.. _nextflow-parameters: 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 :ref:`nextflow-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 -------------------- .. list-table:: Input/Output Parameters :widths: 20 10 10 60 :header-rows: 1 * - 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 :ref:`nextflow-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 ------------------------ .. list-table:: Mode Selection Parameters :widths: 20 10 10 60 :header-rows: 1 * - Parameter - Type - Default - Description * - ``--type`` - string - ``shortreads`` - Analysis mode to use. Options: ``shortreads``, ``longreads``, ``assemfree``. See mode-specific documentation for details. Quality Control Options ------------------------- .. list-table:: Quality Control Parameters :widths: 20 10 10 60 :header-rows: 1 * - 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 --------------- .. list-table:: Kraken2 Parameters :widths: 20 10 10 60 :header-rows: 1 * - 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. .. list-table:: Short Reads Assembly Parameters :widths: 20 10 10 60 :header-rows: 1 * - Parameter - Type - Default - Description * - ``--subsample`` - boolean - ``false`` - Enable subsampling mode. Downsample each sample before assembly to reduce computational requirements. Mutually exclusive with ``--coassembly``. See :ref:`shortreads-subsample` 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 :ref:`shortreads-coassembly` for details. Long Reads Options ------------------ These parameters are only applicable when ``--type longreads`` is used. .. list-table:: Long Reads Parameters :widths: 20 10 10 60 :header-rows: 1 * - 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 ---------------- .. list-table:: Database Parameters :widths: 20 10 10 60 :header-rows: 1 * - 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 --------------- .. list-table:: MultiQC Parameters :widths: 20 10 10 60 :header-rows: 1 * - 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. .. list-table:: Generic Parameters :widths: 20 10 10 60 :header-rows: 1 * - 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: .. code-block:: bash nextflow run main.nf \ --input samplesheet.csv \ --outdir results \ --type shortreads \ -profile docker Short reads with subsampling: .. code-block:: bash nextflow run main.nf \ --input samplesheet.csv \ --outdir results \ --type shortreads \ --subsample \ --subsample_size 5000000 \ -profile docker Long reads analysis: .. code-block:: bash nextflow run main.nf \ --input samplesheet.csv \ --outdir results \ --type longreads \ --flye_mode --nano-raw \ -profile docker Assembly-free analysis: .. code-block:: bash nextflow run main.nf \ --input samplesheet.csv \ --outdir results \ --type assemfree \ -profile docker With custom databases: .. code-block:: bash 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: .. code-block:: bash nextflow run main.nf \ --input samplesheet.csv \ --outdir results \ --type shortreads \ --skip_fastqc \ --skip_trimming \ -profile docker Using parameter files: .. code-block:: bash nextflow run main.nf \ -profile docker \ -params-file params.yaml With ``params.yaml``: .. code-block:: yaml input: './samplesheet.csv' outdir: './results/' type: 'shortreads' subsample: true subsample_size: 5000000 skip_kraken_extraction: false kraken_tax: '9606'