Disable GATK filters when joint calling

[amizeranschi]

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[asp8200]

With the change introduced by this PR, the pipeline will "silently" skip the haplotypecaller-filter on joint-germline runs, right? I'm just wondering whether it would be better to stop the pipeline (with meaningful err msg) if the user tries to run joint-germline with filtering or at least inform the user that the filtering is being skipped 🤔

Here are some somewhat related scenarios where the pipeline issues a warning:

[log.warn "If Haplotypecaller is specified, without --dbsnp or --known_indels no filtering will be done. For filtering, please provide at least one of --dbsnpor--known_indels`. ....](

sarek/workflows/sarek.nf

Lines 113 to 124 in c87f4eb

	if (params.tools && params.tools.split(',').contains('haplotypecaller')){
	log.warn "If Haplotypecaller is specified, without `--dbsnp` or `--known_indels no filtering will be done. For filtering, please provide at least one of `--dbsnp` or `--known_indels`.\nFor more information see FilterVariantTranches (single-sample, default): https://gatk.broadinstitute.org/hc/en-us/articles/5358928898971-FilterVariantTranches\nFor more information see VariantRecalibration (--joint_germline): https://gatk.broadinstitute.org/hc/en-us/articles/5358906115227-VariantRecalibrator\nFor more information on GATK Best practice germline variant calling: https://gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-discovery-SNPs-Indels-"
	}
	}
	if (params.joint_germline && (!params.tools || !params.tools.split(',').contains('haplotypecaller'))){
	log.error "The Haplotypecaller should be specified as one of the tools when doing joint germline variant calling. (The Haplotypecaller could be specified by adding `--tools haplotypecaller` to the nextflow command.) "
	exit 1
	}
	if (params.joint_germline && (!params.dbsnp || !params.known_indels || !params.known_snps || params.no_intervals)){
	log.warn "If Haplotypecaller is specified, without `--dbsnp`, `--known_snps`, `--known_indels` or the associated resource labels (ie `known_snps_vqsr`), no variant recalibration will be done. For recalibration you must provide all of these resources.\nFor more information see VariantRecalibration: https://gatk.broadinstitute.org/hc/en-us/articles/5358906115227-VariantRecalibrator \nJoint germline variant calling also requires intervals in order to genotype the samples. As a result, if `--no_intervals` is set to `true` the joint germline variant calling will not be performed."
	}

)

[amizeranschi]

I'm just wondering whether it would be better to stop the pipeline (with meaningful err msg) if the user tries to run joint-germline with filtering or at least inform the user that the filtering is being skipped

My worry here is that, in this scenario, the user doesn't really have a choice about turning VCF filtering on in the first place. It's just on by default, with an option for disabling it via --skip_tools haplotypecaller_filter. So we'd essentially stop the pipeline or warn the users about some pipeline logic that they didn't initiate, which might be confusing.

[asp8200]

I'm just wondering whether it would be better to stop the pipeline (with meaningful err msg) if the user tries to run joint-germline with filtering or at least inform the user that the filtering is being skipped

My worry here is that, in this scenario, the user doesn't really have a choice about turning VCF filtering on in the first place. It's just on by default, with an option for disabling it via --skip_tools haplotypecaller_filter. So we'd essentially stop the pipeline or warn the users about some pipeline logic that they didn't initiate, which might be confusing.

Also valid points. I don't have a strong opinion on this; just wanted to share my two cents. Perhaps somebody else will chip in as well.

Anyways, thanks for the PR.

[FriederikeHanssen]

So this established back the old behavior. The pipeline was not suppoed to do filtering for joint germline, but single sample only, (where it sometimes can be skipped because it takes a long time): https://gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-discovery-SNPs-Indels-

I think we might need to refactor this subworkflow a bit to make it more intuitive. and put the whole FilterVarianttranches/CNNScore part into a singlesample haplotypecaller subworkflow, but I would do that in a separate PR