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new modules for tempo's fastq alignment #13

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anoronh4 opened this issue Dec 14, 2023 · 0 comments
Open
1 of 12 tasks

new modules for tempo's fastq alignment #13

anoronh4 opened this issue Dec 14, 2023 · 0 comments
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anoronh4 commented Dec 14, 2023 •
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We want to convert the bwa_markdup_bqsr subworkflow to a non-hybrid workflow, i.e. use only msk modules. the following should be added:

  • bwa/mem
  • gatk4/markduplicates
  • gatk4spark/markduplicates
  • gatk4/applybqsr
  • gatk4spark/applybqsr
  • gatk4/baserecalibrator
  • gatk4spark/baserecalibrator
  • samtools/index

for testing, we might add:

  • bwa/index
  • gatk4/createsequencedictionary
  • samtools/faidx

An additional module might be added as well:

  • custom/splitfastqbylane (once proposed to the nf-core modules repository, but the PR was never approved)
@anoronh4 anoronh4 changed the title new modules: new modules for fastq alignment Dec 14, 2023
@anoronh4 anoronh4 mentioned this issue Dec 14, 2023
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@anoronh4 anoronh4 mentioned this issue Jan 9, 2024
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@anoronh4 anoronh4 changed the title new modules for fastq alignment new modules for tempo's fastq alignment Jan 26, 2024
@buehlere buehlere added the module adding new module label Feb 9, 2024
@anoronh4 anoronh4 self-assigned this May 2, 2024
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