Detailed dataset (yaml) file example

See the README for a basic introduction to the setup of the dataset (yaml/json) spec.

A more fully fleshed out example can be seen below:

id: laura-mb-v14
samples:
  # some particular sample id in our dataset
  Hs-LN-D-5RACE-IgG:
    meta: {isotype: g, species: human, subject: BF520, timepoint: M9}
    locus: igh
    parameter-dir: /path/to/Hs-LN-D-5RACE-IgG/parameter-dir
    partition-file: /path/to/Hs-LN-D-5RACE-IgG/partition.csv
    cluster-annotation-file: /path/to/Hs-LN-D-5RACE-IgG/partition-cluster-annotations.csv
    per-sequence-meta-file: /path/to/Hs-LN-D-5RACE-IgG/seqmeta.csv
    seeds:
      # unique seed id
      BF520.1-igh:
        partition-file: /path/to/Hs-LN-D-5RACE-IgG/seeds/BF520.1-igh/partition.csv
        cluster-annotation-file: /path/to/Hs-LN-D-5RACE-IgG/seeds/BF520.1-igh/partition-cluster-annotations.csv
      BF520.2-igh:
        partition-file: /path/to/Hs-LN-D-5RACE-IgG/seeds/BF520.2-igh/partition.csv
        cluster-annotation-file: /path/to/Hs-LN-D-5RACE-IgG/seeds/BF520.2-igh/partition-cluster-annotations.csv
      # other seed partitions...

    # other partitions can be any other runs of partis on the same sample or subsample of the data, as you like.
    # You can also just create separate sample entries for these if you'd rather.
    other-partitions:
      subset-1:
        partition-file: /path/to/Hs-LN-D-5RACE-IgG/other-subsets/subset-1/partition.csv
        cluster-annotation-file: /path/to/Hs-LN-D-5RACE-IgG/other-subsets/subset-1/partition-cluster-annotations.csv
      subset-2:
        partition-file: /path/to/Hs-LN-D-5RACE-IgG/other-subsets/subset-2/partition.csv
        cluster-annotation-file: /path/to/Hs-LN-D-5RACE-IgG/other-subsets/subset-2/partition-cluster-annotations.csv
      # other subsets...

  # some other sample in our dataset...
  Hs-LN-D-5RACE-IgK:
    meta: {isotype: k, species: human, subject: BF520, timepoint: M9}
    locus: igh
    parameter-dir: /path/to/Hs-LN-D-5RACE-IgG/parameter-dir
    partition-file: /path/to/Hs-LN-D-5RACE-IgG/partition.csv
    cluster-annotation-file: /path/to/Hs-LN-D-5RACE-IgG/partition-cluster-annotations.csv
    per-sequence-meta-file: /path/to/Hs-LN-D-5RACE-IgG/seqmeta.csv
    seeds:
      #etc...
    other-partitions:
      #etc...

  # etc. for other samples...

Eventually we may also support adding per-subject metadata. Also if you aren't a fan of yaml but would prefer to use json for these specs, we can add an option for that fairly easily. If you're interested in either, please submit an issue.