[FEATURE] port pytest to nf-test for sarek modules

[maxulysse]

Consider using the automated tool to facilitate this https://nf-co.re/docs/contributing/modules#migrating-from-pytest-to-nf-test

Is your feature request related to a problem? Please describe

• [ ] #5170
• [x] bcftools/concat
• [x] bcftools/mpileup
• [x] bcftools/sort #5165
• [x] #5255
• [x] bwa/index
• [x] bwa/mem
• [x] #5169
• [x] bwamem2/mem
• [x] cat/cat
• [x] cat/fastq
• [x] cnvkit/antitarget
• [x] cnvkit/batch
• [x] cnvkit/reference
• [x] controlfreec/assesssignificance
• [x] controlfreec/freec
• [x] controlfreec/freec2bed
• [x] #5376
• [x] controlfreec/makegraph
• [x] controlfreec/makegraph2
• [x] deepvariant #5234
• [x] dragmap/align
• [x] dragmap/hashtable #5438
• [x] #5364
• [x] ensemblvep/vep
• [x] fastp
• [x] fastqc
• [x] fgbio/callmolecularconsensusreads
• [x] fgbio/fastqtobam
• [x] fgbio/groupreadsbyumi
• [x] freebayes
• [x] gatk4/applybqsr
• [x] gatk4spark/applybqsr
• [x] gatk4/applyvqsr
• [x] gatk4/baserecalibrator
• [ ] gatk4spark/baserecalibrator
• [x] gatk4/calculatecontamination
• [ ] gatk4/cnnscorevariants
• [x] gatk4/createsequencedictionary
• [ ] gatk4/estimatelibrarycomplexity
• [x] gatk4/filtermutectcalls
• [ ] gatk4/filtervarianttranches
• [ ] gatk4/gatherbqsrreports
• [ ] gatk4/gatherpileupsummaries
• [x] gatk4/genomicsdbimport
• [ ] gatk4/genotypegvcfs
• [x] gatk4/getpileupsummaries
• [x] gatk4/haplotypecaller
• [ ] gatk4/intervallisttobed
• [ ] gatk4/learnreadorientationmodel
• [x] gatk4/markduplicates
• [x] gatk4spark/markduplicates
• [x] gatk4/mergemutectstats
• [x] gatk4/mergevcfs
• [x] gatk4/mutect2 #5242
• [ ] gatk4/variantrecalibrator
• [x] #5360
• [x] #5308
• [x] #5361
• [x] mosdepth
• [ ] msisensorpro/msisomatic
• [ ] msisensorpro/scan
• [x] multiqc
• [x] samblaster
• [x] samtools/bam2fq
• [x] samtools/collatefastq
• [x] samtools/convert
• [x] samtools/faidx #5437
• [x] samtools/index
• [x] samtools/merge
• [x] samtools/mpileup
• [x] samtools/stats
• [x] samtools/view
• [ ] sentieon/applyvarcal #5223
• [x] sentieon/bwamem
• [x] sentieon/dedup
• [ ] sentieon/dnamodelapply
• [ ] sentieon/dnascope
• [x] sentieon/gvcftyper
• [x] sentieon/haplotyper
• [ ] sentieon/varcal
• [ ] snpeff/download
• [x] #5185
• [x] #5338
• [x] #5318
• [x] svdb/merge
• [x] tabix/bgziptabix
• [x] tabix/tabix
• [x] #5365
• [x] untar
• [x] unzip
• [x] #5374

Describe the solution you'd like

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Describe alternatives you've considered

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Additional context

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[famosab]

freebayes was already ported: https://github.com/nf-core/modules/tree/master/modules/nf-core/freebayes