nf-core/funcscan

Path to comma-separated file containing sample names and paths to corresponding FASTA files, and optional annotation files.

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

Email address for completion summary.

MultiQC report title. Printed as page header, used for filename if not otherwise specified.

Activate antimicrobial peptide genes screening tools.

Activate antimicrobial resistance gene screening tools.

Activate biosynthetic gene cluster screening tools.

Activates the taxonomic classification of input nucleotide sequences.

Specifies the tool used for taxonomic classification.

If MMseqs2 is chosen as taxonomic classification tool: Specifies if the output of all MMseqs2 subcommands shall be compressed.

Specify a path to MMseqs2-formatted database.

Specify the label of the database to be used.

Specify whether the temporary files should be saved.

Specify whether to save the temporary files.

Specify the alignment type between database and query.

Specify the taxonomic levels to display in the result table.

Specify whether to include or remove the taxonomic lineage.

Specify the speed and sensitivity for taxonomy assignment.

Specify the ORF search sensitivity in the prefilter step.

Specify the mode to assign the taxonomy.

Specify the weights of the taxonomic assignment.

Specify which annotation tool to use for some downstream tools.

Specify whether to save gene annotations in the results directory.

Specify a path to a local copy of a BAKTA database.

Download full or light version of the Bakta database if not supplying own database.

Use the default genome-length optimised mode (rather than the metagenome mode).

Specify the minimum contig size.

Specify the genetic code translation table.

Specify the type of bacteria to be annotated to detect signaling peptides.

Specify that all contigs are complete replicons.

Changes the original contig headers.

Clean the result annotations to standardise them to Genbank/ENA conventions.

Activate tRNA detection & annotation.

Activate tmRNA detection & annotation.

Activate rRNA detection & annotation.

Activate ncRNA detection & annotation.

Activate ncRNA region detection & annotation.

Activate CRISPR array detection & annotation.

Skip CDS detection & annotation.

Activate pseudogene detection & annotation.

Skip sORF detection & annotation.

Activate gap detection & annotation.

Activate oriC/oriT detection & annotation.

Activate generation of circular genome plots.

Supply a path of an HMM file of trusted hidden markov models in HMMER format for CDS annotation

Use the default genome-length optimised mode (rather than the metagenome mode).

Suppress the default clean-up of the gene annotations.

Specify the kingdom that the input represents.

Specify the translation table used to annotate the sequences.

Minimum contig size required for annotation (bp).

E-value cut-off.

Set the assigned minimum coverage.

Allow transfer RNA (trRNA) to overlap coding sequences (CDS).

Use RNAmmer for rRNA prediction.

Force contig name to Genbank/ENA/DDJB naming rules.

Add the gene features for each CDS hit.

Retains contig names.

Specify whether to use Prodigal’s single-genome mode for long sequences.

Does not allow partial genes on contig edges.

Specifies the translation table used for gene annotation.

Forces Prodigal to scan for motifs.

Specify whether to use Pyrodigal’s single-genome mode for long sequences.

Does not allow partial genes on contig edges.

Specifies the translation table used for gene annotation.

Forces Pyrodigal to scan for motifs.

This forces Pyrodigal to append asterisks (*) as stop codon indicators. Do not use when running AMP workflow.

Activates the functional annotation of annotated coding regions to provide more information about the codon regions classified.

Specifies the tool used for further protein annotation.

Change the database version used for annotation.

Path to pre-downloaded InterProScan database.

Assigns the database(s) to be used to annotate the coding regions.

Pre-calculates residue mutual matches.

Specify whether to save pipeline-downloaded databases in your results directory.

Skip AMPlify during AMP screening.

Skip ampir during AMP screening.

Specify which machine learning classification model to use.

Specify minimum protein length for prediction calculation.

Run hmmsearch during AMP screening.

Specify path to the AMP hmm model file(s) to search against. Must have quotes if wildcard used.

Saves a multiple alignment of all significant hits to a file.

Save a simple tabular file summarising the per-target output.

Save a simple tabular file summarising the per-domain output.

Skip Macrel during AMP screening.

The name of the database used to classify the AMPs.

The path to the folder containing the reference database files.

Specifies the prediction tools’ cut-offs.

Filter out all amino acid fragments shorter than this number.

Remove all DRAMP annotations that have an e-value greater than this value.

Retain HMM hits that have an e-value lower than this.

Assign the number of codons used to look for stop codons, upstream and downstream of the AMP hit.

Assign the number of CDSs upstream and downstream of the AMP to look for a transport protein.

Remove hits that have no stop codon upstream and downstream of the AMP.

Assigns the file extension used to identify AMPIR output.

Assigns the file extension used to identify AMPLIFY output.

Assigns the file extension used to identify MACREL output.

Assigns the file extension used to identify HMMER/HMMSEARCH output.

MMseqs2 coverage mode.

Remove hits that have no stop codon upstream and downstream of the AMP.

Remove clusters that don’t have more AMP hits than this number.

MMseqs2 clustering mode.

MMseqs2 alignment coverage.

MMseqs2 sequence identity.

Remove any hits that form a single member cluster.

Skip AMRFinderPlus during the ARG screening.

Specify the path to a local version of the ARMFinderPlus database.

Minimum percent identity to reference sequence.

Minimum coverage of the reference protein.

Specify which NCBI genetic code to use for translated BLAST.

Add the plus genes to the report.

Add identified column to AMRFinderPlus output.

Skip DeepARG during the ARG screening.

Specify the path to the DeepARG database.

Specify the numeric version number of a user supplied DeepaRG database.

Specify which model to use (short or long sequences).

Specify minimum probability cutoff under which hits are discarded.

Specify E-value cutoff under which hits are discarded.

Specify percent identity cutoff for sequence alignment under which hits are discarded.

Specify alignment read overlap.

Specify minimum number of alignments per entry for DIAMOND step of DeepARG.

Skip fARGene during the ARG screening.

Specify comma-separated list of which pre-defined HMM models to screen against

Specify to save intermediate temporary files to results directory.

The threshold score for a sequence to be classified as a (almost) complete gene.

The minimum length of a predicted ORF retrieved from annotating the nucleotide sequences.

Defines which ORF finding algorithm to use.

The translation table/format to use for sequence annotation.

Skip RGI during the ARG screening.

Path to user-defined local CARD database.

Save RGI output .json file.

Specify to save intermediate temporary files in the results directory.

Specify the alignment tool to be used.

Include all of loose, strict and perfect hits (i.e. ≥ 95% identity) found by RGI.

Suppresses the default behaviour of RGI with --arg_rgi_includeloose.

Include screening of low quality contigs for partial genes.

Specify a more specific data-type of input (e.g. plasmid, chromosome).

Run multiple prodigal jobs simultaneously for contigs in a fasta file.

Skip ABRicate during the ARG screening.

Specify the name of the ABRicate database to use. Names of non-default databases can be supplied if --arg_abricate_db provided.

Path to user-defined local ABRicate database directory for using custom databases.

Minimum percent identity of alignment required for a hit to be considered.

Minimum percent coverage of alignment required for a hit to be considered.

Specifies summary output format.

Skip argNorm during ARG screening.

Specify the minimum length of contigs that go into BGC screening.

Specify to save the length-filtered (unannotated) FASTAs used for BGC screening.

Skip antiSMASH during the BGC screening.

Path to user-defined local antiSMASH database.

Minimum length a contig must have to be screened with antiSMASH.

Turn on clusterblast comparison against database of antiSMASH-predicted clusters.

Turn on clusterblast comparison against known gene clusters from the MIBiG database.

Turn on clusterblast comparison against known subclusters responsible for synthesising precursors.

Turn on ClusterCompare comparison against known gene clusters from the MIBiG database.

Generate phylogenetic trees of secondary metabolite group orthologs.

Defines which level of strictness to use for HMM-based cluster detection.

Run Pfam to Gene Ontology mapping module.

Run RREFinder precision mode on all RiPP gene clusters.

Specify which taxonomic classification of input sequence to use.

Run TFBS finder on all gene clusters.

Skip DeepBGC during the BGC screening.

Path to local DeepBGC database folder.

Average protein-wise DeepBGC score threshold for extracting BGC regions from Pfam sequences.

Run DeepBGC’s internal Prodigal step in single mode to restrict detecting genes to long contigs

Merge detected BGCs within given number of proteins.

Merge detected BGCs within given number of nucleotides.

Minimum BGC nucleotide length.

Minimum number of proteins in a BGC.

Minimum number of protein domains in a BGC.

Minimum number of known biosynthetic (as defined by antiSMASH) protein domains in a BGC.

DeepBGC classification score threshold for assigning classes to BGCs.

Skip GECCO during the BGC screening.

Enable unknown region masking to prevent genes from stretching across unknown nucleotides.

The minimum number of coding sequences a valid cluster must contain.

The p-value cutoff for protein domains to be included.

The probability threshold for cluster detection.

The minimum number of annotated genes that must separate a cluster from the edge.

Run hmmsearch during BGC screening.

Specify path to the BGC hmm model file(s) to search against. Must have quotes if wildcard used.

Saves a multiple alignment of all significant hits to a file.

Save a simple tabular file summarising the per-target output.

Save a simple tabular file summarising the per-domain output.

Custom MultiQC yaml file containing HTML including a methods description.

Display the help message.

Display the full detailed help message.

Display hidden parameters in the help message (only works when —help or —help_full are provided).