.. _entry-points:

Entry Points Sub-workflow
=========================

**Workflow File**:
   https://github.com/NCI-CGR/GwasQcPipeline/blob/default/src/cgr_gwas_qc/workflow/sub_workflows/entry_points.smk

**Config Options**: see :ref:`config-yaml` for more details

   - ``user_files.gtc_pattern``
   - ``user_files.idat_pattern``
   - ``user_files.ped``
   - ``user_files.map``
   - ``user_files.bed``
   - ``user_files.bim``
   - ``user_files.fam``
   - ``user_files.bcf``

**Major Outputs**:

   - ``sample_level/samples.bed``
   - ``sample_level/samples.bim``
   - ``sample_level/samples.fam``

The pipeline accepts either per-sample GTC files or an aggregated dataset file:

**per-sample GTC files**:

The pipeline supports two different methods for converting per-sample GTCs to aggregated BED/BIM/FAM:

1. If GTC files are provided using ``user_files.gtc_pattern`` and ``workflow_params.convert_gtc2bcf=false`` (default) then following rulegraph will be followed:

.. figure:: ../static/entry-points_gtc.png
   :name: fig-entry-points-gtc

   The entry-point workflow with GTCs and ``convert_gtc2bcf=false``.
   If per sample GTC files are provided and convert_gtc2bcf is false, then we will convert these files to the PED/MAP format and merge them together.

2. If GTC files are provided using ``user_files.gtc_pattern`` and ``workflow_params.convert_gtc2bcf=true`` then the following rulegraph will be followed:

.. figure:: ../static/entry-points_gtc-to-bcf.svg
   :name: fig-entry-points_gtc-to-bcf

   The entry-point workflow with GTCs and ``convert_gtc2bcf=true``.
   If per sample GTC files are provided and convert_gtc2bcf is true, then we will convert these files to an aggregated BCF file and load the BCF file into Plink to create a BED/BIM/FAM set.

**Aggregated dataset**:

If a reanalysis for previous dataset is desired or GTC files are unavailable, an aggregated file encoding genotypes for all samples can be provided. The pipeline currently supports following three aggregated file formats:

1. If an aggregated PED/MAP is provided using ``user_files.ped`` and ``user_files.map`` then we will convert the PED/MAP to BED/BIM/FAM.
2. If an aggregated BED/BIM/FAM is provided using ``user_files.bed``, ``user_files.bim``, ``user_files.fam`` then we will create a symbolic link.
3. If an aggregated BCF file is provided using ``user_files.bcf`` then we will convert the BCF to BED/BIM/FAM.