \
  -v /data/study/megflow:/output \
  -v /data/study/smri:/smri \
  -v /data/license.txt:/fs_license.txt:ro \
  -v /data/study/project.config:/config/project.config:ro \
  cplmeg/megflow:1.0.0 \
  --config /config/project.config \
  --input /input \
  --output /output \
  --fs_license_file /fs_license.txt \
  --fs_subjects_dir /smri \
  --steps meg_all \
  --resume

Command Structure#

Argument

Purpose

--rm -it

Removes the stopped container and keeps an interactive terminal attached.

/input mount

Container-visible MEG dataset root.

/output mount

Processing derivatives, work cache, and static report output.

/smri mount

Existing or generated FreeSurfer SUBJECTS_DIR.

/fs_license.txt mount

Read-only FreeSurfer license used by anatomy-dependent stages.

/config/project.config mount

Project overlay selected explicitly by --config.

--steps

Temporary stage override. Omit it to retain the stage in the project config.

--resume

Reuse valid Nextflow work-cache entries from the same output/work tree.

The entrypoint prepares the mounted output directory, then runs Nextflow with the host UID/GID inferred from /input. Report-only runs infer ownership from /output. If neither mount has the desired owner, add -e LOCAL_UID="$(id -u)" -e LOCAL_GID="$(id -g)" before the volume mounts.

This command runs the Nextflow driver and local tasks inside the distributed container. It is different from launching Nextflow from a source checkout with -profile docker, where the driver remains on the host and starts one container per task.

See Quickstart for the first-pass workflow, Full Workflow for anatomy and source stages, and Configuration Reference for the ordered configuration reference.

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