===================================
Output & Results
===================================

Command Line Output
===================
When running the workflow you should see output similar to:

.. code-block:: console

    N E X T F L O W  ~  version 23.04.1
    Launching `https://github.com/mriffle/nf-ms-dda-casanovo` [serene_kilby] DSL2 - revision: 84ddf777cd [initial]
    executor >  slurm (3)
    [81/7fb137] process > wf_casanovo:CASANOVO (1)                 [100%] 1 of 1 ✔
    [4b/67c6e4] process > wf_casanovo:CONVERT_TO_LIMELIGHT_XML (1) [100%] 1 of 1 ✔
    [fe/3fa18d] process > wf_casanovo:UPLOAD_TO_LIMELIGHT (1)      [100%] 1 of 1 ✔
    Completed at: 17-Jul-2024 16:15:53
    Duration    : 7h 39m 13s
    CPU hours   : 458.7
    Succeeded   : 3

The first line shows the version of Nextflow you are running. The second line shows the version of the workflow
you are running. The third line shows the executor you are using. An executor in Nextflow describes the actual
system the steps of the workflow are running on. In this case the *Slurm* executor was used, which is software for computer clusters.
The next several lines show the actual steps of the workflow as they are running. The final four lines appear when the workflow completes,
showing the completion time, how long it took, and the number of steps that succeeded.

Workflow Log
============
The log file called ``.nextflow.log`` will appear in the directory in which the workflow was run. It can be helpful
for determining the cause of any problems. A log file will also be generated for each task executed by the workflow,
which will be described below.

Workflow Results
================
By default, all results will be output to the ``results/nf-ms-dda-casanovo`` subdirectory in the directory in which the workflow was
run. In this directory is a subdirectory for each program that was run as part of the workflow. A full description
of output files can be found below.

Output Files
============
Below are each subdirectory created in ``results/nf-ms-dda-casanovo`` and a description of files
that will be found in those directories.

``casanovo`` Subdirectory
^^^^^^^^^^^^^^^^^^^^^^^^^
This directory holds logs and output related to running Casanovo. The following files are present:

- ``scan_file_base.casanovo.stderr`` - The output to standard error generated by Casanovo while searching the scan file.
- ``scan_file_base.casanovo.stdout`` - The standard output generated by Casanovo while searching the scan file.
- ``results.log`` - The log file produced by Casanovo.
- ``results.mztab`` - The final results produced by Casanovo.

``limelight`` Subdirectory
^^^^^^^^^^^^^^^^^^^^^^^^^^^
If uploading to Limelight, this directory holds logs and output related to the upload. The following files are present:

- ``results.limelight.xml`` - The final results of Casanovo that have been converted to Limelight XML.
- ``limelight-xml-convert.stdout`` - The standard output of the conversion process to Limelight XML.
- ``limelight-xml-convert.stderr`` - The standard error of the conversion process to Limelight XML.
- ``limelight-submit-upload.stdout`` - The standard output of the upload process to Limelight.
- ``limelight-submit-upload.stderr`` - The standard error of the upload process to Limelight.