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

type: string

Run on CPUs (default) or GPUs

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

Alphafold2 options.

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

type: string
default: 2020-05-14

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

type: string

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

Colabfold options.

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

type: string

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 PARAMS path used by ‘esmfold’ mode

type: string

Specifies the number of recycles used by Esmfold

type: integer
default: 4

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

type: string

Options to skip various steps within the workflow.

Skip MultiQC.

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

Set the top limit for requested resources for any single job.

Maximum number of CPUs that can be requested for any single job.

hidden
type: integer
default: 16

Maximum amount of memory that can be requested for any single job.

hidden
type: string
default: 128.GB
pattern: ^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$

Maximum amount of time that can be requested for any single job.

hidden
type: string
default: 240.h
pattern: ^(\d+\.?\s*(s|m|h|d|day)\s*)+$

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.

Path to BFD dababase

type: string

Path to a reduced version of the BFD database

type: string

Path to the Alphafold2 parameters

type: string

Path to the MGnify database

type: string

Path to the PDB70 database

type: string

Path to the PDB mmCIF database

type: string

Path to the Uniref30 database

type: string

Path to the UniRef90 database

type: string

Path to the PDB SEQRES database

type: string

Path to UniProt database containing the SwissProt and the TrEMBL databases

type: string

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 links to the DBs and parameters public resources to Colabfold.

Link to the Colabfold database

type: string

Link to the UniRef30 database

type: string

Link to the Alphafold2 parameters for Colabfold

type: string

Dictionary with Alphafold2 parameters tags

type: string

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 links to the parameters public resources to Esmfold.

Link to the Esmfold parameters

type: string

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

Display help text.

hidden
type: boolean

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

Show all params when using --help

hidden
type: boolean

Validation of parameters fails when an unrecognised parameter is found.

hidden
type: boolean

Validation of parameters in lenient more.

hidden
type: boolean

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

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