64 lines
4.4 KiB
Markdown
64 lines
4.4 KiB
Markdown
### Input Options
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| Nextflow parameter name | Type | Description | Help | Default |
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|--------------------------|------|-------------|------|---------|
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| 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. | |
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| 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. | |
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| analyse_unclassified | boolean | Include unclassified reads from multiplexed input directories. | | False |
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| analyse_fail | boolean | Include fail reads from multiplexed input directories. | | False |
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| fastq_chunk | integer | Maximum number of reads per ingress chunk. | Useful mainly for testing or for splitting very large inputs into smaller pieces. | |
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### Reference Options
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| Nextflow parameter name | Type | Description | Help | Default |
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|--------------------------|------|-------------|------|---------|
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| ref_genome | string | Reference genome FASTA. | Required in both discover and fixed_annotation modes. | |
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| ref_annotation | string | Reference transcript annotation in GTF or GFF format. | Required in both discover and fixed_annotation modes. | |
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| 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 |
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| direct_rna | boolean | Set this for direct RNA sequencing libraries. | | False |
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| cdna_preprocess | boolean | Apply the optional cDNA preprocessing stage before alignment. | This is only relevant for cDNA libraries and must not be combined with `--direct_rna`. | False |
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### Sample Options
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| Nextflow parameter name | Type | Description | Help | Default |
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| 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`. | |
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| sample | string | Single sample name for singleplexed input or to restrict multiplexed analysis to one sample. | | |
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### Analysis Options
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| Nextflow parameter name | Type | Description | Help | Default |
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|--------------------------|------|-------------|------|---------|
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| de_analysis | boolean | Run differential gene expression and differential transcript usage analyses. | | False |
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| condition_column | string | Main comparison column in the sample sheet. | | condition |
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| 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. | |
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| reference_level | string | Baseline group for the main comparison column. | If omitted, the workflow will use control when that level exists. | |
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### Output Options
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| Nextflow parameter name | Type | Description | Help | Default |
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| out_dir | string | Directory for user-facing workflow outputs. | | output |
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| igv | boolean | Generate an IGV configuration file for the aligned BAM outputs. | | False |
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### Advanced Options
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| Nextflow parameter name | Type | Description | Help | Default |
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|--------------------------|------|-------------|------|---------|
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| threads | integer | Thread count to use for the core workflow processes. | | 4 |
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| minimap2_opts | string | Extra command-line options to pass to minimap2. | | |
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| ndr | number | Optional bambu novel discovery rate override. | | |
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| cdna_kit | string | ONT cDNA kit identifier used for pychopper preprocessing. | Only used when `--cdna_preprocess` is enabled. The workflow derives the pychopper kit code from this value. | SQK-PCS109 |
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| pychopper_backend | string | Primer-detection backend to use for pychopper preprocessing. | | edlib |
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| pychopper_opts | string | Extra command-line options to pass to pychopper. | | |
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| skip_sqanti | boolean | Skip SQANTI3 transcript classification and QC. | | False |
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| sqanti_skip_orf | boolean | Skip ORF prediction during SQANTI3 QC. | | True |
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| sqanti_extra_args | string | Extra command-line options to pass to SQANTI3. | | |
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