Run ``GPSW`` with test data
================================================================================

First activate the `GPSW` Conda environment:

.. code-block:: shell

   $ conda activate gpsw

Download workflow code and small test data set:

.. code-block:: shell

   $ cd /path/to/test/dir
   $ gpsw fetch --test-data

This will download the workflow code, configuration files and test data, and should look as follows:

.. dropdown:: Directory structure
   :icon: info
   :color: primary

   .. code-block:: text

      .
      ├── config
      │   └── config.yml
      ├── reads
      │   ├── Control_1.fastq.gz
      │   ├── Control_2.fastq.gz
      │   ├── Control_3.fastq.gz
      │   ├── Control_4.fastq.gz
      │   ├── Control_5.fastq.gz
      │   ├── Control_6.fastq.gz
      │   ├── Test_1.fastq.gz
      │   ├── Test_2.fastq.gz
      │   ├── Test_3.fastq.gz
      │   ├── Test_4.fastq.gz
      │   ├── Test_5.fastq.gz
      │   └── Test_6.fastq.gz
      ├── resources
      │   └── orfs.csv
      └── workflow
         ├── envs
         │   └── stats.yaml
         ├── report
         │   ├── alignment-rates.rst
         │   ├── barcoderank.rst
         │   ├── drugz.rst
         │   ├── lfc_neg.rst
         │   ├── lfc_pos.rst
         │   ├── missed-barcodes.rst
         │   ├── multiqc.rst
         │   ├── pca.rst
         │   └── plot-coverage.rst
         ├── rules
         │   ├── count.smk
         │   ├── qc.smk
         │   └── stats.smk
         ├── schemas
         │   └── config.schema.yaml
         ├── scripts
         │   ├── calculate_proportion_of_reads_in_bins.py
         │   ├── calculate_psi.py
         │   ├── count_barcodes.sh
         │   ├── create_count_table.py
         │   ├── csv_to_fasta.py
         │   ├── general_functions.smk
         │   ├── plot_alignment_rate.R
         │   ├── plot_barcode_multi_conditions_profiles.R
         │   ├── plot_barcode_profiles.R
         │   ├── plot_barcoderank.R
         │   ├── plot_coverage.R
         │   ├── plot_dotplot.R
         │   ├── plot_lfc.R
         │   ├── plot_missed_barcodes.R
         │   ├── plot_pca.R
         │   └── rename_to_barcode.py
         └── Snakefile

      10 directories, 45 files

To start the workflow on the test data:

.. code-block:: shell

   $ cd /path/to/test/dir
   $ gpsw run --profile $HOME/.config/snakemake/standard/


.. note::
   The ``--profile`` argument will only have to be provided on the first run of `GPSW`, as it will create a config file (``~/.gpsw/config.ini``) that will store the profile path. To run `GPSW` without a profile use ``--profile None``.