# CytoPipeline 1.3

## CytoPipeline 1.3.6
- `execute()` now stores the nb of events retained at each pre-processing step,
to speed-up `collectNbOfRetainedEvents()`

## CytoPipeline 1.3.5
- added CITATION file

## CytoPipeline 1.3.4
- in execute(), when cache does already exist, make it clean before executing 
the pipeline steps (= preventing inconsistent cache upon crash/forced 
interruption)

## CytoPipeline 1.3.3
- added `collectNbOfRetainedEvents()` function

## CytoPipeline 1.3.2
- systematically override `pData` in cache upon execute() to allow running 
consistently running several times for increasing number of samples
- `sampleFiles<-` and `pData<-`: make sure that order of sample files 
follow the one of `pData` rownames if `pData` exists.
- added 'verbose' argument in `estimateScaleTransforms()`

## CytoPipeline 1.3.1
- refactored documentation files

# CytoPipeline 1.1

## CytoPipeline 1.1.5
- areSignalCols(), are FluoCols() can now accept a flowSet as input, 
on top of a flowFrame
- applyScaleTransforms() processing step has been improved (can take flowSet 
as input, checks channel concordance between transList and data object)

## CytoPipeline 1.1.4
- updated fcs files, that are at the source of OMIP021Samples dataset

## CytoPipeline 1.1.3
- in subSample(), renamed parameter 'nSamples' into 'nEvents', and added 
possibility for passing unused parameters, in order to support 
the use of the function as a processing step. Also amended the function
as to keep the original order of the events (keep chronology).
Finally, adds a 'keepOriginalCellIDs' parameter (default=TRUE).
- simplified the arguments of execute() related to the storage of the results
after last pre-processing step.

## CytoPipeline 1.1.2
- storage of phenoData into cache upon execution of CytoPipeline object
(and back into CytoPipeline object when re-built from cache)
- changed the default behaviour of estimateScaleTransforms() so that
the default method for scatter channels is now "none" instead of 
"linearQuantile"
- changed default behaviour of ggplotEvents() and ggplotFilterEvents(), when
logicle scale is used but no logicle parameters provided, these are now
estimated using flowCore::estimateLogicle(), instead of explicit default values

## CytoPipeline 1.1.1
- tiny modifications to support upgrade to Bioc 3.18

## CytoPipeline 0.99

## CytoPipeline 0.99.6
- corrected the OMIP021Samples fcs data in order to keep the original file
name
- bug correction: error message on execution with no sample file
- added `phenoData` slot in CytoPipeline object
- updated `readSamples()` to allow passing a `pData` parameters
- updated `compensateFromMatrix()` to allow passing a mapping 
based on a `pData` variable
- updated `readSamples()` to allow selecting a random number of samples and
removed `selectSamples()`
- vignette with demo and links to videos

## CytoPipeline 0.99.5
- reactivated unit tests for ggplot2 objects
- added man page for CytoPipeline package
- a few modifs in the vignette related to Bioc review process
- replaced withr::local_tempdir() by base::tempdir()
- removed extraneous whitespaces in CytoPipeline show() method
- removed `LazyData: true` in DESCRIPTION file 
- replaced `paste0(path, "/", filename)` by `file.path(path, filename)`
- updated License field in DESCRIPTION file

## CytoPipeline 0.99.4

- improved CytoPipeline constructors (`experimentName` and `sampleFiles` are
now parameters of all constructor version)
- centralized the production of standard outputs during pipeline execution, 
set all tuning parameters in execute() instead of slots 
in CytoPipeline object.  

## CytoPipeline 0.99.3

- some minor changes for BiocCheck()

## CytoPipeline 0.99.2

- removed dependencies to a number of packages, moved corresponding 
implementations of CytoProcessingSteps (wrappers) into `CytoPipelineUtils` 
package

## CytoPipeline 0.99.1

- Maintenance due to Bioc version change (3.17)
- removed use of openCyto::gate_tail() (disappeared w/o deprecation), replaced
by flowDensity::deGate()
- implemented export of pre-processed file (writeFlowFrame as a 
CytoProcessingStep implementation)
- extended readSampleFiles : mapping between channels and markers
- selectRandomSamples (new CytoProcessing step implementation)


## CytoPipeline 0.99.0

- Prior to Bioconductor submission
