Config reference

Key-by-key reference for the metapipeline .yaml format. See YAML representation overview for how these fit together and Cross-workflow references for the ${...} syntax usable in params values.

Top level

Key	Type	Required	Default	Notes
config_version	string	yes	—	Must be between 0.0.1 and the current maximum (0.3.0). Rejected outside that range.
workflows	mapping (id → workflow)	yes	—	See Workflow (common fields) below. A list form exists for backward compatibility but is deprecated.
globals	mapping	no	none	See globals below.
transitions	list	no	none	Legacy edge list ({source, target} pairs). Deprecated in favor of each workflow's own from:; still readable but triggers a warning.

globals

Key	Type	Required	Default	Notes
profile	string	no	none	Nextflow -profile applied to every workflow that doesn't set its own profile. Whitespace is stripped.
config_file	path to an existing .config file	no	none	Passed as a Nextflow -c to every workflow, in addition to any per-workflow config_file.
params	mapping (str → scalar)	no	none	Merged under each workflow's own params, with the workflow's values taking precedence on key collision. Values must be str/int/float/bool.
nextflow_version	string, int, or float	no	none	e.g. "25.10", "25.10.4-edge", 25. Checked against the actually-installed nextflow -version before a run; mismatch is reported, not silently ignored.

Workflow (common fields)

Every entry under workflows: is one of two types, selected by type: (default nf-pipeline when omitted). These fields apply to both:

Key	Type	Required	Default	Notes
type	nf-pipeline | nf-module	no	nf-pipeline	Selects NfPipeline vs. NfModule below.
(id)	—	yes	—	Not a field inside the entry; it's the entry's own key under workflows:, e.g. n01:. Referenced by from:, ${id:params:key}, and the CLI's --start/--target.
name	string, non-empty	yes	—	Pipeline/module name, e.g. nf-core/rnaseq. For nf-core pipelines, also used to auto-resolve url/description.
version	string, non-empty	yes	—	A release tag (1.12.0, v1.12.0) or a full/short commit SHA (7-40 hex chars). A branch name (e.g. dev, master) is rejected, since reproducibility requires a pinned revision.
from	string or list of strings	no	none	Id(s) of the workflow(s) that must complete before this one runs. Determines execution (DAG) order.
params	mapping (str → scalar)	no	none	Passed to the pipeline as -params-file. Values must be str/int/float/bool; real types are preserved through to the generated params file, not stringified. May contain ${...} references (string values only).
config_file	path to an existing .config file	no	none	Workflow-specific Nextflow -c, in addition to globals.config_file.

nf-pipeline additional fields

For a nextflow run-style pipeline step (the default type):

Key	Type	Required	Default	Notes
url	string	conditional	auto-resolved for nf-core pipelines	Required for non-nf-core pipelines (must start with https://). For an nf-core pipeline matched by name, auto-filled from the nf-core pipeline list; an explicit mismatching url is rejected.
description	string	no	auto-filled for nf-core pipelines	Free text; auto-populated from nf-core's own description when available.
params_file	path to an existing .yaml/.yml file	no	none	An external base params file. Merged with params at run time (params overrides on key collision) and included in schema validation.
profile	string	no	none	Overrides globals.profile for this workflow specifically.
main_script	string	no	none	Alternate entry script within the pipeline repo. Not settable for nf-core pipelines.

nf-module additional fields

For a nextflow module run-style step:

Key	Type	Required	Default	Notes
container_engine	docker | singularity | conda | podman	no	none	Passed as -with-<engine>.

Legacy transitions: entries

Each entry is {source: <id>, target: <id>}, equivalent to adding from: <source> to the target workflow. Prefer from: in new configs; opening and saving a config with legacy transitions: in the editor rewrites it automatically.