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    "# Singularity changeo clonotype calling\n",
    "\n",
    "Dandelion has a pair of functions, `ddl.pp.calculate_threshold()` and `ddl.tl.define_clones()`, that come together to run the [changeo clonotype calling pipeline](https://changeo.readthedocs.io/en/stable/examples/cloning.html). However, this can be quite fiddly to properly set up - one part of the process is in R, so it requires an operational rpy2 and appropriate dependencies. Meanwhile the other is a command line script which can be difficult to recognise properly within some virtual environments. In summary, creating a simple singularity pipeline to circumvent the need for annoying setup creates a user-friendly way to access this functionality.\n",
    "\n",
    "Once in possession of a `.h5ddl` file, a saved form of the Dandelion object, the changeo clonotype calling can be ran like so:\n",
    "\n",
    "```\n",
    "singularity run -B $PWD /path/to/sc-dandelion_latest.sif changeo-clonotypes \\\n",
    "     --h5ddl vdj.h5ddl\n",
    "```\n",
    "\n",
    "By default, this will save the changeo clones into a new column called `changeo_clone_id` in the output `.h5ddl` file. All Dandelion functions that operate on clone calls can be directed to this column by providing `clone_id=\"changeo_clone_id\"` as an argument. If wishing to save the clones to a different column, provide its desired name via `--key_added`.\n",
    "\n",
    "If wishing to override the threshold determined by SHazaM, provide it via `--manual_threshold`.\n",
    "\n",
    "The SHazaM plot and Dandelion object with changeo clones identified are saved to files named after the original input file (with `_shazam.pdf` and `_changeo.h5ddl` appended respectively). These destinations can be controlled via `--plot_file` and `--h5ddl_out`."
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