--- a
+++ b/examples/chip-nexus/dataspec.yml
@@ -0,0 +1,39 @@
+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