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.

type: string

pattern: ^\S+\.csv$

You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See usage docs.

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

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

pattern:

^(alphafold2|alphafold3|colabfold|esmfold|rosettafold_all_atom|helixfold3|boltz|)(,(alphafold2|alphafold3|colabfold|esmfold|rosettafold_all_atom|helixfold3|boltz)?,?)*(?<!,)$

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})$

Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (~/.nextflow/config) then you don't need to specify this on the command line for every run.

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

UniRef major release

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

Alphafold2 parameters version

type: string

Alphafold3 options.

Specifies the DB and PARAMS path used by 'AlphaFold3' mode

type: string

ColabFold options.

Specifies the MSA server used by ColabFold

type: string

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

Specify your custom MMSeqs2 API server url

type: string

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.

Use the cloud MSA server

type: boolean

default: true

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

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

If you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.

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://storage.googleapis.com/alphafold-databases/v2.3/mgy_clusters_2022_05.fa.gz

Link to the PDB70 database

type: string

default: http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/old-releases/pdb70_from_mmcif_200916.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://storage.googleapis.com/alphafold-databases/v2.3/UniRef30_2021_03.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.

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

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/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/*

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

Link to the ColabFold database

type: string

default: http://wwwuser.gwdg.de/~compbiol/colabfold/colabfold_envdb_202108.tar.gz

Link to the UniRef30 database

type: string

default: https://wwwuser.gwdg.de/~compbiol/colabfold/uniref30_2302.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

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

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

The Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.

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})$

An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.

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

Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.

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

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

type: string

default: http://wwwuser.gwdg.de/~compbiol/uniclust/2020_06/UniRef30_2020_06_hhsuite.tar.gz

type: string

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

type: string

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

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.

type: string

default: null/uniref30/*

type: string

default: null/bfd/*

type: string

default: null/pdb100/*

type: string

default: null/params/RFAA_paper_weights.pt

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

type: string

default: null/params/HelixFold3-240814.pdparams

type: string

default: null/uniref30/*

type: string

default: null/params/ccd_preprocessed_etkdg.pkl.gz

type: string

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

type: string

default: null/bfd/*

type: string

default: null/small_bfd/*

type: string

default: null/uniprot/*

type: string

default: null/pdb_seqres/*

type: string

default: null/uniref90/*

type: string

default: null/mgnify/*

type: string

default: null/pdb_mmcif/mmcif_files

type: string

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

type: string

default: null/pdb_mmcif/obsolete.dat

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

type: string

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

type: string

default: https://storage.googleapis.com/alphafold-databases/casp14_versions/uniclust30_2018_08_hhsuite.tar.gz

type: string

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

type: string

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

type: string

default:

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

type: string

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

type: string

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

type: string

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

type: string

default: https://storage.googleapis.com/alphafold-databases/casp14_versions/mgy_clusters_2018_12.fa.gz

type: string

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

type: string

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

type: string

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

type: string

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

nf-core/proteinfold