neuropipe run

neuropipe run [OPTIONS]

Required Arguments¶

Argument	Description	Example
`--subjects`	Subject IDs — comma-separated string or path to a text file (one ID per line, or comma-separated)	`001,002` or `subjects.txt`
`--input`	Input data directory	`/data/BIDS`
`--output`	Output base directory	`/data/processed`
`--work`	Work base directory (logs, database, temp files)	`/data/work`
`--config-dir`	Path to config directory — must contain `config.yaml`, `hpc_config.yaml`, and `project_config/`. Optional if `$NEUROPIPE_CONFIG_DIR` is set.	`/data/config`
`--project`	Project name — loads `{project}_config.yaml` from `--config-dir/project_config/`	`my_study`
`--session`	Session or wave ID	`01`

Processing Options¶

The pipeline uses two categories of multi-step pipelines:

BIDS pipelines (--bids-prep/--bids-post): containerized tools (fMRIPrep, XCP-D, QSIPrep) that take BIDS input directly. Depend on recon when --prep recon or --prep unzip_recon is also requested.
Staged pipelines (--staged-prep/--staged-post): AFNI-based task fMRI that optionally depend on the structural step.

Option	Values	Description
`--prep`	`unzip` \| `recon` \| `unzip_recon`	Data preparation
`--intermed`	`volume` \| `volume,bfc` \| ...	Intermed tasks (comma-separated); required before `--staged-prep`
`--bids-prep`	`rest` \| `dwi` \| `rest,dwi`	BIDS pipeline preprocessing
`--bids-post`	`rest` \| `dwi` \| `rest,dwi`	BIDS pipeline postprocessing
`--staged-prep`	`cards` \| `kidvid` \| `cards,kidvid`	Staged pipeline preprocessing
`--staged-post`	`cards` \| `kidvid` \| `cards,kidvid`	Staged pipeline postprocessing
`--mriqc`	`individual` \| `group` \| `all`	Quality control (MRIQC)

Pipeline section names (e.g. rest, dwi, cards) must match section names defined in config.yaml.

Task Expansion Rules¶

For full dependency and parallel execution behavior, see Pipeline Reference → CLI Flags Overview.

Execution Options¶

Option	Description
`--dry-run`	Print SLURM commands without submitting. Wrapper scripts are still written to `log/wrapper/` so you can inspect them.
`--resume`	Skip subjects whose outputs already pass checks in `{project}_checks.yaml`. Submits full count with warning if file is missing.
`--skip-preflight`	Skip pre-flight config schema and filesystem checks.
`--skip-bids-validation`	Skip BIDS format validation (runs automatically when `--bids-prep` or `--mriqc individual/all` is used).
`--wait`	Wait for all submitted jobs to complete before exiting
`--polling-interval N`	Seconds between SLURM status polls when `--wait` is active (default: 60)

Passing Subjects¶

Comma-separated:

--subjects 001,002,003

Repeated flags (both forms are equivalent):

--staged-prep cards,kidvid
--staged-prep cards --staged-prep kidvid

From a text file (one ID per line, or comma-separated):

# one per line
printf "001\n002\n003" > subjects.txt

# or comma-separated
echo "001,002,003" > subjects.txt

neuropipe run --subjects subjects.txt ...

The subject prefix (sub-) comes from the project config prefix field; do not include it in subject IDs.

`--dry-run`¶

Generates all wrapper scripts and prints the exact sbatch commands, but does not queue anything. Use it to:

Verify module names and paths before a large run
Preview SLURM array sizes
Inspect generated env-vars in {work}/log/wrapper/

`--resume`¶

Before submitting each task’s array job, the pipeline calls OutputChecker to find which subjects already have valid outputs. Only pending subjects are included in the array. If a task has no pending subjects at all, it is skipped entirely and downstream tasks lose their afterok dependency on it.

If {project}_checks.yaml is missing, --resume is silently ignored (with a warning) and all subjects are submitted.