Nextflow Pipeline: Parameters Reference

This document provides a comprehensive reference for all parameters available in the Nextflow pipeline for CAZyme annotation in microbiome data. Parameters are organized by functional category.

Note

Before running the pipeline, make sure you have cloned the repository. See Nextflow Pipeline: Usage for installation instructions. All examples assume you are in the dbcan-nf directory or use the full path to main.nf.

Input/Output Options

Input/Output Parameters

Parameter	Type	Required	Description
--input	string	Yes	Path to comma-separated file containing information about the samples in the experiment. Must have 3 columns (sample, fastq_1, fastq_2) and a header row. See Nextflow Pipeline: Usage for samplesheet format details.
--outdir	string	Yes	The output directory where the results will be saved. Use absolute paths for Cloud infrastructure.
--email	string	No	Email address for completion summary. Set this to receive a summary email when the workflow exits. Can be set in ~/.nextflow/config to avoid specifying on every run.
--email_on_fail	string	No	Email address for completion summary, only sent when pipeline fails.
--plaintext_email	boolean	No	Send plain-text email instead of HTML. Default: false.

Analysis Mode Selection

Mode Selection Parameters

Parameter	Type	Default	Description
--type	string	shortreads	Analysis mode to use. Options: shortreads, longreads, assemfree. See mode-specific documentation for details.

Quality Control Options

Quality Control Parameters

Parameter	Type	Default	Description
--skip_fastqc	boolean	false	Skip FastQC quality control analysis. When enabled, FastQC steps are bypassed.
--skip_trimming	boolean	false	Skip TrimGalore adapter trimming. When enabled, trimming steps are bypassed.

Kraken2 Options

Kraken2 Parameters

Parameter	Type	Default	Description
--skip_kraken_extraction	boolean	false	Skip Kraken2 taxonomic classification and read extraction. When enabled, all reads are used without filtering.
--kraken_db	string	null	Path to custom Kraken2 database directory. If not specified, the pipeline will build a standard database automatically.
--kraken_tax	string	9606	NCBI taxonomy ID for taxonomic filtering. Default 9606 corresponds to Homo sapiens. Reads matching this taxon are extracted for downstream analysis.

Assembly Options (Short Reads Mode)

These parameters are only applicable when --type shortreads is used.

Short Reads Assembly Parameters

Parameter	Type	Default	Description
--subsample	boolean	false	Enable subsampling mode. Downsample each sample before assembly to reduce computational requirements. Mutually exclusive with --coassembly. See Short Reads: Subsampling Mode for details.
--subsample_size	integer	20000000	Number of reads per file to retain when subsampling is enabled. Only used when --subsample is set.
--coassembly	boolean	false	Enable co-assembly mode. Combine all samples and perform a single MEGAHIT assembly. Requires at least 2 samples. Mutually exclusive with --subsample. See Short Reads: Co-assembly Mode for details.

Long Reads Options

These parameters are only applicable when --type longreads is used.

Long Reads Parameters

Parameter	Type	Default	Description
--flye_mode	string	--pacbio-hifi	Flye assembly mode. Options include --pacbio-hifi, --pacbio-raw, --nano-raw, --nano-hq. See Flye documentation for details.

Database Options

Database Parameters

Parameter	Type	Default	Description
--dbcan_db	string	null	Path to custom dbCAN database directory. If not specified, the pipeline will download the database automatically.

MultiQC Options

MultiQC Parameters

Parameter	Type	Default	Description
--multiqc_title	string	null	MultiQC report title. Printed as page header, used for filename if not otherwise specified.
--multiqc_config	string	null	Custom config file to supply to MultiQC.
--multiqc_logo	string	null	Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file.
--multiqc_methods_description	string	null	Custom MultiQC YAML file containing HTML including a methods description.
--max_multiqc_email_size	string	25.MB	File size limit when attaching MultiQC reports to summary emails.

Generic Options

These options are common to all nf-core pipelines and are typically set in a Nextflow config file.

Generic Parameters

Parameter	Type	Default	Description
--publish_dir_mode	string	copy	Method used to save pipeline results to output directory. Options: symlink, rellink, link, copy, copyNoFollow, move.
--monochrome_logs	boolean	false	Do not use coloured log outputs.
--hook_url	string	null	Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.
--validate_params	boolean	true	Boolean whether to validate parameters against the schema at runtime.

Parameter Usage Examples

Basic short reads analysis:

nextflow run main.nf \
  --input samplesheet.csv \
  --outdir results \
  --type shortreads \
  -profile docker

Short reads with subsampling:

nextflow run main.nf \
  --input samplesheet.csv \
  --outdir results \
  --type shortreads \
  --subsample \
  --subsample_size 5000000 \
  -profile docker

Long reads analysis:

nextflow run main.nf \
  --input samplesheet.csv \
  --outdir results \
  --type longreads \
  --flye_mode --nano-raw \
  -profile docker

Assembly-free analysis:

nextflow run main.nf \
  --input samplesheet.csv \
  --outdir results \
  --type assemfree \
  -profile docker

With custom databases:

nextflow run main.nf \
  --input samplesheet.csv \
  --outdir results \
  --type shortreads \
  --dbcan_db /path/to/dbcan_db \
  --kraken_db /path/to/kraken_db \
  -profile docker

Skipping quality control steps:

nextflow run main.nf \
  --input samplesheet.csv \
  --outdir results \
  --type shortreads \
  --skip_fastqc \
  --skip_trimming \
  -profile docker

Using parameter files:

nextflow run main.nf \
  -profile docker \
  -params-file params.yaml

With params.yaml:

input: './samplesheet.csv'
outdir: './results/'
type: 'shortreads'
subsample: true
subsample_size: 5000000
skip_kraken_extraction: false
kraken_tax: '9606'