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║    Hyper Divergent Region Nextflow Pipeline   ║
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A reproducible Nextflow pipeline to call HDRs in selfing nematodes.

Pipeline Parameters

Most input parameters are optional. If they are not provided, the pipeline automatically selects the appropriate defaults based on the value of --species.

Parameter	Description	Default
--species <string>	Target species.	NULL. Accepted values: c_elegans, c_briggsae, c_tropicalis.
--vcf <full_path>	Reference VCF file used for extracting variant information.	Inferred from --species.
--refgen <full_path>	Reference genome (FASTA).	Inferred from --species.
--bam <full_path>	Directory containing input BAM files.	Inferred from --species.
--str <string>	Reference strain identifier.	Inferred from --species.
--pbt <float>	Percent bases covered threshold for calling HDRs.	Inferred from --species.
--vct <int>	Variant count threshold for calling HDRs.	Inferred from --species.
--output <string>	Name of the output directory.	results_MM-DD-YY
-profile <string>	Nextflow configuration profile.	NULL. Only -profile rockfish is accepted currently.

Note: Unless explicitly specified, the values for --vcf, --reference, --bam, --ref, --pbt, and --vct are automatically determined from the selected --species. These parameters are determined from the most recent releases as of 07/30/26. Manually define each custom parameter (except for HDR calling thresholds) when using a newer release.

Usage

Disclaimer

This pipeline is designed to run within the nf24_env environment. Ensure this environment is activated before executing any of the commands below.

Standard run

Run the pipeline using the default reference files for the selected species.

nextflow run main.nf --species c_elegans -profile rockfish

This is the recommended command for most users. The pipeline automatically uses the most recent released VCF and BAM files available as of 07/30/26 for the specified species.

Using an updated VCF

Run the pipeline with a custom VCF while using the default reference genome and BAM directory.

nextflow run main.nf --species c_elegans --vcf <path_to_vcf_file> -profile rockfish

When a custom VCF is provided, the pipeline assumes that any newly introduced samples have corresponding BAM files located in:

/vast/<allocation>/data/<species>/WI/alignments

Custom HDR thresholds

Run the pipeline with user-defined HDR calling thresholds.

nextflow run main.nf \
    --species c_elegans \
    --vct 15 \
    --pbt 0.7 \
    --output CE_VCT15_PBT70 \
    -profile rockfish

This command specifies custom variant count (--vct) and percent bases covered (--pbt) thresholds, as well as a custom output directory. Modifying these thresholds is intended only for experimental analyses and is strongly discouraged unless there is a well-justified reason.

Development workflows

The following parameters are reserved for alternative workflows that are currently under development for C. briggsae:

• --bam
• --refgen
• --str

These parameters are not intended for routine use.

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Current Release Files (Revised: 08/04/26)

The pipeline automatically selects the appropriate reference files based on the value of --species.

Species	Reference Genome	Reference VCF
c_elegans	c_elegans.PRJNA13758.WS283.genome.fa	WI.20250625.hard-filter.isotype.vcf.gz
c_briggsae	c_briggsae.QX1410_nanopore.Feb2020.genome.fa	WI.20250626.hard-filter.isotype.vcf.gz
c_tropicalis	c_tropicalis.NIC58_nanopore.June2021.genome.fa	WI.20250627.hard-filter.isotype.vcf.gz