Parameters

⚙️ Pipeline Parameters

This page documents all parameters available for PoODLE.

Pipeline parameters use double hyphens (--), while Nextflow runtime options use single hyphens (-).

Example:

nextflow run MDHHS-Bioinformatics/poodle \
  -profile singularity \
  --input samplesheet.csv \
  --outdir results

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📥 Core Pipeline Parameters

These parameters are required for most pipeline runs.

Parameter	Type	Required	Default	Description
--input	string	✓	–	Path to the input samplesheet (CSV) describing the samples to process.
--outdir	string	✓	./poodle_results	Directory where pipeline results will be written.
--annotation_format	string	✓	gff	Format of the annotation files used for pangenome analysis. Options: gff (standard GFF3 with embedded FASTA by tools such as Prokka or Bakta), split_gff (for annotations lacking embedded FASTA sequences, e.g. RefSeq-style), or genbank (.gbk, .gb, .gbff). All samples in a run must use the same format.

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🧬 Analysis Options

These parameters enable optional analysis steps.

Parameter	Type	Default	Description
--gubbins	boolean	false	Perform recombination filtering using Gubbins.
--mashtree	boolean	false	Generate an genomic composition tree using MashTree.
--previous_results	string	–	Path to previous pipeline results used to reuse existing analyses. By default, the pipeline looks for prior Snippy results for the same cluster in the outdir.
--save_snippy_run	boolean	true	Save Snippy run outputs for each sample.

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⚙️ Execution Configuration

These parameters control compute resource limits.

Parameter	Type	Default	Description
--max_cpus	integer	16	Maximum CPUs that can be requested by any job.
--max_memory	string	128.GB	Maximum memory that can be requested by any job.
--max_time	string	24.h	Maximum execution time for any job.

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🔧 Generic Pipeline Options

These parameters control pipeline behavior.

Parameter	Type	Default	Description
--help	boolean	–	Display help message and exit.
--version	boolean	–	Print pipeline version and exit.
--validate_params	boolean	true	Validate parameters against schema.
--show_hidden_params	boolean	false	Show advanced parameters in help output.
--monochrome_logs	boolean	false	Disable colored logging output.

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🧠 Core Nextflow Arguments

These options are part of Nextflow itself and use a single hyphen (-).

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-profile

Select the execution configuration profile.

Example:

-profile singularity

Available profiles typically include:

Profile	Description
docker	Run using Docker containers
singularity	Run using Singularity containers
apptainer	Run using Apptainer containers
test	Run pipeline with bundled test data

Multiple profiles can be combined:

-profile test,singularity

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-r (Pipeline Release Version)

Specify the pipeline version or Git revision to run.

Example:

nextflow run MDHHS-Bioinformatics/poodle -r v1.0.0

This ensures that the exact same pipeline version is used for analysis.

You can also run:

Example	Description
-r v1.0.0	Run a tagged release
-r main	Run the latest development version
-r <commit>	Run a specific Git commit

⚠️ For reproducible analyses, it is strongly recommended to run a tagged release.

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-resume

Resume a previously failed or interrupted pipeline run.

-resume

Nextflow will reuse cached results when possible.

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-c

Provide a custom Nextflow configuration file.

-c custom.config

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🏛 Institutional Configuration Options

These parameters are used when loading configurations from nf-core/configs.

Parameter	Description
--custom_config_version	Git commit ID for institutional configs
--custom_config_base	Base URL for institutional configuration repository
--config_profile_name	Name of institutional profile
--config_profile_description	Description of institutional profile
--config_profile_contact	Contact information
--config_profile_url	Documentation URL

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⚡ Custom Configuration (Advanced)

Users can override pipeline resource requirements using custom configuration files.

Example:

process {
    withName: ALIGNMENT {
        memory = 100.GB
        cpus = 8
    }
}

Run with:

nextflow run poodle -c custom.config

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🧰 Troubleshooting Resource Issues

If a job fails due to insufficient memory or CPUs, you can increase global resource limits:

--max_memory 200.GB \
--max_cpus 32 \
-resume