config.yaml

# list of sample names as used by genpipes: ["sample1", "sample2"]
SAMPLES: []

# list marks as used by genpipes: ["H3K27me3", "H3K27ac"]
MARKS: []


# path to genpipes output folder
GENPIPES: "/lustre06/project/6004736/alvann/from_narval/220408_SJG2_A29P/ChIP/out/01A_genpipes_chipseq"

# path to output folder
OUT_PATH: ""

CPU: 10
CPU_COMPUTE_MATRIX: 10

# path to black list file
BLACK_LIST: "/lustre06/project/6004736/alvann/from_narval/REFERENCES/annotation_files/ENCODE.blacklist.wgEncodeHg19ConsensusSignalArtifactRegions.hg19.noOverlaps.bed"

# bin size to use for bigwig summary
BIN_SIZE: [5000]

# bed files used for bigwig summary
SUMMARY_REGIONS:
  gene.ens.hg19: "/lustre06/project/6004736/alvann/from_narval/REFERENCES/annotation_files/Ensembl.ensGene.whole.hg19.collapsed.can.bed"
  promoter5kb.ens.hg 19: "/lustre06/project/6004736/alvann/from_narval/REFERENCES/annotation_files/Ensembl.ensGene.whole.hg19.collapsed.promoter5kb.can.bed"
  cgi10kb.UCSC.hg19: "/lustre06/project/6004736/alvann/from_narval/REFERENCES/annotation_files/UCSC.regulation.CpGIslands.cpgIslandExt.hg19.10kb.bed"

# PCs to compute
PC:
  pc12: [1, 2]
  pc34: [3, 4]

# normalization method: RPKM, CPM etc (see deeptools for options)
NORM_METHOD: ["CPM"]

# scale factrs to use (numeric or rx)
SCALE_FACTOR: [1, "rx"]

# if SCALE_FACTOR = "rx" provide path to csv file with rx scale factors for each sample
# file needs to have column Sample and column rx
SCALE_FACTOR_FILE_RX: ""

# params to run compute matrix (used as input for heatmaps etc)
# change <name> to meaningful matrix name 
COMPUT_MATRIX_PARAM:
  <name>: 
    type: "scale"
    ref_point: ""
    region_bed: "Ensembl.ensGene.whole.hg19.collapsed.bed"
    length: 10000
    up: 2500
    down: 2500
    samples: ["", "", ""]
  <name>: 
    type: "ref_point"
    ref_point: "center"
    region_bed: "Ensembl.ensGene.whole.hg19.collapsed.promoter5kb.bed"
    length: ""
    up: 2500
    down: 2500
    samples: ["", "", ""]

# params plot heatmap and plot profile. See deeptols for options.
PLOT_HEATMAP_PARAM:
  name:
    color: "#1e5385,#f8f79d,#cc2200"
    colorLine: 
    plotType: se
    samples: ""
    lables: ""
    startLabel: ""
    endLabel: ""
    title: ""
    height: 15
    kmeans: 2

PLOT_PROFILE_PARAM:
  name:
    lables: ""
    startLabel: ""
    endLabel: ""
    title: ""
    plotType: se
    colors:

# samples used when calculating Z-score
Z_SCORE_PARAM:
  control: [""]
  condition:
    condition1: [""]
    condition2: [""]