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maxplanck-ie / nanoporeReads_dataTransfer

A pipeline to transfer the Nanopore reads to end users
MIT License
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Updates in base code #148

Closed caballero closed 6 months ago

caballero commented 7 months ago

This PR is for:

  1. capture software versions from HTML or JSON
  2. merge bam files if available
  3. set smart triggers for basecall, align and modbed files
  4. change modbam2bed to modkit
  5. capture model used from report JSON
  6. dorado align using Fastq instead of BAM as input
  7. fix parsing of species in multiqc_data in final report

Linked issues: