proteinfold
nf-core/proteinfold
Protein 3D structure prediction pipeline
Key tools
Run it
nfclaw run proteinfold --input samplesheet.csv --outdir results -profile dockernextflow run pipelines/proteinfold/upstream -profile docker --input samplesheet.csv --outdir resultsnfclaw run proteinfold --demo --outdir results # adds the upstream test profile (-profile test,docker)Inputs
| column | type | required | allowed values | constraints |
|---|---|---|---|---|
sequence | string | no | matches ^\S+$ | |
id | string | no | matches ^\S+$ | |
fasta | string (file path) | yes | matches ^\S+\.(fa(sta)?|faa|yaml|yml|json)$ |
--input must match ^\S+\.csv$.
The samplesheet is a CSV with this header (the columns the schema requires); fill each value per the table above and reference.md (no example value is invented here):
fastaAny of the optional columns above may be appended to the header when your data needs them: sequence, id.
From data files. --input may also be the data files — a directory (searched recursively), a quoted glob, or files (--input once per file) — from which nfclaw writes this samplesheet: id from file names; fasta from files matching their patterns, by sample name. Set other columns with --sheet-set COLUMN=VALUE. Preview it with --check; a run records it in <outdir>/provenance/ for replay.
Resources
Resource requests follow the pipeline's configs and selected profiles. nf-core's resource labels often assume a server — a single step can request far more memory than a workstation has, and retry rules can increase requests. If a run fails with Process requirement exceeds available memory (or CPUs), cap every request, and every retry, at what this machine actually has:
nfclaw run proteinfold --input samplesheet.csv --outdir results -profile docker \ --limit-cpus 4 --limit-memory 15.GBnfclaw turns those into Nextflow's process.resourceLimits and passes them as a -c config — the mechanism nf-core prescribes for exactly this (docs). Set them to the machine's real capacity. --limit-time DURATION also caps how long any one task may run: a task that needs longer is stopped, and so is every retry, so set it only as a deliberate ceiling, never as a guess at how long the analysis takes. The generated config is kept in <outdir>/provenance/, so commands.sh replays the run under the same ceiling.
Nextflow engine
This release declares nextflowVersion = '!>=25.10.2'.
To pin this release's declared minimum engine — useful when a newer Nextflow has incompatible config parsing:
nfclaw run proteinfold ... --nxf-ver 25.10.2--nxf-ver is recorded in <outdir>/provenance/, so the replay uses the same engine. See known-issues.
Demo
nfclaw run proteinfold --demo --outdir results # adds the upstream test profile (-profile test,docker)This release's test profile sets stubRun = true: the demo runs every task's stub block, which writes placeholder files instead of running its tool. It checks the workflow's wiring and publication, not its analysis, and its outputs hold no results; nfclaw status reports the success with a stub run: caveat.
Samplesheet
A CSV with this header (the columns the schema requires). Fill each value per the constraints below; optional columns from the table may be appended.
fasta| Column | Type | Required | Allowed / constraints |
|---|---|---|---|
sequence | string | optional | matches ^\S+$ |
id | string | optional | matches ^\S+$ |
fasta | string (file path) | required | matches ^\S+\.(fa(sta)?|faa|yaml|yml|json)$ |
Required parameters
--inputstring (file path)Path to comma-separated file containing information about the samples in the experiment.
Constraint · matches ^\S+\.csv$
--outdirstring (directory path)The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
Parameter explorer
182 parameters · 27 groupsEvery parameter from the pinned nextflow_schema.json. nfclaw checks explicit values before launch; complex rules use the pinned pipeline's runtime validation. Search, filter by group, and expand any parameter for its default, allowed values and constraints.
164 parameters · 18 hidden
Alphafold2 Dbs And Parameters Link options12
Link to BFD dababase
Link to the MGnify database
Link to the AlphaFold2 parameters
Link to the PDB70 database
Link to the PDB mmCIF database
Link to the PDB obsolete database
Link to the PDB SEQRES database
Link to a reduced version of the BFD dababase
Link to the SwissProt UniProt database
Link to the TrEMBL UniProt database
Link to the Uniclust30 database
Link to the UniRef90 database
Alphafold2 Dbs And Parameters Paths options12
Path to BFD dababase
Specifies the DB and PARAMS path used by 'AlphaFold2' mode
Path to the MGnify database
Path to the AlphaFold2 parameters
Path to the PDB70 database
Path to the PDB mmCIF database
Path to the PDB obsolete file
Path to the PDB SEQRES database
Path to a reduced version of the BFD database
Path to UniProt database containing the SwissProt and the TrEMBL databases
Path to the Uniref30 database
Path to the UniRef90 database
Alphafold2 options6
If true uses the full version of the BFD database otherwise, otherwise it uses its reduced version, small bfd
Maximum date of the PDB templates used by 'AlphaFold2' mode
Specifies the mode in which AlphaFold2 will be run
Model preset for 'AlphaFold2' mode
Alphafold2 parameters version
Random seed to control stochastic alphafold inference.
Alphafold3 Dbs And Parameters Link options10
Specifies the DB and PARAMS path used by 'AlphaFold3' mode
Link to the MGnify database
Link to the nt_rna database
Link to the PDB mmCIF database
Link to the PDB SEQRES database
Link to the Rfam database
Link to the RNAcentral database
Link to a reduced version of the BFD dababase
Link to the UniProt database
Link to the UniRef90 database
Alphafold3 Dbs And Parameters Path options10
Path to the MGnify database
Path to the nt_rna database
Path to the Alphafold3 parameters
Path to the PDB mmCIF database
Path to the PDB SEQRES database
Path to the Rfam database
Path to the RNAcentral database
Path to the reduced version of the BFD database
Path to UniProt database containing the SwissProt and the TrEMBL databases
Path to the UniRef90 database
Boltz Dbs And Model Links options5
Link to download boltz affinity file
Link to download boltz-2 conf file
Link to download boltz-2 mols
Link to download CCD file
Link to download model file
Boltz Dbs And Parameters Paths options6
Path to boltz affinity file
Path to boltz-2 conf file
Path to boltz-2 mols
Path to CCD file
Path to boltz databases
Path to boltz Model file
Boltz options3
Sets the model to use for prediction. Default is boltz2
Use optimized Triton-based CUDA kernels for Boltz inference
run Boltz-2 using inference time potentials
Colabfold Dbs And Parameters Link options3
Link to the Alphafold2 parameters for Colabfold
Link to the ColabFold database
Link to the UniRef30 database
Colabfold Dbs And Parameters Paths options5
Link to the Alphafold2 parameters for Colabfold
Dictionary with Alphafold2 parameters tags
Specifies the PARAMS and DB path used by 'colabfold' mode
Link to the ColabFold database
Link to the UniRef30 database
Colabfold options7
Create databases indexes when running colabfold_local mode
Specify the way that MMSeqs2 will load the required databases in memory
Model preset for 'colabfold' mode
Number of recycles for ColabFold
Use Amber minimization to refine the predicted structures
Use GPU for Amber relaxation in ColabFold
Use PDB templates
Esmfold options2
Specifies whether is a 'monomer' or 'multimer' prediction
Specifies the number of recycles used by ESMFold
Esmfold Parameters Link options3
Link to the ESMFold t36-3B-UR50D model
Link to the ESMFold t36-3B-UR50D-contact-regression model
Link to the ESMFold 3B-v1 model
Esmfold Parameters Paths options2
Specifies the PARAMS path used by 'esmfold' mode
Link to the ESMFold parameters
Foldseek options4
The ID of Foldseek databases
Specifies the path to foldseek databases used by 'foldseek'.
Specifies the arguments to be passed to foldseek easysearch command
Skip foldseek structural similarity search.
Generic options4
Display the help message.
Display the full detailed help message.
Custom MultiQC yaml file containing HTML including a methods description.
Display hidden parameters in the help message (only works when --help or --help_full are provided).
Helixfold3 Dbs And Parameters Link options14
Link to BFD database for HelixFold3
Link to CCD preprocessed file for HelixFold3
Link to HelixFold3 init models
Link to Maxit Suite for HelixFold3
Link to MGnify database for HelixFold3
Link to obsolete PDB file for HelixFold3
Link to PDB mmCIF database for HelixFold3
Link to PDB SEQRES database for HelixFold3
Link to Rfam database for HelixFold3
Link to reduced BFD database for HelixFold3
Link to UniRef30 database for HelixFold3
Link to UniProt SwissProt database for HelixFold3
Link to UniProt TrEMBL database for HelixFold3
Link to UniRef90 database for HelixFold3
Helixfold3 Dbs And Parameters Paths options14
Path to BFD database for HelixFold3
Path to CCD preprocessed file for HelixFold3
Path to HelixFold3 database
Path to HelixFold3 init models
Path to Maxit Suite for HelixFold3
Path to MGnify database for HelixFold3
Path to obsolete PDB file for HelixFold3
Path to PDB mmCIF database for HelixFold3
Path to PDB SEQRES database for HelixFold3
Path to Rfam database for HelixFold3
Path to reduced BFD database for HelixFold3
Path to UniRef30 database for HelixFold3
Path to UniProt database for HelixFold3
Path to UniRef90 database for HelixFold3
Helixfold3 options3
Number of independent predictions made with the HelixFold3 model
No PDB template released after this date will be used to guide predictions.
The numerical precision used by the HelixFold3 model.
Input Output options13
The directory where reference data is stored. Individual methods can be overwritten with method-specific paths.
Email address for completion summary.
Global toggle for full database usage.
Path to comma-separated file containing information about the samples in the experiment.
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', 'rosettafold2na'] separated by a comma (',') with no spaces.
Specify your custom MMSeqs2 API server url
MultiQC report title. Printed as page header, used for filename if not otherwise specified.
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
Keep raw intermediate files
Split input multi-fasta file in separated fasta files each of them containing one sequence to be folded
UniRef major release
Run on CPUs (default) or GPUs
Use the cloud MSA server
Process Skipping options2
Skip MultiQC.
Skip visualisation reports.
Rosettafold2na Dbs And Parameters Link options9
Rosettafold2na Dbs And Parameters Path options5
Path to the RNA folder containing all necessary RNA databases for RF2NA
Rosettafold2na options1
Specifies the DB and PARAMS path used by 'RosettaFold2NA' mode
Rosettafold All Atom Dbs And Parameters Links options4
Link to the BFD database for RoseTTAFold All Atom
Link to the RoseTTAFold All Atom paper weights
Link to the PDB100 database for RoseTTAFold All Atom
Link to the UniRef30 database for RoseTTAFold All Atom
Rosettafold All Atom Dbs And Parameters Paths options5
Path to BFD database for RoseTTAFold All Atom
Path to RoseTTAFold All Atom database
Path to RoseTTAFold All Atom paper weights
Path to PDB100 database for RoseTTAFold All Atom
Path to UniRef30 database for RoseTTAFold All Atom
Outputs
Results land in --outdir; the files and directory layout depend on the selected workflow, parameters and publication settings. Run metadata is normally placed in <outdir>/pipeline_info/ (execution report, software versions), when those outputs are enabled. The pinned tree includes MultiQC support; a report is produced only when its workflow step runs. --skip-multiqc true disables that report. nfclaw run also writes <outdir>/provenance/ with the exact params file and the run log, <outdir>/provenance/logs/run.log — the whole launch, whose last line states the outcome (Nextflow's own log is <outdir>/.nextflow.log); unless --no-provenance it adds a run manifest (pinned version, commit and exact command), input/output SHA-256 checksums, and a replayable commands.sh.
The exact output files and directory layout for this release are documented upstream: github.com/nf-core/proteinfold/blob/2.0.0/docs/output.md
Check a run — in the foreground or the background — with nfclaw status <outdir>: success, still running, how it ended (with the error), or stopped without an outcome; exit 0 success, 3 running, 1 otherwise.