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Options / Parameters

InterProScan 6 is distributed as a Nextflow workflow, so a typical command combines:

  • Nextflow options with a single dash, such as -profile, -r, and -w
  • InterProScan workflow parameters with a double dash, such as --input and --formats

The tables below describe the InterProScan 6 parameters, plus the main Nextflow options that are part of almost every invocation.

Core invocation options

Option Description
-r, -revision <VERSION> Tells Nextflow which InterProScan version to run. Recommended for reproducibility. For example, use -r 6.0.1 to pin a specific InterProScan release.
-profile <PROFILE> Selects the runtime environment, such as docker, slurm, etc. Common combinations include docker,test and singularity,slurm.
--input <FASTA> Path to the input FASTA file. Required unless a profile such as test supplies it automatically.
--datadir <DATADIR> Directory used for InterPro and member-database data files.
--interpro <VERSION> InterPro release to use. The default is latest. A pinned version such as 108.0 is better for reproducibility.

Tip

--datadir is only required when at least one selected analysis needs external data files. It is not required if you run only self-contained analyses such as COILS, MobiDB-lite, or TMbed.

Input interpretation

Option Description
--nucleic Treats the input as nucleotide FASTA. The workflow translates all six reading frames and analyses the resulting ORFs. Disabled by default; protein FASTA is assumed otherwise.

Analysis selection

Option Description
--applications <LIST> Comma-separated list of analyses to run. By default, InterProScan runs all analyses except the deep-learning-based analyses.
--skip-applications <LIST> Comma-separated list of analyses to exclude. The default is to skip none.
--run-ml Enables deep-learning-based analyses such as DeepTMHMM, SignalP, and TMbed. Disabled by default because these analyses are more resource-intensive.

Info

Some analyses rely on separately licensed third-party applications. This affects the external software component, not your ability to run InterProScan on your own sequences. See Licensed applications.

Tip

Analysis names passed to --applications and --skip-applications are case-insensitive, and hyphens, underscores, and spaces are ignored.

Warning

  • --applications cannot be combined with --skip-applications.
  • --applications cannot be combined with --run-ml.

Output control

Option Description
--outdir <DIR> Directory where output files are written. The default is the current working directory (.).
--outprefix <PREFIX> Base name for output files, without directory or extension. The default is the input filename. It must not contain slashes.
--formats <LIST> Comma-separated output formats. Supported values are gff3, json, jsonl, tsv, and xml. The default is all formats.
--goterms Includes Gene Ontology annotations in supported output files. Disabled by default.
--pathways Includes pathway annotations in supported output files. Disabled by default.
--skip-repr-locations Skips the representative-location selection step. Disabled by default.

Info

--outprefix controls only the filename stem. Use --outdir to choose the output directory.

Execution and resource control

Option Description
--cpus <N> Number of CPU threads allocated per task for applications that support multithreading. The default is 1.
--use-gpu Enables GPU acceleration for compatible deep-learning-based analyses. This only has an effect when GPU-capable analyses are selected and configured.
--max-workers <N> Maximum number of parallel tasks when running locally. If unset, Nextflow uses its normal scheduler behaviour.

External services and data

Option Description
--matches-api-url <URL> Uses an alternative InterPro Matches API endpoint for precomputed results. Default: https://www.ebi.ac.uk/interpro/matches/api.
--no-matches-api Disables the Matches API and forces all analyses to run locally. Disabled by default.
--globus Downloads InterProScan data from the Globus mirror instead of the EMBL-EBI FTP site. Disabled by default.
--skip-interpro-version-check Skips the compatibility check between the workflow version and the selected InterPro data release. Disabled by default.

Other options

Option Description
--help Prints the usage message and exits