Pipeline Parameters

Auto-Generated Documentation

This page is automatically generated from nextflow_schema.json. Parameter defaults and descriptions reflect the current pipeline version.

Overview

Pipeline: nf-proteindesign pipeline parameters

Nextflow pipeline for Boltzgen protein design using pre-made design YAML specifications

Input/output options

Define where the pipeline should find input data and save output data.

--input

Required. Path to comma-separated samplesheet file.

• Type: string
• Default: "null"
• Pattern: ^\S+\.csv$

--outdir

Required. The output directory where the results will be saved.

• Type: string
• Default: "./results"

Boltzgen design parameters

Core parameters for Boltzgen protein design execution.

--cache_dir

Cache directory for model weights (~6GB).

• Type: string
• Default: "null"

--boltzgen_config

Optional path to custom Boltzgen config YAML to override defaults.

• Type: string
• Default: "null"

--steps

Optional comma-separated list of steps to run (e.g., 'filtering' to rerun only filtering).

• Type: string
• Default: "null"

ProteinMPNN sequence optimization

Options for ProteinMPNN sequence optimization of designed structures.

--run_proteinmpnn

Enable ProteinMPNN sequence optimization of Boltzgen designs.

• Type: boolean
• Default: false

--mpnn_sampling_temp

Sampling temperature (lower = more conservative).

• Type: number
• Default: 0.1

--mpnn_num_seq_per_target

Number of sequence variants to generate per structure.

• Type: integer
• Default: 8

--mpnn_batch_size

Batch size for ProteinMPNN inference.

• Type: integer
• Default: 1

--mpnn_seed

Random seed for reproducibility.

• Type: integer
• Default: 37

--mpnn_backbone_noise

Backbone noise level (lower = more faithful to input).

• Type: number
• Default: 0.02

--mpnn_save_score

Save per-residue scores.

• Type: boolean
• Default: true

--mpnn_save_probs

Save per-residue probabilities (large files, use for detailed analysis).

• Type: boolean
• Default: false

--mpnn_fixed_chains

Chains to keep fixed (e.g., 'A,B' - typically the target chains).

• Type: string
• Default: "null"

--mpnn_designed_chains

Chains to design (e.g., 'C' - typically the binder chain).

• Type: string
• Default: "null"

Boltz-2 structure prediction

Options for Boltz-2 multimer structure prediction of ProteinMPNN sequences.

--run_boltz2_refold

Enable Boltz-2 structure prediction for ProteinMPNN sequences.

• Type: boolean
• Default: false

--boltz2_num_diffusion

Number of diffusion samples per sequence (higher = more diversity).

• Type: integer
• Default: 200

--boltz2_num_recycling

Number of recycling iterations for structure refinement.

• Type: integer
• Default: 3

--boltz2_use_msa

Use multiple sequence alignments (MSAs) for prediction.

• Type: boolean
• Default: false

--boltz2_predict_affinity

Predict binding affinity for protein complexes.

• Type: boolean
• Default: true

Analysis and scoring options

Options for scoring and evaluating designed structures.

--run_ipsae

Enable IPSAE scoring of Boltzgen predictions.

• Type: boolean
• Default: false

--ipsae_pae_cutoff

PAE cutoff for IPSAE calculation (Angstroms).

• Type: number
• Default: 10

--ipsae_dist_cutoff

Distance cutoff for CA-CA contacts (Angstroms).

• Type: number
• Default: 10

--run_prodigy

Enable PRODIGY binding affinity prediction on final designs.

• Type: boolean
• Default: false

--prodigy_selection

Chain selection for PRODIGY (e.g., 'A,B'). If null, auto-detects from structure.

• Type: string
• Default: "null"

--run_foldseek

Enable Foldseek structural similarity search for budget designs and Boltz-2 structures.

• Type: boolean
• Default: false

--foldseek_database

Path to Foldseek database directory (required if run_foldseek is true).

• Type: string
• Default: "null"

--foldseek_database_name

Name of the Foldseek database within the directory.

• Type: string
• Default: "afdb"

--foldseek_evalue

E-value threshold for reporting matches (lower = more stringent).

• Type: number
• Default: 0.001

--foldseek_max_seqs

Maximum number of target sequences to report per query.

• Type: integer
• Default: 100

--foldseek_sensitivity

Search sensitivity (1.0-9.5, higher = more sensitive but slower).

• Type: number
• Default: 9.5

--foldseek_coverage

Minimum fraction of aligned residues (0.0-1.0, higher = more global alignment).

• Type: number
• Default: 0.0

--foldseek_alignment_type

Alignment type: 0=3Di only, 1=TMalign (global), 2=3Di+AA (local, default).

• Type: integer
• Default: 2
• Allowed values: 0, 1, 2

--run_consolidation

Enable consolidated metrics report generation.

• Type: boolean
• Default: false

--report_top_n

Number of top designs to highlight in consolidated report.

• Type: integer
• Default: 10

Resource allocation

Maximum resource limits for pipeline execution.

--max_cpus

Maximum number of CPUs per process.

• Type: integer
• Default: 16

--max_memory

Maximum memory per process.

• Type: string
• Default: "128.GB"
• Pattern: ^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$

--max_time

Maximum time per process.

• Type: string
• Default: "240.h"
• Pattern: ^\d+(\.\d+)?\.?\s*(m|h|d|s)?$

--max_gpus

Maximum number of GPUs per process.

• Type: integer
• Default: 1

Generic options

Less common options for the pipeline, typically set in a config file.

--publish_dir_mode

Method for publishing outputs.

• Type: string
• Default: "copy"
• Allowed values: copy, symlink, move

--tracedir

Directory to store pipeline execution traces.

• Type: string
• Default: "${params.outdir}/pipeline_info"

--validate_params

Validate parameters against the schema at runtime.

• Type: boolean
• Default: true

--show_hidden_params

Show hidden parameters in help message.

• Type: boolean
• Default: false

--help

Display help text.

• Type: boolean
• Default: "null"

--version

Display version and exit.

• Type: boolean
• Default: "null"

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Quick Reference Table

Parameter	Type	Default	Description
--input	string	"null"	**Required
--outdir	string	"./results"	**Required
--cache_dir	string	"null"	Cache directory for model weights (~6GB)
--boltzgen_config	string	"null"	Optional path to custom Boltzgen config YAML to...
--steps	string	"null"	Optional comma-separated list of steps to run (e
--run_proteinmpnn	boolean	false	Enable ProteinMPNN sequence optimization of Bol...
--mpnn_sampling_temp	number	0.1	Sampling temperature (lower = more conservative)
--mpnn_num_seq_per_target	integer	8	Number of sequence variants to generate per str...
--mpnn_batch_size	integer	1	Batch size for ProteinMPNN inference
--mpnn_seed	integer	37	Random seed for reproducibility
--mpnn_backbone_noise	number	0.02	Backbone noise level (lower = more faithful to ...
--mpnn_save_score	boolean	true	Save per-residue scores
--mpnn_save_probs	boolean	false	Save per-residue probabilities (large files, us...
--mpnn_fixed_chains	string	"null"	Chains to keep fixed (e
--mpnn_designed_chains	string	"null"	Chains to design (e
--run_boltz2_refold	boolean	false	Enable Boltz-2 structure prediction for Protein...
--boltz2_num_diffusion	integer	200	Number of diffusion samples per sequence (highe...
--boltz2_num_recycling	integer	3	Number of recycling iterations for structure re...
--boltz2_use_msa	boolean	false	Use multiple sequence alignments (MSAs) for pre...
--boltz2_predict_affinity	boolean	true	Predict binding affinity for protein complexes
--run_ipsae	boolean	false	Enable IPSAE scoring of Boltzgen predictions
--ipsae_pae_cutoff	number	10	PAE cutoff for IPSAE calculation (Angstroms)
--ipsae_dist_cutoff	number	10	Distance cutoff for CA-CA contacts (Angstroms)
--run_prodigy	boolean	false	Enable PRODIGY binding affinity prediction on f...
--prodigy_selection	string	"null"	Chain selection for PRODIGY (e
--run_foldseek	boolean	false	Enable Foldseek structural similarity search fo...
--foldseek_database	string	"null"	Path to Foldseek database directory (required i...
--foldseek_database_name	string	"afdb"	Name of the Foldseek database within the directory
--foldseek_evalue	number	0.001	E-value threshold for reporting matches (lower ...
--foldseek_max_seqs	integer	100	Maximum number of target sequences to report pe...
--foldseek_sensitivity	number	9.5	Search sensitivity (1
--foldseek_coverage	number	0.0	Minimum fraction of aligned residues (0
--foldseek_alignment_type	integer	2	Alignment type: 0=3Di only, 1=TMalign (global),...
--run_consolidation	boolean	false	Enable consolidated metrics report generation
--report_top_n	integer	10	Number of top designs to highlight in consolida...
--max_cpus	integer	16	Maximum number of CPUs per process
--max_memory	string	"128.GB"	Maximum memory per process
--max_time	string	"240.h"	Maximum time per process
--max_gpus	integer	1	Maximum number of GPUs per process
--publish_dir_mode	string	"copy"	Method for publishing outputs
--tracedir	string	"${params.outdir}/pipeline_info"	Directory to store pipeline execution traces
--validate_params	boolean	true	Validate parameters against the schema at runtime
--show_hidden_params	boolean	false	Show hidden parameters in help message
--help	boolean	"null"	Display help text
--version	boolean	"null"	Display version and exit