ChangeLog

CHANGES
=======

* allow underscores
* set python/numpy/macs version
* Update seqtools.yml

v0.0.1
------

* Wd (#14)
* Wd (#13)
* Update README.md
* Wd (#9)
* Wd (#8)
* Wd (#6)
* update readme
* Shuffling
* fix batch vs non batch in 1 run
* batch effects parse
* FDR cutoff maPlot == edgeR
* countmatrix update, FDR 0.05
* ruleOrder ambigious compcond cond
* matrix bugfix
* bug logs
* Fix logpaths
* escape metadat files with dryrun
* restruct fin
* restruct
* readme update
* readme update
* prePeak done
* done until peak
* macs2 - merge noss
* bamMerge - noss
* fragSize - nonpeakSet
* work in progress
* invoke bam processing without sampleSheet
* restructure exec
* init layout wrap
* different modes for peak generation
* change variable bammerge DAG conflict
* union working
* DAG arg
* strip graphviz, fix dryrun
* mergeComp mode complete
* merge conds
* start on merge
* clean smk
* non bam merge working
* restruct for outDir
* init sampleMerge
* graphviz for DAG
* help msg
* ship dryrun to subprocess, include DAG
* outdir spec + mergeB
* PCA 5k
* LFC out change, ntop 500 PCA
* Batch effect parser
* readme update
* Fix no batch run
* Batcheffect
* Batch effects
* incorp batch effects
* Include Batch parsing ss
* include alternative TSS for scoring
* bypass gtf parse in dryrun
* another fix
* fix dryrun
* dryrun action test
* escape flag for dryrun, pave the way for tests
* remove flake from reqs
* remove snake clutter
* flake test
* hardCode python version seqtools
* comment rich bug
* bugFix Genes
* init reqs
* remove pytest
* revert wheel deps
* Create flake.yml
* exec updates
* bugFix downstream
* Snakefile rename
* update readme, small arg updates
* bugFix
* pep8 args
* uropa outdir bugfix
* Delete .coverage
* ignore
* debug AOS outdir, future ideas
* Create LICENSE
* Further pep8
* pep8 misc
* pep8 setup
* add flake, update todo
* Simplify the environment forest to only 2
* remove duplicate snakemake
* downstream init
* add meme, clean uropa env add meme
* include mito check fly
* Allow variable max frag size
* updateWorkflow
* Update README.md
* General functions, fullMerge peak and annotations
* Break up workflows, diffAcc counter impl
* revert diffPeak
* figLegends
* label maPlot according to conditions
* remove hardcode conda path
* Force input order for factor levels DE
* Typos
* todo update
* Major readme update
* revert SummitInc
* Individual peak calling, merge later
* Todo / snake update
* gsize bugfixes, param eval etc
* Changes macs2, fix up genomeSize
* Split init tobias
* Switch to edgeR, cant believe it actually works
* bugfix DESEQ
* homer revisit
* Todo argument handling
* Error handling samplesheet malformat, log alSieve
* Simplify peak annotations / mergings
* meme start / cleaning
* Partial rollbacks + readme updates
* Revisit workflow
* Switch to pval, plot init output full list
* working frip plotter
* running updates
* blackList alignmentsieve
* IDR implementation + short TODO
* working FRIP + update todo
* todo list
* Annotate peaks uropa
* typos
* readme
* pval down and slurm submission
* conda env fixes
* Init other analysis
* Seperate conda envs
* Start multiple environments
* Tex reports
* Init texbuilder
* Init tex, match colors of PCA with plot
* envs update
* Cluster execution + deal with logs
* DESeq2 Typo
* Finalise group comparisons
* Multiple comparisons finished
* Update README.md
* multicompare untill bwz
* Begin allowing multiple comparisons
* Env update
* DESeq implementation
* todolist
* deeptools progress
* Init Rscripts
* snakemake progress
* snakemake implementation
* SS parsing
* Further init
* readme
* initrepo
* Initial commit