wf-transcriptomes-v202/docs/07_input_parameters.md

Input Options

Nextflow parameter name	Type	Description	Help	Default
fastq	string	FASTQ reads to analyse.	You can provide a single FASTQ, a folder of FASTQs, or a multiplexed folder containing one sub-folder per sample or barcode.
bam	string	BAM or uBAM reads to analyse.	You can provide a single BAM or uBAM, a folder of BAMs, or a multiplexed folder containing one sub-folder per sample or barcode.
analyse_unclassified	boolean	Include unclassified reads from multiplexed input directories.		False
analyse_fail	boolean	Include fail reads from multiplexed input directories.		False
fastq_chunk	integer	Maximum number of reads per ingress chunk.	Useful mainly for testing or for splitting very large inputs into smaller pieces.

Reference Options

Nextflow parameter name	Type	Description	Help	Default
ref_genome	string	Reference genome FASTA.	Required in both discover and fixed_annotation modes.
ref_annotation	string	Reference transcript annotation in GTF or GFF format.	Required in both discover and fixed_annotation modes.
transcriptome_mode	string	How bambu should prepare the transcriptome model.	Use discover for reference-guided transcript discovery and quantification, or fixed_annotation for quantification only against the supplied annotation.	discover
direct_rna	boolean	Set this for direct RNA sequencing libraries.		False

Sample Options

Nextflow parameter name	Type	Description	Help	Default
sample_sheet	string	CSV file describing barcodes, aliases, and optional experimental design columns.	For multiplexed runs, the sample sheet should contain both barcode and alias. For differential analysis it must also contain alias, the condition column, and any extra columns named in --covariates.
sample	string	Single sample name for singleplexed input or to restrict multiplexed analysis to one sample.

Analysis Options

Nextflow parameter name	Type	Description	Help	Default
de_analysis	boolean	Run differential gene expression and differential transcript usage analyses.		False
condition_column	string	Main comparison column in the sample sheet.		condition
covariates	string	Comma-separated extra sample-sheet columns to adjust for, for example batch.	Each listed name must exist as a column in the sample sheet.
reference_level	string	Baseline group for the main comparison column.	If omitted, the workflow will use control when that level exists.

Output Options

Nextflow parameter name	Type	Description	Help	Default
out_dir	string	Directory for user-facing workflow outputs.		output
igv	boolean	Generate an IGV configuration file for the aligned BAM outputs.		False

Advanced Options

Nextflow parameter name	Type	Description	Help	Default
threads	integer	Thread count to use for the core workflow processes.		4
mod_codes	string	Comma-separated modified base codes to pass to modkit pileup.	Provide values accepted by modkit pileup --modified-bases, for example A:a,C:m. If omitted, the workflow infers primary_base:mod_code pairs from the BAM with modkit modbam check-tags.
minimap2_opts	string	Extra command-line options to pass to minimap2.
force_alignment	boolean	Force re-alignment of input BAM files.	Read alignment is skipped if the existing sequence names in the aligned BAM match the provided reference. Enable this if the existing alignments used incorrect minimap2 presets (e.g. missing --splice or direct RNA settings).	False
ndr	number	Optional bambu novel discovery rate override.
skip_sqanti	boolean	Skip SQANTI3 transcript classification and QC.		False
sqanti_skip_orf	boolean	Skip ORF prediction during SQANTI3 QC.		True
sqanti_extra_args	string	Extra command-line options to pass to SQANTI3.