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megSAP cleanup #314

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8 of 16 tasks
marc-sturm opened this issue Nov 26, 2024 · 0 comments
Open
8 of 16 tasks

megSAP cleanup #314

marc-sturm opened this issue Nov 26, 2024 · 0 comments
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@marc-sturm @leonschuetz @Ott-Alexander

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marc-sturm commented Nov 26, 2024 •
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ToDo:

  • remove unneeded Primer tools
  • reomve MIP tools
  • replace numdiff/SampleDiff with TsvDiff
    • remove SampleDiff and SampleOverview from ngs-bits
  • move NGS tools into Tools folder, move Scripts specific to Tübingen into IMGAG folder, move install scripts to Install folder, move auxilary scripts to Auxilary folder, move unneeded scripts to Deprecated folder
  • check cronjobs, doc and ngs-bits doc for path updates needed because of the moving
  • check PHP warnings/errors
  • check for absolute paths
  • perform tests
    • WES: NA12878_58 - freebayes - 10threads (MS)
      -old: 1h 52m
      -new: 1h 53m
    • WGS: NA12878x2_93 - freebayes - 15threads (MS)
      -old: 16h 42m
      -new: 8h 32m + TODO
    • lrGS: 23014LRa023_01 - 15threads (MS)
      -old: 15h 44m
      -new: h m
    • cfDNA: (LS)
    • somatic T/N WES: (ALO)
    • somatic T/N WGS: (ALO)
    • somatic TO WES: (ALO)
    • RNA: (ALO)
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@Ott-Alexander Ott-Alexander

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@marc-sturm @leonschuetz @Ott-Alexander