Adding annotate module in the cp_process_singlecells workflow

[axiomcura]

About PR

In this PR, the cp_process_singlecells will have the annotation module imported for analysis.

[MikeLippincott]

LGTM. Left a couple of comments to address. Minor documentation.

[MikeLippincott]

I don't have a lot of experience with what the norm is for these .yaml files but is it possible to add hints to what the possibilities are for each param? ex. dest_datatype: parquet what are the possible input types? I am not sure is this is doable or a norm just a thought

[axiomcura]

Good point. We are still figuring out what is the best way to document all the different types of parameters that each workflow module have to offer. Our current approach is to direct the user to the documentation inside the

If you look at the documentation in the workflow configs, the description of each technology is used along with it's corresponding link.

In terms of "what are the available parameters", we are currently discussing in developing a schema #55 which we will define the data type, options, etc of the parameters in the workflow config.

[MikeLippincott]

less ambiguous, I like basename better!

[MikeLippincott]

Looking at line 30-32: how do multiple config files know which rules they belong to?

[axiomcura]

Each module represented by the include takes in the same workflow config.

Here's an example from: https://github.com/WayScience/CytoSnake/blob/aa852f9f4886057cb96f5aa19e648e2d760adc22/configs/wf_configs/cp_process_singlecells.yaml

cytotable_convert:
  params:
    dest_datatype: parquet
    source_datatype: sqlite
    concat: True
    join: True
    infer_common_schema: True
    drop_null: True
    preset: cellprofiler_sqlite
    log_level: ERROR

annotate_configs:
  params:
    join_on:
      - Metadata_well_position
      - Image_Metadata_Well
    add_metadata_id_to_platemap: True
    format_broad_cmap: False
    clean_cellprofiler: True
    external_metadata: "none"
    external_join_left: "none"
    external_join_right: "none"
    compression_options:
      method: "gzip"
      mtime: 1
    float_format: null
    cmap_args: {}

The corresponding parameters are selected by the name of the module. Above presents the parameters for both:

include: "../rules/cytotable_convert.smk"
include: "../rules/annotate.smk"

Here's an simple image:

[axiomcura]

Thanks for the discussion points, merging!