config.yaml

---
units: units.tsv

# files and directories
working_dir: "temp/"
result_dir: "results/"

# trimmomatic parameters
trimmomatic:
  adapters:               "adapters.fasta"
  seedMisMatches:         '2'
  palindromeClipTreshold: '30'
  simpleClipThreshold:    '10'
  LeadMinTrimQual:        '3'
  TrailMinTrimQual:       '3'
  windowSize:             '4'
  avgMinQual:             '15'
  minReadLength:          '40'
  phred:                  '-phred33' # phred: for illumina >1.8 the quality score are encoded by phred33

## Genomic references, annotations and aligner indexes
refs:
  genome_url:  "ftp://ftp.solgenomics.net/tomato_genome/assembly/build_3.00/S_lycopersicum_chromosomes.3.00.fa"
  gff_url: "ftp://ftp.solgenomics.net/tomato_genome/annotation/ITAG3.0_release/ITAG3.0_gene_models.gff"

# bowtie2 parameters
bowtie2:
  params:
    mode:             "--local"
    sensitivity:      "--very-sensitive-local"
    max_fragment_len: "--maxins 500"                # maximum fragment length for valid paired-end alignments
    min_fragment_len: "--minins 80"                 # minimum fragment length for valid paired-end alignments
    verbose:          "-q"

# bamCoverage parameters:
bamCoverage:
  params:
    EFFECTIVEGENOMESIZE: '820000000' #source = http://plant-plasticity.github.io/resources/3_ATAC-seq%20data%20processing.pdf #option is --effectiveGenomeSize
    EXTENDREADS: '200'              # extend each reads with a 200bp to match the average fragment size of the ChIP experiment
    binSize: "1000"
    ignoreForNormalization: "SL3.0ch00" #list here space-delimited chromosomes that should be ignored for normalization, sex chromosomes usually.
    smoothLength: "40"
    normalizeUsing: "RPKM"

bamcompare:
  binSize: "1000"
  normalizeUsing: "RPKM"          #others choices are CPM, BPM, RPGC, None more documentation:https://deeptools.readthedocs.io/en/develop/content/tools/bamCompare.html?highlight=bamcompare
  EFFECTIVEGENOMESIZE: '820000000'
  operation : "log2"              #others choices are ratio, subtract, add, mean, reciprocal_ratio, first, second more documentation:https://deeptools.readthedocs.io/en/develop/content/tools/bamCompare.html?highlight=bamcompare
  smoothLength: "40"
  scaleFactorsMethod: "None"       #others choices are readCount, ,SES
  ignoreForNormalization: "SL3.0ch00" #list here space-delimited chromosomes that should be ignored for normalization, sex chromosomes usually.


# macs2 Parameters:
          # for information over macs2, refer to https://github.com/taoliu/MACS
          # regular peak calling : macs2 callpeak -t ChIP.bam -c Control.bam -f BAM -g hs -n test -B -q 0.01
          # broad peak calling : macs2 callpeak -t ChIP.bam -c Control.bam --broad -g hs --broad-cutoff 0.1
macs2:
  genomesize: "--gsize mm"        #here I used 'mm' because it's the closest to tomato, for human change to 'hs'
  format: "--format BAMPE"        #Use BAMPE to activate the paired end data, MACS will use the actual insert size of pairs of reads to build the fragemnt pileup.
  qvalue: "0.05"                  #default is 0.05
  outdir : "results/bed/"
  bandwidth: "--bw 350"           #the bandwidth is used to scan the genome for model building. To be set to the expected sonication fragment size.

multiBamSummary:
  binSize: "1000"

computeMatrix:
  binSize   : "1000"
  upstream  : "3000"
  downstream: "3000"

plotCorrelation:
  corMethod : "pearson"            # Can be replaced by spearman
  whatToPlot: "heatmap"            # Can be replaced by scatterplot
  color     : "PuBuGn"             # see [here](https://matplotlib.org/examples/color/colormaps_reference.html) for alternative colors

plotHeatmap:
  kmeans    : "1"
  color     : "PuBuGn"
  plot      : "plot, heatmap and colorbar"    # Others options are : “plot and heatmap”, “heatmap only” and “heatmap and colorbar”


plotFingerprint:
    EXTENDREADS: '200'
    binSize: "1000"

plotProfile:
    kmeans : "1"                  # choose the number of kmeans to compute
    startLabel : "TSS"            # default is TSS but could be anything, like "peak start"
    endLabel : "TES"              # TES is default but can be changed like for startLabel