Parameters

All parameters can be set via command line (--param value) or in a params file.

nextflow run rec3141/microscape-nf --help

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Input / Output

Parameter	Default	Description
--input	required	Directory of paired-end *.fastq.gz files
--outdir	results	Output directory
--store_dir	off	Persistent cache directory (skip completed steps across runs)

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Language and Engine

Parameter	Default	Description
--lang	python	Script language: python (papa2 + microscape) or R (dada2 + microscapeR)
--dada_engine	follows --lang	Override DADA2 engine independently: python or R

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Primer Removal

Parameter	Default	Description
--skip_primer_removal	false	Skip if input is already trimmed
--primer_auto	true	Auto-select primer file by filename prefix (16S/18S/ITS)
--primers	auto	Override with a specific primer FASTA
--primer_error_rate	0.12	Cutadapt max error rate

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DADA2 Quality Filtering

Parameter	Default	Description
--maxEE	2	Max expected errors per read
--truncQ	11	Truncate at first base with quality <= Q
--maxN	0	Max Ns allowed
--truncLen_fwd	0	Truncate forward reads at position N (0 = off)
--truncLen_rev	0	Truncate reverse reads at position N (0 = off)
--min_overlap	10	Minimum overlap for paired-read merging

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QC Filtering

Parameter	Default	Description
--min_seq_length	50	Remove ASVs shorter than N bp
--min_samples	2	Remove ASVs present in fewer than N samples
--min_seqs	3	Remove ASVs with fewer than N total reads
--min_reads	100	Remove samples with fewer than N reads

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Taxonomy

Parameter	Default	Description
--ref_databases	required	Reference databases, semicolon-separated: "name:path:Level1,Level2,..."
--run_phylogeny	false	Build MSA + NJ phylogenetic tree

Example:

--ref_databases "silva:/db/silva_nr99_v138.1_train_set.fa.gz:Domain,Phylum,Class,Order,Family,Genus;pr2:/db/pr2_train.fasta:Domain,Supergroup,Division,Class,Order,Family,Genus,Species"

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Metadata

Parameter	Default	Description
--metadata	off	Path to MIMARKS-compliant TSV/CSV metadata file
--sample_id_column	sample_name	Column name in metadata matching sample IDs

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Network

Parameter	Default	Description
--min_prevalence	5	Min samples an ASV must appear in for network analysis

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Resources

Parameter	Default	Description
--threads	8	General thread count
--dada_cpus	8	CPUs for DADA2 processes
--dada_memory	16 GB	Memory for DADA2 processes