fasta_file: ../data/mm10.subset.fa  # reference genome fasta file

task_specs:  # specifies multiple tasks (e.g. Oct4, Sox2 Nanog)

  Oct4:

    tracks:

      - ../data/chip-nexus/Oct4/counts.pos.subset.bw

      - ../data/chip-nexus/Oct4/counts.neg.subset.bw

    peaks: ../data/chip-nexus/Oct4/idr-optimal-set.summit.subset.bed.gz

  Sox2:

    tracks:

      - ../data/chip-nexus/Sox2/counts.pos.subset.bw

      - ../data/chip-nexus/Sox2/counts.neg.subset.bw

    peaks: ../data/chip-nexus/Sox2/idr-optimal-set.summit.subset.bed.gz

  Nanog: # Nanog is the task name

    tracks:

      # List of bigwig files (1 or more) corresponding to the task

      # The model will predict each track individually (here coverage of

      # reads mapping to the positive and negative strand) and

      # the contribution scores will be averaged across all of these tracks

      - ../data/chip-nexus/Nanog/counts.pos.subset.bw

      - ../data/chip-nexus/Nanog/counts.neg.subset.bw

    # Peaks associated with Nanog task (optional)

    # These are used to later run TF-MoDISco for Nanog contrib scores

    # only in the Nanog peaks.

    peaks: ../data/chip-nexus/Nanog/idr-optimal-set.summit.subset.bed.gz

bias_specs:  # specifies multiple bias tracks

  input:  # first bias track

    tracks:  # can specify multiple tracks

      - ../data/chip-nexus/patchcap/counts.pos.subset.bw

      - ../data/chip-nexus/patchcap/counts.neg.subset.bw

    tasks:  # applies to Oct4, Sox2, Nanog tasks

      - Oct4

      - Sox2

      - Nanog

  # NOTE: bias_specs don't specify peaks since they are only used

  # to correct for biases