Parameters

Full parameter reference for clystere. All parameters can be passed on the command line (--parameter_name value) or set in a params YAML/JSON file (-params-file params.yml).

---

Input / output

Parameter	Default	Description
--input	null	Required. Path to a samplesheet CSV.
--outdir	results	Output directory for published files.
--publish_dir_mode	copy	How Nextflow stages outputs: copy, symlink, move, rellink, link.

---

antiSMASH — basic options

Parameter	Default	Description
--antismash_db	null	Path to an antiSMASH database directory. Downloaded automatically if absent.
--antismash_taxon	bacteria	Taxon preset: bacteria or fungi.
--antismash_genefinding_tool	prodigal	Gene-finding tool: prodigal, prodigal-m, none, or error.
--antismash_minlength	1000	Minimum sequence length (bp) to annotate.
--antismash_limit	-1	Maximum number of sequences to annotate (-1 = no limit).
--antismash_minimal	true	Run in minimal mode (core detection only).
--antismash_accept_failure	false	Continue the pipeline even if antiSMASH exits non-zero.
--antismash_reuse_results	false	Skip antiSMASH and reuse existing results from --outdir/antismash/.
--antismash_extra_args	''	Arbitrary extra arguments appended verbatim to the antiSMASH command.

---

antiSMASH — detection modules

These flags enable additional detection modules. All require --antismash_minimal false (or set the flag alongside --antismash_minimal to override it):

Parameter	antiSMASH flag	Description
--antismash_enable_nrps_pks	--enable-nrps-pks	Full NRPS/PKS analysis
--antismash_enable_terpene	--enable-terpene	Terpene pathway detection
--antismash_enable_lanthipeptides	--enable-lanthipeptides	Lanthipeptide detection
--antismash_enable_lassopeptides	--enable-lassopeptides	Lasso peptide detection
--antismash_enable_sactipeptides	--enable-sactipeptides	Sactipeptide detection
--antismash_enable_thiopeptides	--enable-thiopeptides	Thiopeptide detection
--antismash_enable_t2pks	--enable-t2pks	Type II PKS detection
--antismash_enable_tta	--enable-tta	TTA codon detection
--antismash_enable_genefunctions	--enable-genefunctions	Gene function annotation
--antismash_enable_html	--enable-html	Generate HTML reports
--antismash_fullhmmer	--fullhmmer	Full-genome Pfam HMM scan
--antismash_clusterhmmer	--clusterhmmer	Cluster-focused Pfam scan
--antismash_tigrfam	--tigrfam	TIGRFam annotation
--antismash_cassis	--cassis	CASSIS promoter motif detection
--antismash_asf	--asf	Active site finder
--antismash_pfam2go	--pfam2go	Pfam-to-GO mapping
--antismash_rre	--rre	RiPP recognition element detection
--antismash_smcog_trees	--smcog-trees	SMCOG phylogenetic trees
--antismash_tfbs	--tfbs	Transcription factor binding sites

---

antiSMASH — ClusterBlast

Parameter	Default	antiSMASH flag	Description
--antismash_cc_mibig	false	--cc-mibig	Compare clusters to MIBiG reference clusters
--antismash_cb_general	false	--cb-general	GeneralClusterBlast (NCBI database)
--antismash_cb_knownclusters	false	--cb-knownclusters	KnownClusterBlast (MIBiG). Also adds hit columns to all_regions.tsv.
--antismash_cb_subclusters	false	--cb-subclusters	SubClusterBlast
--antismash_cc_custom_dbs	null	--cc-custom-dbs	Comma-separated paths to custom ClusterCompare DB config files
--antismash_cb_nclusters	null	--cb-nclusters	Maximum clusters to report (default: 10)
--antismash_cb_min_homology_scale	null	--cb-min-homology-scale	Minimum homology scale threshold (0.0–1.0)

---

antiSMASH — HMM detection

Parameter	Default	Description
--antismash_hmmdetection_strictness	relaxed	Detection strictness: strict, relaxed, or loose.
--antismash_hmmdetection_fungal_cutoff_multiplier	null	Override fungal HMM score cutoff multiplier.
--antismash_hmmdetection_fungal_neighbourhood_multiplier	null	Override fungal neighbourhood multiplier.
--antismash_hmmdetection_limit_to_rule_names	null	Comma-separated rule names to restrict detection.
--antismash_hmmdetection_limit_to_rule_categories	null	Comma-separated rule categories to restrict detection.

---

antiSMASH — output

Parameter	Default	Description
--antismash_zip_output	false	true = force zip; false = force no-zip; null = antiSMASH default.
--antismash_summary_gbk	null	Toggle summary GenBank output (true/false/null).
--antismash_region_gbks	null	Toggle per-region GenBank files (true/false/null).
--antismash_allow_long_headers	true	Allow sequence headers longer than antiSMASH's default limit.

---

GECCO

Parameter	Default	Description
--gecco_run	true	Run GECCO for each input genome.
--gecco_extra_args	''	Arbitrary extra arguments passed to GECCO.

---

deepBGC

Parameter	Default	Description
--deepbgc_run	true	Run deepBGC for each input genome.
--deepbgc_data_dir	null	Path to deepBGC downloads/models. Auto-downloaded when absent/empty.
--deepbgc_extra_args	''	Arbitrary extra arguments passed to deepBGC.

---

comBGC unification

These parameters control filtering while combining antiSMASH, GECCO, and deepBGC predictions prior to BiG-SCAPE or BiG-SLiCE.

Parameter	Default	Description
--combgc_min_length	3000	Minimum BGC length retained by comBGC.
--combgc_contig_edge	2	Exclude BGCs near contig edges in comBGC.

---

BiG-SCAPE

--bigscape_run and --bigslice_run are mutually exclusive.

BiG-SCAPE in clystere runs on unified comBGC-filtered regions and requires --gecco_run true and --deepbgc_run true.

Parameter	Default	Description
--bigscape_run	false	Enable BiG-SCAPE GCF clustering.
--bigscape_dereplicate	true	Run bigscape dereplicate before clustering.
--bigscape_dereplicate_cutoff	0.8	Similarity cutoff used for BiG-SCAPE dereplication.
--bigscape_pfam_path	null	Path to Pfam-A.hmm. Resolved automatically from --antismash_db if absent.
--bigscape_gcf_cutoffs	0.3 0.5 0.7	Space-separated list of GCF similarity cutoffs.
--bigscape_mix	true	Include a mixed-class network alongside class-specific networks.
--bigscape_classify	none	Classification mode: none or classify.
--bigscape_include_singletons	true	Include singleton BGCs (no GCF membership) in output.
--bigscape_zip_output	false	Compress BiG-SCAPE output directory.
--bigscape_extra_args	''	Arbitrary extra arguments passed to BiG-SCAPE.

BiG-SLiCE

BiG-SLiCE requires its HMM model bundle. The pipeline bootstraps this bundle automatically during the first BiG-SLiCE task execution.

BiG-SLiCE in clystere runs on unified comBGC-filtered regions and requires --gecco_run true and --deepbgc_run true.

Parameter	Default	Description
--bigslice_run	false	Enable BiG-SLiCE clustering. Mutually exclusive with --bigscape_run.
--bigslice_zip_output	false	Compress BiG-SLiCE output directory.
--bigslice_extra_args	''	Arbitrary extra arguments passed to BiG-SLiCE.

---

Tabulation

Parameter	Default	Description
--run_tabulation	true	Run TABULATE_REGIONS and COUNT_REGIONS after antiSMASH.
--count_per_contig	false	Emit one row per contig in region_counts.tsv instead of per assembly.
--split_hybrids	false	Count each product class in a hybrid BGC individually. total_count is always the number of regions.

---

Pipeline internals

Parameter	Default	Description
--max_memory	14.GB	Hard ceiling on memory per process (overridden by hpc/slurm profiles).
--max_cpus	8	Hard ceiling on CPUs per process.
--max_time	240.h	Hard ceiling on wall-time per process.
--monochrome_logs	false	Disable colour in Nextflow log output.
--help	false	Print parameter help and exit.
--version	false	Print pipeline version and exit.