Publish Modules
===============

Nextflow module that fires once per dataset after both the NSForest
and scsilhouette branches have completed.

It clones ``NIH-NLM/cell-kn``, copies outputs into the
``data/prod/{organ}/`` tree, commits, pushes a new branch, and
opens a pull request against ``main``.

.. warning::

   ``params.github_token`` must be a GitHub personal access token
   with ``repo`` write access. Never hardcode it — pass via
   ``-params-file params.json`` or an environment variable.


Publish Results Process
^^^^^^^^^^^^^^^^^^^^^^^

.. rubric:: ``publish_results_process``

*Source:* ``modules/publish/publish_results.nf``

Publish Results to cell-kn GitHub Repository

Fires once per dataset. Reads files from S3 results path derived
from workflow.workDir (works on CloudOS and other platforms).


Branch naming:
~~~~~~~~~~~~~~
  {YYYY}-{mon}-{DD}-{organ}-{first_author}-{year}-sc_nsforest_qc_nf
  e.g. 2026-mar-06-skin-of-body-Wiedemann-2023-sc_nsforest_qc_nf


Platform notes:
~~~~~~~~~~~~~~~
  CloudOS: publishDir files land at s3://.../jobs/{id}/results/{label}/
           derived by replacing /work with /results in workflow.workDir

**Params referenced:**

- ``params.github_token``
- ``params.publish_dest_dir``
- ``params.publish_repo``