proteinfold: Parameters

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

Path to comma-separated file containing information about the samples in the experiment.

required

type: string

pattern: ^\S+\.csv$

The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.

required

type: string

Specifies the mode in which the pipeline will be run. mode can be any combination of [‘alphafold2’, ‘alphafold3’, ‘colabfold’, ‘esmfold’, ‘rosettafold_all_atom’, ‘boltz’, ‘helixfold3’] separated by a comma (’,’) with no spaces.

type: string

default: alphafold2

Run on CPUs (default) or GPUs

type: boolean

Split input multi-fasta file in separated fasta files each of them containing one sequence to be folded

type: boolean

Email address for completion summary.

type: string

pattern: ^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$

MultiQC report title. Printed as page header, used for filename if not otherwise specified.

type: string

The directory where reference data is stored. Individual methods can be overwritten with method-specific paths.

type: string

Global toggle for full database usage.

type: boolean

UniRef major release

type: string

Use the cloud MSA server

type: boolean

Specify your custom MMSeqs2 API server url

type: string

AlphaFold2 options.

Maximum date of the PDB templates used by ‘AlphaFold2’ mode

type: string

default: 2038-01-19

pattern: ^\d{4}-\d{2}-\d{2}$

If true uses the full version of the BFD database otherwise, otherwise it uses its reduced version, small bfd

type: boolean

Specifies the mode in which AlphaFold2 will be run

type: string

Model preset for ‘AlphaFold2’ mode

type: string

Random seed to control stochastic alphafold inference.

type: string

Alphafold2 parameters version

type: string

ColabFold options.

Model preset for ‘colabfold’ mode

type: string

Number of recycles for ColabFold

type: integer

default: 3

Use Amber minimization to refine the predicted structures

type: boolean

default: true

Specify the way that MMSeqs2 will load the required databases in memory

type: integer

Use PDB templates

type: boolean

default: true

Create databases indexes when running colabfold_local mode

type: boolean

ESMFold options.

Specifies the number of recycles used by ESMFold

type: integer

default: 4

Specifies whether is a ‘monomer’ or ‘multimer’ prediction

type: string

Boltz options.

run Boltz-2 using inference time potentials

type: boolean

Sets the model to use for prediction. Default is boltz2

type: string

Foldseek options.

Specifies the mode of foldseek search.

type: string

The ID of Foldseek databases

type: string

Specifies the path to foldseek databases used by ‘foldseek’.

type: string

Specifies the arguments to be passed to foldseek easysearch command

type: string

HelixFold3 options

The numerical precision used by the HelixFold3 model.

type: string

Number of independent predictions made with the HelixFold3 model

type: integer

default: 4

No PDB template released after this date will be used to guide predictions.

type: string

default: 2038-01-19

Options to skip various steps within the workflow.

Skip MultiQC.

type: boolean

Skip visualisation reports.

type: boolean

Parameters used to describe centralised config profiles. These should not be edited.

Git commit id for Institutional configs.

hidden

type: string

default: master

Base directory for Institutional configs.

hidden

type: string

default: https://raw.githubusercontent.com/nf-core/configs/master

Institutional config name.

hidden

type: string

Institutional config description.

hidden

type: string

Institutional config contact information.

hidden

type: string

Institutional config URL link.

hidden

type: string

Parameters used to provide the links to the DBs and parameters public resources to AlphaFold2.

Link to BFD dababase

type: string

default:

https://storage.googleapis.com/alphafold-databases/casp14_versions/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt.tar.gz

Link to a reduced version of the BFD dababase

type: string

default: https://storage.googleapis.com/alphafold-databases/reduced_dbs/bfd-first_non_consensus_sequences.fasta.gz

Link to the AlphaFold2 parameters

type: string

default: https://storage.googleapis.com/alphafold/alphafold_params_2022-12-06.tar

Link to the MGnify database

type: string

default: https://ftp.ebi.ac.uk/pub/databases/metagenomics/peptide_database/2024_04/mgy_clusters.fa.gz

Link to the PDB70 database

type: string

default: https://wwwuser.gwdguser.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/pdb70_from_mmcif_220313.tar.gz

Link to the PDB mmCIF database

type: string

default: rsync.rcsb.org::ftp_data/structures/divided/mmCIF/

Link to the PDB obsolete database

type: string

default: https://files.wwpdb.org/pub/pdb/data/status/obsolete.dat

Link to the Uniclust30 database

type: string

default: https://wwwuser.gwdguser.de/~compbiol/uniclust/2023_02/UniRef30_2023_02_hhsuite.tar.gz

Link to the UniRef90 database

type: string

default: https://ftp.ebi.ac.uk/pub/databases/uniprot/uniref/uniref90/uniref90.fasta.gz

Link to the PDB SEQRES database

type: string

default: https://files.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt

Link to the SwissProt UniProt database

type: string

default: https://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz

Link to the TrEMBL UniProt database

type: string

default: https://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.fasta.gz

Parameters used to provide the paths to the DBs and parameters for AlphaFold2.

Specifies the DB and PARAMS path used by ‘AlphaFold2’ mode

type: string

Path to BFD dababase

type: string

default: null/bfd/*

Path to a reduced version of the BFD database

type: string

default: null/small_bfd/*

Path to the AlphaFold2 parameters

type: string

default: null/params/alphafold_params_2022-12-06/*

Path to the MGnify database

type: string

default: null/mgnify/*

Path to the PDB70 database

type: string

default: null/pdb70/**

Path to the PDB mmCIF database

type: string

default: null/pdb_mmcif/mmcif_files

Path to the PDB obsolete file

type: string

default: null/pdb_mmcif/obsolete.dat

Path to the Uniref30 database

type: string

default: null/uniref30/*

Path to the UniRef90 database

type: string

default: null/uniref90/*

Path to the PDB SEQRES database

type: string

default: null/pdb_seqres/*

Path to UniProt database containing the SwissProt and the TrEMBL databases

type: string

default: null/uniprot/*

Parameters used to provide the links to the DBs and parameters public resources to Alphafold3.

Specifies the DB and PARAMS path used by ‘AlphaFold3’ mode

type: string

Link to a reduced version of the BFD dababase

type: string

default: https://storage.googleapis.com/alphafold-databases/v3.0/bfd-first_non_consensus_sequences.fasta.zst

Link to the MGnify database

type: string

default: https://storage.googleapis.com/alphafold-databases/v3.0/mgy_clusters_2022_05.fa.zst

Link to the PDB mmCIF database

type: string

default: https://storage.googleapis.com/alphafold-databases/v3.0/pdb_2022_09_28_mmcif_files.tar.zst

Link to the UniRef90 database

type: string

default: https://storage.googleapis.com/alphafold-databases/v3.0/uniref90_2022_05.fa.zst

Link to the PDB SEQRES database

type: string

default: https://storage.googleapis.com/alphafold-databases/v3.0/pdb_seqres_2022_09_28.fasta.zst

Link to the UniProt database

type: string

default: https://storage.googleapis.com/alphafold-databases/v3.0/uniprot_all_2021_04.fa.zst

Link to the RNAcentral database

type: string

default: https://storage.googleapis.com/alphafold-databases/v3.0/rnacentral_active_seq_id_90_cov_80_linclust.fasta.zst

Link to the nt_rna database

type: string

default: https://storage.googleapis.com/alphafold-databases/v3.0/nt_rna_2023_02_23_clust_seq_id_90_cov_80_rep_seq.fasta.zst

Link to the Rfam database

type: string

default: https://storage.googleapis.com/alphafold-databases/v3.0/rfam_14_9_clust_seq_id_90_cov_80_rep_seq.fasta.zst

Parameters used to provide the paths to the DBs and parameters for Alphafold2.

Path to the reduced version of the BFD database

type: string

default: null/small_bfd/*

Path to the Alphafold3 parameters

type: string

default: null/params/*

Path to the MGnify database

type: string

default: null/mgnify/*

Path to the PDB mmCIF database

type: string

default: null/pdb_mmcif/mmcif_files

Path to the UniRef90 database

type: string

default: null/uniref90/*

Path to the PDB SEQRES database

type: string

default: null/pdb_seqres/*

Path to UniProt database containing the SwissProt and the TrEMBL databases

type: string

default: null/uniprot/*

Path to the RNAcentral database

type: string

default: null/rnacentral/*

Path to the nt_rna database

type: string

default: null/nt_rna/*

Path to the Rfam database

type: string

default: null/rfam/*

Parameters used to provide the links to the DBs and parameters public resources to ColabFold.

Link to the ColabFold database

type: string

default: https://opendata.mmseqs.org/colabfold/colabfold_envdb_202108.db.tar.gz

Link to the UniRef30 database

type: string

default: https://opendata.mmseqs.org/colabfold/uniref30_2302.db.tar.gz

Link to the Alphafold2 parameters for Colabfold

type: string

Parameters used to provide the paths to the DBs and parameters public resources to ColabFold.

Specifies the PARAMS and DB path used by ‘colabfold’ mode

type: string

Link to the ColabFold database

type: string

default: null/colabfold_envdb/*

Link to the UniRef30 database

type: string

default: null/colabfold_uniref30/*

Link to the Alphafold2 parameters for Colabfold

type: string

Dictionary with Alphafold2 parameters tags

type: object

Parameters used to provide the links to the parameters public resources to ESMFold.

Link to the ESMFold 3B-v1 model

type: string

default: https://dl.fbaipublicfiles.com/fair-esm/models/esmfold_3B_v1.pt

Link to the ESMFold t36-3B-UR50D model

type: string

default: https://dl.fbaipublicfiles.com/fair-esm/models/esm2_t36_3B_UR50D.pt

Link to the ESMFold t36-3B-UR50D-contact-regression model

type: string

default: https://dl.fbaipublicfiles.com/fair-esm/regression/esm2_t36_3B_UR50D-contact-regression.pt

Parameters used to provide the paths to the parameters public resources to ESMFold.

Specifies the PARAMS path used by ‘esmfold’ mode

type: string

Link to the ESMFold parameters

type: string

default: null/params/*

Links used to provide model links and weight links to Boltz

Link to download CCD file

type: string

default: https://huggingface.co/boltz-community/boltz-1/resolve/main/ccd.pkl

Link to download model file

type: string

default: https://huggingface.co/boltz-community/boltz-1/resolve/main/boltz1_conf.ckpt

Link to download boltz affinity file

type: string

default: https://huggingface.co/boltz-community/boltz-2/resolve/main/boltz2_aff.ckpt

Link to download boltz-2 conf file

type: string

default: https://huggingface.co/boltz-community/boltz-2/resolve/main/boltz2_conf.ckpt

Link to download boltz-2 mols

type: string

default: https://huggingface.co/boltz-community/boltz-2/resolve/main/mols.tar

Paths used to provide model paths and weight paths to Boltz

Path to boltz databases

type: string

Path to CCD file

type: string

default: null/params/ccd.pkl

Path to boltz Model file

type: string

default: null/params/boltz1_conf.ckpt

Path to boltz affinity file

type: string

default: null/params/boltz2_aff.ckpt

Path to boltz-2 conf file

type: string

default: null/params/boltz2_conf.ckpt

Path to boltz-2 mols

type: string

default: null/params/mols/

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

Display version and exit.

hidden

type: boolean

Method used to save pipeline results to output directory.

hidden

type: string

Email address for completion summary, only when pipeline fails.

hidden

type: string

pattern: ^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$

Send plain-text email instead of HTML.

hidden

type: boolean

File size limit when attaching MultiQC reports to summary emails.

hidden

type: string

default: 25.MB

pattern: ^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$

Do not use coloured log outputs.

hidden

type: boolean

Incoming hook URL for messaging service

hidden

type: string

Custom config file to supply to MultiQC.

hidden

type: string

Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file

hidden

type: string

Custom MultiQC yaml file containing HTML including a methods description.

type: string

Boolean whether to validate parameters against the schema at runtime

hidden

type: boolean

default: true

Base URL or local path to location of pipeline test dataset files

hidden

type: string

default: https://raw.githubusercontent.com/nf-core/test-datasets/

Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.

hidden

type: string

Display the help message.

type: boolean,string

Display the full detailed help message.

type: boolean

Display hidden parameters in the help message (only works when —help or —help_full are provided).

type: boolean

Parameters used to provide the paths to the DBs and parameters for RoseTTAFold All Atom.

Link to the UniRef30 database for RoseTTAFold All Atom

type: string

default: https://wwwuser.gwdguser.de/~compbiol/uniclust/2023_02/UniRef30_2023_02_hhsuite.tar.gz

Link to the BFD database for RoseTTAFold All Atom

type: string

default: https://bfd.mmseqs.com/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt.tar.gz

Link to the PDB100 database for RoseTTAFold All Atom

type: string

default: https://files.ipd.uw.edu/pub/RoseTTAFold/pdb100_2021Mar03.tar.gz

Link to the RoseTTAFold All Atom paper weights

type: string

default: http://files.ipd.uw.edu/pub/RF-All-Atom/weights/RFAA_paper_weights.pt

Parameters used to provide the paths to the DBs and parameters for RoseTTAFold All Atom.

Path to RoseTTAFold All Atom database

type: string

Path to UniRef30 database for RoseTTAFold All Atom

type: string

default: null/uniref30/*

Path to BFD database for RoseTTAFold All Atom

type: string

default: null/bfd/*

Path to PDB100 database for RoseTTAFold All Atom

type: string

default: null/pdb100/*

Path to RoseTTAFold All Atom paper weights

type: string

default: null/params/RFAA_paper_weights.pt

Parameters used to provide the paths to the DBs and parameters for HelixFold3.

Path to HelixFold3 database

type: string

Path to HelixFold3 init models

type: string

default: null/params/HelixFold3-240814.pdparams

Path to UniRef30 database for HelixFold3

type: string

default: null/uniref30/*

Path to CCD preprocessed file for HelixFold3

type: string

default: null/params/ccd_preprocessed_etkdg.pkl.gz

Path to Rfam database for HelixFold3

type: string

default: null/rfam/Rfam-14.9_rep_seq.fasta

Path to BFD database for HelixFold3

type: string

default: null/bfd/*

Path to reduced BFD database for HelixFold3

type: string

default: null/small_bfd/*

Path to UniProt database for HelixFold3

type: string

default: null/uniprot/*

Path to PDB SEQRES database for HelixFold3

type: string

default: null/pdb_seqres/*

Path to UniRef90 database for HelixFold3

type: string

default: null/uniref90/*

Path to MGnify database for HelixFold3

type: string

default: null/mgnify/*

Path to PDB mmCIF database for HelixFold3

type: string

default: null/pdb_mmcif/mmcif_files

Path to Maxit Suite for HelixFold3

type: string

default: null/maxit-v11.200-prod-src

Path to obsolete PDB file for HelixFold3

type: string

default: null/pdb_mmcif/obsolete.dat

Parameters used to provide the links to the parameters public resources to HelixFold3.

Link to HelixFold3 init models

type: string

default: https://paddlehelix.bd.bcebos.com/HelixFold3/params/HelixFold3-params-240814.zip

Link to UniRef30 database for HelixFold3

type: string

default: https://wwwuser.gwdguser.de/~compbiol/uniclust/2023_02/UniRef30_2023_02_hhsuite.tar.gz

Link to CCD preprocessed file for HelixFold3

type: string

default: https://paddlehelix.bd.bcebos.com/HelixFold3/CCD/ccd_preprocessed_etkdg.pkl.gz

Link to Rfam database for HelixFold3

type: string

default: https://paddlehelix.bd.bcebos.com/HelixFold3/MSA/Rfam-14.9_rep_seq.fasta

Link to BFD database for HelixFold3

type: string

default:

https://storage.googleapis.com/alphafold-databases/casp14_versions/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt.tar.gz

Link to reduced BFD database for HelixFold3

type: string

default: https://storage.googleapis.com/alphafold-databases/reduced_dbs/bfd-first_non_consensus_sequences.fasta.gz

Link to PDB SEQRES database for HelixFold3

type: string

default: https://files.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt

Link to UniRef90 database for HelixFold3

type: string

default: ftp://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref90/uniref90.fasta.gz

Link to MGnify database for HelixFold3

type: string

default: https://ftp.ebi.ac.uk/pub/databases/metagenomics/peptide_database/2024_04/mgy_clusters.fa.gz

Link to PDB mmCIF database for HelixFold3

type: string

default: rsync.rcsb.org::ftp_data/structures/divided/mmCIF/

Link to UniProt SwissProt database for HelixFold3

type: string

default: ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz

Link to UniProt TrEMBL database for HelixFold3

type: string

default: ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.fasta.gz

Link to obsolete PDB file for HelixFold3

type: string

default: https://files.rcsb.org/pub/pdb/data/status/obsolete.dat

Link to Maxit Suite for HelixFold3

type: string

default: https://proteinfold-dataset.s3.amazonaws.com/test-data/db/helixfold3/maxit-v11.200-prod-src.tar.gz

nf-core/proteinfold