Outputs _______ RAFT outputs are available in a project's ``outputs/`` directory. The ``outputs/`` directory can contain a variety of subdirectories but generally includes at least ``qc/``, ``reports/``, and ``samples/``. ``reports/`` ============ The ``reports/`` directory contains reports generated by Nextflow: * dag.dot - A directed acyclic graph ``dot`` file that can be used to understand the flow among processes. The ``.dot`` file can be converted to a graph using ``graphviz``. * report.html - A report with a wealth of information regarding each process run by the workflow. Useful for understanding resource limitations within the workflow. * timeline.html - A report showing a graphical representation of each process's run time. * trace.txt - A text file containing information about each process run. Useful for troubleshooting as ``grep`` can be used to find specific processes. This file exists within the project's ``log/`` directory while the workflow is running. Hierarchical Output Directory Structure ======================================= Directories containing sample-level outputs (``qc/`` and ``samples/``) follow: .. code-block:: console samples/ \__ \__ \__ Therefore, samples outputs are defined by the ``Dataset``, ``Pat_Name``, and ``Run_Name`` columns from the user-provided manifest. Some situations, like variant calling, may involve multiple samples from the same patient. In this case, the ``/`` directory is defined as ``_/``. ``samples/`` ============ Sample-level outputs can be found within the ``samples/`` directory. Outputs are partitioned by sample where appropriate. For example, the outputs for samples ``ar-279`` for patient ``Pt01`` in datasets ``Foo_2024`` can be found in ``outputs/samples/Foo_2024/Pt01/ar-279/``. .. code-block:: console ls samples/Foo_2024/Pt01/ar-279/ fastp salmon_aln_quant samtools_coverage seq2hla seqtk_subseq starfusion Each subdirectory, (e.g. ``starfusion/``) contains symbolic links to the output files contained within the project's ``work/`` dirctory. ``qc/`` ======= Quality control data for each sample can be found in the ``qc/`` directory. These outputs are generally tool-level reported metrics.