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NationalGenomicsInfrastructure / ngi_reports

Code to generate reports for use by the NGI in SciLifeLab

Home Page:http://nationalgenomicsinfrastructure.github.io/ngi_reports/

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Project summary report updates

ewels opened this issue · comments

commented

Stage 1

  • Change Contract to Agreement in template
  • Add NGI Facility
    • Genomics Production Stockholm
    • Genomics Applications Stockholm
  • Re-write Library construction
    • Can no longer drop quote in, need to use new code system lookup table
    • Break up into bullet points - skip if blank
      • Input (DNA, RNA, Library)
      • Type (many things - eg. By user, Rubicon Thruplex FD)
      • Option (Depletion, 350bp)
      • Category (Low Input)
    • Talk to Mattias to get this
    • If all bullet points are missing / can't parse field then:
      • Throw a warning on the command line (with the contents of the field)
      • Skip the entire section, including header (use {% if project.variable %} in template)
  • Add to Sequencing Method
    • Add sequencing chemistry to sequencing method
  • Swedac Accreditation section
    • If blank should print an empty string
    • Print Not Applicable if in database
      • Ask Mattias to add this to the LIMS
    • Use [Not] Validated under ISO accreditation 17025:2005 instead of [Not] Swedac accredited
      • Parse in reports from whatever is stored in the database
    • Make all values dynamic from statusdb
    • Rename fields according to what we actually do
      • Library preparation
      • Sequencing data
      • Data Processing
      • Data Analysis

Stage 2

  • Remove tabular data from the report if more than 5 samples
  • Always generate .csv files of tabular data
  • Have explanation of fields in report
  • Sample Table - One row per sample
    • NGI ID
    • User ID
    • Total Reads

    • = Q30

    • Sample Pass / Fail Status (from yield)
  • Library Table - One row per sample prep per sample
    • NGI ID
    • Library Prep
    • Library QC Status
    • Average fragment size
    • Index
  • Run Table - One row per per flow cell lane
    • Date
    • Flow Cell ID
    • Lane
    • Cluster Yield (Passed Filters)
    • % PhiX

    • = Q30

    • Sequencing Method

Only test with projects from 2015 - not J.Lundeberg_14_01

THE FUTURE

  • Make plots where there are tables
  • Use CLICK instead of Argparse for report specific command line parameters
    • Have option for whether to display tables in report or not
commented

wow, this is a cool issue!

commented

It took a three hour long meeting to write 😄

commented

@guillermo-carrasco: Indeed 😂 Was created by Markdown Magician @ewels

commented

Well this is done :)