Molmed / checkQC

CheckQC inspects the content of an Illumina runfolder and determines if it passes a set of quality criteria
http://checkqc.readthedocs.io/
GNU General Public License v3.0
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Support for iSeq, and improved org for testing #67

Closed johandahlberg closed 6 years ago

johandahlberg commented 6 years ago

This adds support for the Illumina iSeq, and also makes some changes to the way that the RuntypeRecognizer works by introducing a separate class for reading the files in the runfolder. This makes this easier to mock in the tests, which makes it easier to test that the correct instrument is returned depending on which type of runfolder is passed in.

The QC criteria that I have added are completely arbitrary, and need to be update.

codecov[bot] commented 6 years ago

Codecov Report

Merging #67 into master will increase coverage by 1%. The diff coverage is 76%.

Impacted file tree graph

@@         Coverage Diff          @@
##           master   #67   +/-   ##
====================================
+ Coverage      91%   92%   +1%     
====================================
  Files          18    19    +1     
  Lines         688   701   +13     
====================================
+ Hits          626   638   +12     
- Misses         62    63    +1
Impacted Files Coverage Δ
checkQC/app.py 87% <100%> (ø) :arrow_up:
checkQC/runfolder_reader.py 71% <71%> (ø)
checkQC/run_type_recognizer.py 92% <89%> (+7%) :arrow_up:

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johandahlberg commented 6 years ago

Go ahead and merge @MatildaAslin