modules icon indicating copy to clipboard operation
modules copied to clipboard

Published 20 hours ago • verified publisher icon nf-core

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

Open maxulysse opened this issue 2 years ago • 6 comments

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

maxulysse avatar Oct 10 '23 07:10 maxulysse

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

maxulysse avatar Oct 10 '23 07:10 maxulysse

Hello ! I will work on samtools/faidx.

vlebars avatar Mar 18 '24 09:03 vlebars

I will do bedtools/merge.

vlebars avatar Mar 18 '24 13:03 vlebars

I will do bedtools/sort.

vlebars avatar Mar 19 '24 08:03 vlebars

I will do gatk4/bedtointervallist.

vlebars avatar Mar 19 '24 10:03 vlebars

I will do gatk4/combinegvcfs.

vlebars avatar Mar 19 '24 14:03 vlebars

All done :)

famosab avatar Feb 13 '25 13:02 famosab