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

[maxulysse]

Is your feature request related to a problem? Please describe

• [x] bedtools/merge
• [x] bedtools/sort
• [ ] cat/fastq
• [ ] custom/dumpsoftwareversions
• [ ] ensemblvep/vep
• [ ] fastqc
• [ ] gatk4/applybqsr
• [x] gatk4/baserecalibrator
• [x] gatk4/bedtointervallist
• [ ] gatk4/combinegvcfs
• [ ] gatk4/createsequencedictionary
• [ ] gatk4/haplotypecaller
• [ ] gatk4/indexfeaturefile
• [ ] gatk4/intervallisttools
• [x] gatk4/markduplicates
• [ ] gatk4/mergevcfs
• [ ] gatk4/splitncigarreads
• [ ] gatk4/variantfiltration
• [ ] gffread
• [ ] gunzip
• [ ] mosdepth
• [ ] multiqc
• [x] samtools/faidx
• [ ] samtools/flagstat
• [ ] samtools/idxstats
• [ ] samtools/index
• [ ] samtools/merge
• [ ] samtools/sort
• [ ] samtools/stats
• [ ] snpeff/snpeff
• [ ] star/align
• [ ] star/genomegenerate
• [ ] tabix/bgziptabix
• [ ] tabix/tabix
• [ ] untar

Describe the solution you'd like

No response

Describe alternatives you've considered

No response

Additional context

No response