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Generate plots and a report from pipeline #25

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noporpoise opened this issue Sep 29, 2015 · 0 comments
Closed

Generate plots and a report from pipeline #25

noporpoise opened this issue Sep 29, 2015 · 0 comments
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enhancement

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@noporpoise
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Would be nice if the McCortex pipeline could automatically generate a report with plots and figures on the processing that has been done, summary of the results, QA etc.

Would require R and Latex as dependencies.
noporpoise added a commit that referenced this issue Nov 15, 2015
@noporpoise
Split report from pipeline makefile (resolves #25)
fa4902d 
make-report.pl:
- generates a latex markup + Makefile
- requires McCortex but not R or latex
- running `make` calls R + latex + McCortex plotting scripts to create PDF

make-pipeline.pl:
- don't include any report generation

scripts/R/*.R:
- add additional information to plots from expected coverage and cleaning cutoffs

tests/pipeline/Makefile:
- test report generation, but don't run latex+pdf

src/commands/ctx_view.c:
- some suggestions for improvements to the command line arguments
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