Complete CLI Reference¶

This page provides the complete command-line interface reference for wf2wf.

Note

Auto-generated CLI documentation requires the sphinx-click package. If not available, use wf2wf --help and wf2wf COMMAND --help for documentation.

wf2wf¶

wf2wf - Workflow-to-Workflow Converter

Convert workflows between different formats using a unified intermediate representation.

Supported formats:

Snakemake (.smk, .snakefile)
HTCondor DAGMan (.dag)
CWL (.cwl)
Nextflow (.nf)
WDL (.wdl)
Galaxy (.ga)
JSON (.json) - IR format
YAML (.yaml, .yml) - IR format

.. program:: wf2wf .. code-block:: shell

wf2wf [OPTIONS] COMMAND [ARGS]...

.. rubric:: Options

.. option:: –version

Show the version and exit.

bco¶

BioCompute Object utilities (packaging, validation, etc.).

.. program:: wf2wf bco .. code-block:: shell

wf2wf bco [OPTIONS] COMMAND [ARGS]...

diff¶

Show domain-level differences between two BCO JSON documents.

.. program:: wf2wf bco diff .. code-block:: shell

wf2wf bco diff [OPTIONS] FIRST SECOND

.. rubric:: Arguments

.. option:: FIRST

Required argument

.. option:: SECOND

Required argument

package¶

Create an FDA eSTAR Technical Data Package from BCO_FILE.

.. program:: wf2wf bco package .. code-block:: shell

wf2wf bco package [OPTIONS] BCO_FILE

.. rubric:: Options

.. option:: –format <pkg_format>

Packaging format (currently only: estar)

:options: estar

.. option:: –out <out_path>

Output ZIP file path

.. option:: –verbose

Verbose output

.. option:: –interactive

Prompt before overwriting output ZIP

.. rubric:: Arguments

.. option:: BCO_FILE

Required argument

sign¶

Compute sha256 digest and produce detached signature using openssl.

The BCO’s etag field is updated to sha256:<hex> if not already.

.. program:: wf2wf bco sign .. code-block:: shell

wf2wf bco sign [OPTIONS] BCO_FILE

.. rubric:: Options

.. option:: –key <priv_key>

**Required** Private key (PEM) for openssl sha256 signing

.. option:: –sig <sig_file>

Output detached signature path (.sig)

.. option:: –verbose

.. option:: –interactive

Prompt before overwriting signature/attestation files

.. rubric:: Arguments

.. option:: BCO_FILE

Required argument

convert¶

Convert workflows between different formats.

Examples: | # Single input file (defaults to IR format with warning) | wf2wf convert -i workflow.smk

# Snakemake to DAGMan
wf2wf convert -i workflow.smk --out-format dagman

# Auto-detect formats from extensions
wf2wf convert -i Snakefile -o workflow.dag

# With additional options
wf2wf convert -i workflow.smk -o pipeline.dag --configfile config.yaml --verbose

# Convert to intermediate JSON format
wf2wf convert -i workflow.smk -o workflow.json

.. program:: wf2wf convert .. code-block:: shell

wf2wf convert [OPTIONS]

.. rubric:: Options

.. option:: -i, –input <input_path>

**Required** Path to the input workflow file

.. option:: –in-format, –input-format <input_format>

Format of the input workflow (auto-detected if not specified)

:options: snakemake | dagman | nextflow | cwl | wdl | galaxy | json | yaml

.. option:: -o, –out, –output <output_path>

Path to output workflow file (auto-generated if not specified)

.. option:: –out-format, –output-format <output_format>

Desired output format (auto-detected from output path if not specified)

:options: snakemake | dagman | nextflow | cwl | wdl | galaxy | bco | json | yaml

.. option:: –snakefile

Path to Snakefile (alias for --input when input format is snakemake)

.. option:: -c, –configfile

Snakemake config file

.. option:: -d, –workdir

Working directory for Snakemake workflow

.. option:: –cores

Number of cores for Snakemake operations (default: 1)

.. option:: –snakemake-args <snakemake_args>

Additional arguments to pass to snakemake commands (can be used multiple times)

.. option:: –parse-only

Parse Snakefile without requiring snakemake executable (limited functionality)

.. option:: –resource-profile <resource_profile>

Apply resource profile to fill in missing resource specifications

:options: shared | cluster | cloud | hpc | gpu | memory_intensive | io_intensive

.. option:: –infer-resources

Infer resource requirements from command/script content

.. option:: –validate-resources

Validate resource specifications and report issues

.. option:: –target-environment <target_environment>

Target execution environment (auto-detected from output format if not specified)

:options: shared_filesystem | distributed_computing | hybrid | cloud_native | unknown

.. option:: –scripts-dir <scripts_dir>

Directory for generated wrapper scripts (DAGMan export)

.. option:: –default-memory <default_memory>

Default memory request for jobs (default: 4GB)

.. option:: –default-disk <default_disk>

Default disk request for jobs (default: 4GB)

.. option:: –default-cpus <default_cpus>

Default CPU request for jobs (default: 1)

.. option:: –inline-submit

Use inline submit descriptions in DAG file instead of separate .sub files

.. option:: –validate, –no-validate

Validate workflow against JSON schema (default: enabled)

.. option:: –fail-on-loss

Exit with non-zero status if any information loss occurred during conversion

.. option:: -v, –verbose

Enable verbose output

.. option:: –debug

Enable debug output

.. option:: –auto-env <auto_env>

Automatically build or reuse Conda/container images and replace env specs (Phase2)

:options: off | reuse | build

.. option:: –oci-backend <oci_backend>

OCI builder backend to use when --auto-env is active (default: buildx)

:options: buildx | podman | buildah

.. option:: –push-registry <push_registry>

Registry to push images (enables push)

.. option:: –confirm-push

Actually push to registry; without this only probing is performed

.. option:: –apptainer

Convert OCI image to Apptainer SIF and reference that

.. option:: –sbom

Generate SBOM via syft and attach to environment metadata

.. option:: –platform

Target platform for OCI buildx/buildah (e.g. linux/arm64)

.. option:: –build-cache <build_cache>

Remote cache location for BuildKit --build-cache

.. option:: –report-md <report_md>

Write human-readable Markdown report to this file

.. option:: –interactive

Enable interactive prompting for missing resource specifications, environment configurations, and execution parameters

.. option:: –intent

Ontology IRI describing workflow intent (can repeat)

.. option:: –adapt-environments

Enable environment adaptation (default: enabled)

.. option:: –adaptation-strategy <adaptation_strategy>

Adaptation strategy for resource scaling (default: balanced)

:options: conservative | aggressive | balanced

.. option:: –source-environment <source_environment>

Source execution environment (auto-detected if not specified)

:options: shared_filesystem | distributed_computing | hybrid | cloud_native | unknown

.. option:: –adaptation-report <adaptation_report>

Write adaptation report to this file

info¶

Display information about a workflow file.

Shows workflow metadata, task count, and dependency structure.

.. program:: wf2wf info .. code-block:: shell

wf2wf info [OPTIONS] WORKFLOW_FILE

.. rubric:: Options

.. option:: -f, –format

Output format (default: json)

:options: json | yaml

.. rubric:: Arguments

.. option:: WORKFLOW_FILE

Required argument

validate¶

Validate a workflow file against the wf2wf JSON schema.

WORKFLOW_FILE can be JSON or YAML format.

.. program:: wf2wf validate .. code-block:: shell

wf2wf validate [OPTIONS] WORKFLOW_FILE

.. rubric:: Arguments

.. option:: WORKFLOW_FILE

Required argument

Main Commands¶

wf2wf convert - Convert workflows between formats
wf2wf validate - Validate workflow files
wf2wf info - Show workflow information
wf2wf bco - Generate BioCompute Objects
wf2wf cache - Manage environment cache

For detailed help on any command, use:

wf2wf COMMAND --help