How to specify ploidy for HaplotypeCaller in the nf-core/sarek pipeline?

[koraykaplan88]

Hello,

I am using the nf-core/sarek pipeline to analyze genomic data. The pipeline works perfectly fine for my diploid plant samples, and I was able to run it without any issues.

However, I am now analyzing polyploid species (specifically tiploid and tetraploid species), and I need to ensure that the VCF files generated by HaplotypeCaller reflect the tetraploid nature of my samples. Unfortunately, I couldn't find a direct way to specify the --ploidy parameter for GATK HaplotypeCaller in the pipeline.

My goal is to ensure that the VCF files generated by HaplotypeCaller reflect the triploid/tetraploid nature of my samples. I have tried adding --haplotypecaller_options '--ploidy 4', but the pipeline flagged this as an invalid parameter:
WARN: The following invalid input values have been detected:

• --haplotypecaller_options: --ploidy 4

Here is the command I used to run the pipeline:
nextflow run nf-core/sarek -profile singularity -c nextflow.config -params-file params.yaml
--input 4n_input.csv --fasta my_reference_genome.fasta
--tools haplotypecaller --skip_tools baserecalibrator

Also params.yml file content:
genome: null
dbsnp: null
known_indels: null
known_snps: null
germline_resource: null
sentieon_dnascope_model: null

Is there a way to specify the ploidy for HaplotypeCaller in the current version of nf-core/sarek?

[FriederikeHanssen]

You can specify tool parameters that are not exposed in the pipeline using a custom.config: https://nf-co.re/docs/usage/getting_started/configuration#customising-tool-arguments

I assume you already set something in the nextflow.config?

[koraykaplan88]

My config file is actually pretty simple:

process {
withSingularity = true
singularity.enabled = true
}

I just want to add haplotypecaller --ploidy 4 to it. Could you help with that? Where can I find the specific name of the haplotypecaller step in the workflow?

[FriederikeHanssen]

You can find it here:

You'd want something like:

process {
    withName: 'GATK4_HAPLOTYPECALLER' {
        ext.args   = { params.joint_germline ? "-ERC GVCF --ploidy 4" : "--ploidy 4" }
    }
}

[koraykaplan88]

Yes, thank you very much!