search

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
25 stars 16 forks source link

Configurable bcl2fastq output #48

Closed johandahlberg closed 6 years ago

johandahlberg commented 6 years ago

This relates to what has been reported in:

Basically this code makes it possible to configure where bcl2fastq has written its output, and switches the default to match the standard output location of bcl2fastq.

The way to configure it from now on is to set it in the newly introduced parser config section in the config, e.g:

parser_configurations:
  StatsJsonParser:
    bcl2fastq_output_path: Data/Intensities/BaseCalls
codecov[bot] commented 6 years ago

Codecov Report

Merging #48 into master will increase coverage by 1%. The diff coverage is 100%.

Impacted file tree graph

@@         Coverage Diff          @@
##           master   #48   +/-   ##
====================================
+ Coverage      90%   90%   +1%     
====================================
  Files          18    18           
  Lines         670   683   +13     
====================================
+ Hits          598   612   +14     
+ Misses         72    71    -1
Impacted Files Coverage Δ
checkQC/qc_engine.py 100% <100%> (ø) :arrow_up:
checkQC/parsers/interop_parser.py 98% <100%> (ø) :arrow_up:
checkQC/parsers/stats_json_parser.py 97% <100%> (+1%) :arrow_up:
checkQC/app.py 88% <100%> (+1%) :arrow_up:
checkQC/config.py 91% <100%> (+3%) :arrow_up:

Continue to review full report at Codecov.

Legend - Click here to learn more Δ = absolute <relative> (impact), ø = not affected, ? = missing data Powered by Codecov. Last update d72b696...d0cf304. Read the comment docs.