add wbuild demo
-
define variables outside report.R - where? maybe in
make.config
or.Rprofile
- use them in i) the wbuild header of report.R
- and ii) in the R-code
- where? maybe in
-
define variables in wbuild header and use them in R-code, e.g. this makeData.R -
compile a single script file with wBuild (to use the variables from the header); best without defining a rule in Snakefile
Tasks for the sprint
-
choose an example dataset to use throughout the demo - go through the whole tutorial
- Pages
-
simple input page - single input file, plot the results (iris dataset)
-
input-output page - script parameters (choose whether it should be rendered or not)
- one script does PCA
- second one plots it
- script parameters (choose whether it should be rendered or not)
-
plain snakefiles inclusion - show how to do this - show how to download the iris dataset if it doesnt exist
- say that if you would have removed the file, everything else would still run
- show how to download the iris dataset if it doesnt exist
-
describe how the markdown inclusion works -
How to use plain python in the header using escape sequences - case-study: apply one script multiple times using wildcards
- run model on three different columns, save all the models to the output
- case-study: apply one script multiple times using wildcards
-
softlinking/scriptMapping the analysis scripts automatically - show how to apply the same pipeline to 2 different datasets (have two scripts)
- for the second one, modify the plot file
-
show the commands implemented in snakemake and also supported by wbuild - DAG
- all
- publish
- explain the config file
- script-mapping
-
adapt the process of getting the dataset for windows -
wget
is a command unique for Linux and doesn't launch on Windows - skip wgetting the dataset and instead ship it already bundled in demo?
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