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[FEATURE] port pytest to nf-test for sarek modules
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
- [ ] fgbio/callmolecularconsensusreads
- [x] fgbio/fastqtobam
- [ ] 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
- [ ] sentieon/bwamem
- [ ] sentieon/dedup
- [ ] sentieon/dnamodelapply
- [ ] sentieon/dnascope
- [ ] sentieon/gvcftyper
- [ ] 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
- [ ] 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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