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

Describe the solution you'd like

No response

Describe alternatives you've considered

No response

Additional context

No response

[maxulysse]

Note that we have overlap with https://github.com/nf-core/modules/issues/3935

[vlebars]

Hello ! I will work on samtools/faidx.

[vlebars]

I will do bedtools/merge.

[vlebars]

I will do bedtools/sort.

[vlebars]

I will do gatk4/bedtointervallist.

[vlebars]

I will do gatk4/combinegvcfs.