Pytest for VQSR-flow

[asp8200]

Description of feature

We are lacking a pytest of the VQSR-flow. (Both the GATK version and the upcoming Sentieon version.)

The challenge is that VQSR crashes on our current testdata for joint-germline. (Problems include too little variation in testdata and testdata based on a different reference-genome than the one used for the VQSR-reference-files in iGenomes.)

Here is a long Slack conversation where I try to explain the problems with constructing the desired pytest.

https://nfcore.slack.com/archives/C02MDBZAYJK/p1684238360591329

This is how I run the VQSR-flow manually:

GATK:
nextflow run main.nf -profile docker --input mapped_joint_bam_HG002_HG003_1perc_of_40x.csv --tools haplotypecaller --step variant_calling --joint_germline --outdir results --skip_tools haplotypecaller_filter

Sentieon:
nextflow run main.nf -profile docker --input mapped_joint_bam_HG002_HG003_1perc_of_40x.csv --tools sentieon_haplotyper --step variant_calling --joint_germline --outdir results --skip_tools haplotypecaller_filter --sentieon_haplotyper_out_format gvcf

(The syntax for the Sentieon-cmd may be changed.)