nf-core/proteinfold
Protein 3D structure prediction pipeline
1.1.0). The latest
stable release is
1.1.1
.
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.
string^\S+\.csv$You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See usage docs.
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringSpecifies the mode in which the pipeline will be run
stringRun on CPUs (default) or GPUs
booleanEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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.
stringAlphafold2 options.
Maximum date of the PDB templates used by 'AlphaFold2' mode
string2020-05-14Specifies the DB and PARAMS path used by 'AlphaFold2' mode
stringIf true uses the full version of the BFD database otherwise, otherwise it uses its reduced version, small bfd
booleanSpecifies the mode in which Alphafold2 will be run
stringModel preset for 'AlphaFold2' mode
stringColabfold options.
Specifies the PARAMS and DB path used by 'colabfold' mode
stringSpecifies the MSA server used by Colabfold
stringModel preset for 'colabfold' mode
stringNumber of recycles for Colabfold
integer3Use Amber minimization to refine the predicted structures
booleantrueSpecify the way that MMSeqs2 will load the required databases in memory
integerSpecify your custom MMSeqs2 API server url
stringUse PDB templates
booleantrueCreate databases indexes when running colabfold_local mode
booleanEsmfold options.
Specifies the PARAMS path used by 'esmfold' mode
stringSpecifies the number of recycles used by Esmfold
integer4Specifies whether is a 'monomer' or 'multimer' prediction
stringOptions to skip various steps within the workflow.
Skip MultiQC.
booleanParameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterIf 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.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1
Maximum amount of memory that can be requested for any single job.
string128.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. --max_memory '8.GB'
Maximum amount of time that can be requested for any single job.
string240.h^(\d+\.?\s*(s|m|h|d|day)\s*)+$Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. --max_time '2.h'
Parameters used to provide the links to the DBs and parameters public resources to Alphafold2.
Link to BFD dababase
stringhttps://storage.googleapis.com/alphafold-databases/casp14_versions/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt.tar.gzLink to a reduced version of the BFD dababase
stringhttps://storage.googleapis.com/alphafold-databases/reduced_dbs/bfd-first_non_consensus_sequences.fasta.gzLink to the Alphafold2 parameters
stringhttps://storage.googleapis.com/alphafold/alphafold_params_2022-12-06.tarLink to the MGnify database
stringhttps://storage.googleapis.com/alphafold-databases/v2.3/mgy_clusters_2022_05.fa.gzLink to the PDB70 database
stringhttp://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/old-releases/pdb70_from_mmcif_200916.tar.gzLink to the PDB mmCIF database
stringrsync.rcsb.org::ftp_data/structures/divided/mmCIF/Link to the PDB obsolete database
stringhttps://files.wwpdb.org/pub/pdb/data/status/obsolete.datLink to the Uniclust30 database
stringhttps://storage.googleapis.com/alphafold-databases/v2.3/UniRef30_2021_03.tar.gzLink to the UniRef90 database
stringhttps://ftp.ebi.ac.uk/pub/databases/uniprot/uniref/uniref90/uniref90.fasta.gzLink to the PDB SEQRES database
stringhttps://files.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txtLink to the SwissProt UniProt database
stringhttps://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gzLink to the TrEMBL UniProt database
stringhttps://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.fasta.gzParameters used to provide the paths to the DBs and parameters for Alphafold2.
Path to BFD dababase
stringPath to a reduced version of the BFD database
stringPath to the Alphafold2 parameters
stringPath to the MGnify database
stringPath to the PDB70 database
stringPath to the PDB mmCIF database
stringPath to the Uniref30 database
stringPath to the UniRef90 database
stringPath to the PDB SEQRES database
stringPath to UniProt database containing the SwissProt and the TrEMBL databases
stringParameters used to provide the links to the DBs and parameters public resources to Colabfold.
Link to the Colabfold database
stringhttp://wwwuser.gwdg.de/~compbiol/colabfold/colabfold_envdb_202108.tar.gzLink to the UniRef30 database
stringhttps://wwwuser.gwdg.de/~compbiol/colabfold/uniref30_2302.tar.gzLink to the Alphafold2 parameters for Colabfold
stringParameters used to provide the links to the DBs and parameters public resources to Colabfold.
Link to the Colabfold database
stringLink to the UniRef30 database
stringLink to the Alphafold2 parameters for Colabfold
stringDictionary with Alphafold2 parameters tags
stringParameters used to provide the links to the parameters public resources to Esmfold.
Link to the Esmfold 3B-v1 model
stringhttps://dl.fbaipublicfiles.com/fair-esm/models/esmfold_3B_v1.ptLink to the Esmfold t36-3B-UR50D model
stringhttps://dl.fbaipublicfiles.com/fair-esm/models/esm2_t36_3B_UR50D.ptLink to the Esmfold t36-3B-UR50D-contact-regression model
stringhttps://dl.fbaipublicfiles.com/fair-esm/regression/esm2_t36_3B_UR50D-contact-regression.ptParameters used to provide the links to the parameters public resources to Esmfold.
Link to the Esmfold parameters
stringLess common options for the pipeline, typically set in a config file.
Display help text.
booleanDisplay version and exit.
booleanMethod used to save pipeline results to output directory.
stringThe 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.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.
Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Do not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringIncoming hook URL for messaging service. Currently, MS Teams and Slack are supported.
Custom config file to supply to MultiQC.
stringCustom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
stringCustom MultiQC yaml file containing HTML including a methods description.
stringBoolean whether to validate parameters against the schema at runtime
booleantrueShow all params when using --help
booleanBy default, parameters set as hidden in the schema are not shown on the command line when a user runs with --help. Specifying this option will tell the pipeline to show all parameters.
Validation of parameters fails when an unrecognised parameter is found.
booleanBy default, when an unrecognised parameter is found, it returns a warinig.
Validation of parameters in lenient more.
booleanAllows string values that are parseable as numbers or booleans. For further information see JSONSchema docs.
Base URL or local path to location of pipeline test dataset files
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/