NEWS.txt

# --------------------------------------------------------------------- #
# DONE
201910
[*]. Add rule for FeatureCombination.rds -> txt
    - export directly in function call
[*]. Configure the pipeline for differential peak calling - ask Alex


181603
[*]. Add peak QC
[*]. Run multiqc
[*]. Add test genome data (genome subset)
[*]. add check for gzipped bowtie reference
[*]. the pipeline does not work without app params - change config check

181503
[*]. enable trimming

181303
[*] Move samplesheet To csv file
[*] detect library type from input, extension for paired end data to be automatically determined from the pairs

182002
[*] Put default settings in etc/settings.yaml.in, do not set them in Snake_ChIPseq.py.
[*] Introduce section 'export_bigwig' in settings with parameters 'extend' and 'scale_bw'. 

181701
[*] Adjusted code to settings.yaml and sample_sheet.yaml. The pipeline now works witwo yaml files.
[*] Custom function for calling Rscript + Rscript parser for yaml like arguments
[*] Any number of feature combinations is now supported.

181201
[*]. Refactored the code so that the output of pipelines is always in bed format
[*]. Annotate peaks with given genomic annotation

171124
[*]. Refactored code - rules separated into multiple files
[*]. sorted out the bigWig/bigBed/UCSC tracks issue

171122
[*]. Annotation Processing
[*]. Signal extraction
[*]. Peak Annotation

170801
[*]. cofigure the pipeline for broad histone data
[*]. bedToBigBed for broadPeak data

170724
[*]. Automatic UCSC hub setup

170620
[*]. add scalling to the bedgraph construction

170615
[*]. Enable running subsections of the pipeline:
    IDR and PEAK calling are not obligatory

170614
[*]. extended the pipeline to accept multiple ChIP/Cont samples for peak calling
[*].  add support for peak calling without control:
    peak calling can be run without control samples - useful for ATAC data

172405
[*]. write checks for the config proper formatting :
    - ChIP and Cont parameters in peak calling
    - idr samples
[*]. Check for params:idr
[*] Add paired end test data
[*]. Extent to paired end reads
    - Testing for paired end reads
    - Mapping
    - Fastqc for paired end reads

Initial commit
[*] 0. Make test data
[*] 1. Variables into config file:
[*]    - genome path
[*]    - read extension
[*] 2. Automatic reference generation
[*] 3. check globbing
[*] 4. Add peak calling
[*]. Extract the input file for the fastqs as a config parameter
[*]. application placeholders in config files
[*]. Format messages
[*] Add interactive macs parameters
[*] Add possible pseudonims for samples

# --------------------------------------------------------------------- #
# TODO
## Main
[]. IDR - column index is hardcoded, should be enabled and tested for bed files
[]. Check_Config:
    - check that IDR and Peak names and Feature combination names do not overlap!
    
[]. Feature combination:
    - construct default feature combination for all peaks
    


    
[]. Check for spaces in genome fasta headers
[]. Check whether the fasta sequence names are the same as gtf sequence names
[]. Feature combination singnal extraction 200
[]. QC for Peaks - ask alex for Peak QC rule
[]. Report with figures



[]. extract signal:
    - Comprehensive
            [x] basic mapping stats
            [x] peakQC
            - annotation per genomic category
            [*] profiles over TSS and TTS
            [*] cumulative profiles over the gene body
            - peak co-occurence matrix
            - sample correlation

            - motif discovery



[#]. enable sample specific parameter deposition - works for macs
[#]. write tests
[]. write markdown
        - Sample Specific

[]. add differential analysis feature
	[x] add section to settings file
	- add counting rules 
	- add report 
		- add DEseq2
		- add edger
	- explain issues with different normalizations


[]. omit manually filtering bam files
	- verify downstream tools can filter mapq and duplicates if needed



[]. write yaml schema
    https://github.com/Grokzen/pykwalify,
    http://www.kuwata-lab.com/kwalify/ruby/users-guide.01.html#schema


[]. make BigWigExtend a streaming function

[]. Tests:
        - for no control sample
        - for multiple chip and control samples
        - add test if control not set in yaml file - check for multiple types of input
        - check whether IDR test works

[]. Tests for hub
[]. Check yaml:
    - hub
    - feature combination:
        - keys must be idr and peaks
    - uniqueness of peak names
    - check for annotation - gtf file existence



## Additional
[]. rewrite fastqc to go through each individual file


[]. Set default for genome name if genome specified but genome name is not
[]. Delete temporary files - bed and bedGraph files
[]. Sample specific read extension
[]. Motif Discovery


#
link to the sample sheet
https://docs.google.com/spreadsheets/d/1SokqvaLEhR_tJhkxDwXGg1OzmGErbKv5Vq41dxz3qlQ/edit#gid=0