Parameter Reference¶
Every pipeline parameter, grouped by pipeline stage. nextflow_schema.json at the repo root
is the source of truth for types, defaults, and validation.
For a walkthrough of the parameters needed for a first run, see Running the CLI.
-- vs -
Pipeline parameters (listed below) are passed with a double dash, e.g. --aligner MAFFT.
Nextflow's own built-in options use a single dash, e.g. -profile, -output-dir, -c.
Core parameters¶
Required for every run.
| Parameter | Type | Default | Description |
|---|---|---|---|
run_name |
string | (required) | Identifier for this run. Used in logging, reports, and the default output path. |
samplesheet |
file path | (required) | CSV of samples and metadata. See Samplesheet Reference. |
sample_base_dir |
directory path | (required) | Base directory for resolving samplesheet file paths. |
reference_file |
file path | (required) | Reference sequence containing the gene/CDS of interest. Expected format depends on trim_method. |
region_of_interest |
string | (required) | CDS or protein to extract. Required even without AGA preprocessing; no fixed naming convention. |
-output-dir |
directory path | ./results/${run_name} |
Nextflow built-in, not a pipeline parameter. Where output files are saved. |
Preprocessing parameters¶
Stage 1 (Trim) — see Pipeline Overview.
| Parameter | Type | Default | Description |
|---|---|---|---|
trim_method |
enum: MINIMAP2, AGA |
AGA |
Trimming tool. MINIMAP2 is faster; AGA handles complex overlapping reading frames. |
skip_trim |
boolean | false |
Skip trimming — input is already trimmed to the region of interest. |
region_shorthand |
string | (none) | Short name for the region of interest. |
aga_args |
string | --local |
Extra arguments for AGA. |
minimap_trim_from |
integer | (none) | Start coordinate for MINIMAP2 trimming. |
minimap_trim_to |
integer | (none) | End coordinate for MINIMAP2 trimming. |
Filtering parameters¶
Stage 2 (Functional Filtering) — see Pipeline Overview.
| Parameter | Type | Default | Description |
|---|---|---|---|
functional_filter_method |
enum: ELLPACA, LENGTH_BASED_FILTERING |
ELLPACA |
ELLPACA filters on stop codons (below); LENGTH_BASED_FILTERING filters on length (next section). |
skip_functional_filter |
boolean | false |
Skip functional filtering — all sequences proceed to alignment. |
ff_max_stop_pct |
integer | 100 |
Latest point along the read (as a percentage) a stop codon can occur and still count as functional. |
ff_include_no_stop_codons |
boolean | true |
Whether sequences with no stop codons are functional. |
ff_include_frameshifts |
boolean | false |
Whether sequences with a potential frameshift are functional. |
ff_acceptable_pct_loss |
number (0–1) | 0.2 |
Proportion of median protein length allowed to be lost before a sequence is non-functional. |
ff_expected_length |
number | (median of input) | Expected protein length. Unset uses the median of the input. |
Length-based filtering¶
Used when functional_filter_method is LENGTH_BASED_FILTERING.
| Parameter | Type | Default | Description |
|---|---|---|---|
lbf_threshold_mode |
enum: FIXED, MEDIAN, MEAN |
MEDIAN |
How the minimum-length threshold ("center") is determined. |
lbf_min_length |
integer | (none) | Minimum length to keep. Required, and only used, in FIXED mode. |
lbf_tolerance |
string (e.g. 20, 20%) |
(none — strict minimum) | Sets both lbf_min_tolerance and lbf_max_tolerance to the same value. Not combinable with either. |
lbf_min_tolerance |
string (e.g. 20, 20%) |
(none) | How much shorter than center a sequence may be. Not combinable with lbf_tolerance. |
lbf_max_tolerance |
string (e.g. 20, 20%) |
(none — no upper bound) | How much longer than center a sequence may be. Not combinable with lbf_tolerance. |
K-mer filtering¶
Independent filtering pass matching sequence ends against expected k-mers.
| Parameter | Type | Default | Description |
|---|---|---|---|
use_kmer_filtering |
boolean | false |
Turns k-mer filtering on. |
match_kmers_start |
string | (none) | K-mer(s) to match at the sequence start. Comma-separated. |
match_kmers_end |
string | (none) | K-mer(s) to match at the sequence end. Comma-separated. |
Alignment parameters¶
Stage 3 (Alignment) — see Aligner Reference for choosing an aligner.
| Parameter | Type | Default | Description |
|---|---|---|---|
aligner |
enum (see Aligner Reference) | MAFFT |
Aligner used for the main alignment. |
Pass-through arguments, one per aligner:
| Parameter | Default | Applies to |
|---|---|---|
mafft_args |
--localpair --maxiterate 1000 |
MAFFT |
mafft_fast_align_args |
--retree 1 --maxiterate 0 |
MAFFT, used internally by AGA's preprocessing |
tcoffee_args |
(none) | T-Coffee |
tcoffee_regressive_args |
-nseq 100 -tree mbed -method clustalo_msa |
T-Coffee Regressive |
prank_args |
+F |
PRANK |
pagan_args |
(none) | PAGAN |
clustalo_args |
--iterations 2 |
Clustal Omega |
clustalw_args |
-CLUSTERING=NJ -ITERATION=NONE -NUMITER=3 -MATRIX=BLOSUM |
ClustalW |
virulign_args |
--maxFrameShifts 3 --exportReferenceSequence no |
VIRULIGN |
macse_args |
(none) | MACSE |
MUSCLE, MUSCLE-FAST, and PROBCONS have no pass-through arguments parameter.
Panel alignment¶
| Parameter | Type | Default | Description |
|---|---|---|---|
panel_alignment |
file path | (none) | Pre-aligned sequences used as a scaffold, when aligner is MAFFT-SEED. |
Reference sequence insertion¶
Inserts a reference sequence directly into the alignment, instead of mapping it on afterward.
| Parameter | Type | Default | Description |
|---|---|---|---|
add_reference_to_sequences |
enum: BEFORE, AFTER, null |
null |
Whether, and where, a reference is added to the sequences being aligned. null disables this. |
reference_to_add |
file path | (none) | Reference sequence to insert. Can differ from reference_file, which is used for trimming/mapping. |
Phylogeny parameters¶
Infers a phylogenetic tree from the computed alignment(s).
| Parameter | Type | Default | Description |
|---|---|---|---|
build_phylogeny |
boolean | false |
Infer a phylogenetic tree from the computed alignment(s). |
phylogeny_alignment_type |
enum: NT, AA, BOTH |
NT |
Which computed alignment(s) feed tree inference. |
phylogeny_baseline_method |
enum: REFERENCE, CONSENSUS, MINDIST |
REFERENCE |
How the baseline sequence for tree rooting is chosen. Also intended for a per-site variation heatmap, not yet implemented. |
iqtree_args |
string | (none) | Extra arguments for IQ-TREE, when build_phylogeny is enabled. |
Deprecated
multi_timepoint_alignment is deprecated. Don't use it in new runs.
Execution / resource parameters¶
| Parameter | Type | Default | Description |
|---|---|---|---|
-profile |
string | (none) | Nextflow config profile(s). Container runtimes: docker, singularity, apptainer. Others: test (caps resources for the test dataset), debug (verbose logging, no cleanup), slurm. Site-specific: ilifu, hex, zoidberg — see the Developer Guide to add your own. |
max_memory |
string | 128.GB |
Memory cap per process. |
max_cpus |
integer | 16 |
CPU cap per process. |
max_time |
string | 240.h |
Time cap per process. |
slurm_queue |
string | Main |
SLURM queue, when using the slurm profile. |