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mgi-qc / cwl_wgs_report

Create wgs report from cwl metrics.
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reporting script to judge pass/fail metric is not judging #6

Open awollam opened 4 years ago

awollam commented 4 years ago

e.g. cwl.metrics.parser.py -wgs -w 2859352 put in 20 as the metric to judge:

report says this below: QC Pass Metrics (samples must meet all requirements) HAPLOID COVERAGE: 20 (User defined) discordant_rate < 5 inter-chromosomal_Pairing rate < 0.05 FREEMIX < 0.05 FOP: PF_MISMATCH_RATE < 0.05 SOP: PF_MISMATCH_RATE < 0.05

Additional Metrics: No other metric required/reviewed for assignment of QC pass/fail judgement

SEQUENCING_NOTE: https://confluence.ris.wustl.edu/pages/viewpage.action?spaceKey=AD&title=WorkOrder+2859352

Number of Flow Cell or Desired Coverage: See Special Instructions

Special Instructions:

The sample will have an automated library constructed. The library will be pooled with the library from work order 2859351. The pooled libraries will be sequenced on 0.047 of an NovaSeq S4 flow cell (300 XP, targeting ~20x). The deliverables are fastq files.

Number of Flow Cell Lanes or Desired Coverage: Special Instructions:

QC Summary Report: Number of samples QC'ed = 1 Number of samples that pass = 0 Number of samples that fail = 0

Samples That Failed QC Failed Metrics: HAPLOID COVERAGE = NA discordant_rate = NA inter-chromosomal_Pairing rate= NA FREEMIX = NA FOP: PF_MISMATCH_RATE = NA SOP: PF_MISMATCH_RATE = NA

QC Summary Statistics: AVERAGE HAPLOID COVERAGE = 36.570571711385384 AVERAGE discordant_rate = 2.9200000000000017

antonaccitj commented 4 years ago

Terminal output for this metrics file:

_------------------------- Report for 2859352.cwl.metrics.011320.tsv: Confluence link: https://confluence.ris.wustl.edu/pages/viewpage.action?spaceKey=AD&title=WorkOrder+2859352

QC based on:

  1. Haploid Coverage
  2. Haploid Coverage and Total Base Pairs

  3. Total Base Pairs in place of Haploid Coverage Make a selection: 1

    Enter Haploid Coverage value: 20

    Would you like to add a SEQUENCING_NOTE? y/n: n Skipping SEQUENCING_NOTE

    No missing metircs FREEMIX missing for M_II-LSL-Nras_G12D-5217 No report generated as no samples were QC'd -------------------------_

I think we decided back in September??? that this would not fail pass, or include samples in the metric averages if they are missing metrics(I think this last one was a counting issue). Freemix was one of the non optional ones.