TODO for improvements and finalisation

[evezeyl]

TODO

• reread purge haplotigs and explain better
• read more about the variant normalisation
• more nextflow training ... need to improve / groovy

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Pipeline itself

• include the version notes ... check version output and add if missing
  • debug - R.version is empty - quarto R script for filtering contigs-> sessionInfo not working on qmd ? or sink ? find a way to get it. -> see eg https://stackoverflow.com/questions/39131017/sink-wont-print-output-to-text-file-in-rmarkdown (tried {sink ..} but did not work
• modules config - selection output
• include R packages - script ? session info
• adjust the system configs (now I have modified the saga.config) for other institutions can use / adjust the pipeline fast (but not urgent yet)
  • base.config
  • hpc.config

Documentation

• track description visual (until now)

  • FILTER_CONTIGS
  • COMPASS
  • HAPLOPURGE
  • VARWRRUM:

• 1_Pipeline_description.mdshort description tracks, purpose and references

  • FILTER_CONTIGS
  • COMPASS
  • HAPLOPURGE
  • VARWRRUM:

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• 2_Installation.md
• SAGA_USERS_instructions.md
• 3_How_to_Run.md

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Details tracks choices - need review - improvements

• 4_Choices.md
  • Filtering_contigs.md
  • Haplopurge_choices.md
  • VARWRRUM_choices.md

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Description of output and options

Then send to review - colleagues
TRACKING :
Thomas : review

• 1_Pipeline_description.md
• 2_Installation.md
• SAGA_USERS_instructions.md
• 3_How_to_Run.md
• 4_Choices.md
  • Filtering_contigs.md
  • Haplopurge_choices.md
  • VARWRRUM_choices.md