===================================
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 22.10.5
    Launching `https://github.com/mriffle/nf-ms-dda-tpp` [backstabbing_northcutt] DSL2 - revision: fa5741ac09 [main]
    executor >  slurm (4)
    [skipped  ] process > get_mzmls:MSCONVERT (1)               [100%] 1 of 1, stored: 1 ✔
    [f4/45f66a] process > wf_comet_tpp:COMET (1)                [100%] 1 of 1 ✔
    [90/c407a9] process > wf_comet_tpp:TPP                      [100%] 1 of 1 ✔
    [5c/cc87fa] process > wf_comet_tpp:CONVERT_TO_LIMELIGHT_XML [100%] 1 of 1 ✔
    [2f/81cfe0] process > wf_comet_tpp:UPLOAD_TO_LIMELIGHT      [100%] 1 of 1 ✔
    Completed at: 24-Jul-2024 12:45:57
    Duration    : 9m 13s
    CPU hours   : 12.4
    Succeeded   : 4

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-tpp`` 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-tpp`` and a description of files
that will be found in those directories.

``comet`` Subdirectory
^^^^^^^^^^^^^^^^^^^^^^^^^
For each input scan file (e.g., each input raw file), the following set of files will exist:

- ``scan_file_base.comet.stderr`` - The output of any errors generating by running Comet on this scan file.
- ``scan_file_base.comet.stdout`` - The standard output generated by Comet for this scan file.
- ``scan_file_base.pep.xml`` - The results, in PepXML format, generated by Comet for this scan file.

``tpp`` Subdirectory
^^^^^^^^^^^^^^^^^^^^^^^^^
This directory holds logs and output related to running the TPP. The following files are present:

- ``interact.ipro.ptm.pep.xml`` - If running PTMProphet, this will be the final output that includes Comet, PeptideProphet, InterProphet, and PTMProphet results.
- ``interact.ipro.pep.xml`` - If not running PTMProphet, this will be the final output that includes Comet, PeptideProphet, and InterProphet results.
- ``InteractParser.stderr`` - Standard error from running InteractParser. Check here for errors.
- ``InteractParser.stdout`` - Standard out from running InteractParser. This is what is normally displayed on the console.
- ``interact.pep.xml`` - The output of PeptideProphet.
- ``interact.ptm.pep.xml`` - If running PTMProphet, this is the output of PTMProphet. Includes output from Comet, PeptideProphet, and PTMProphet.
- ``InterProphetParser.stderr`` - Standard error from running InterProphetParser. Check here for errors.
- ``InterProphetParser.stdout`` - Standard out from running InterProphetParser. This is what is normally displayed on the console.
- ``PeptideProphetParser.stderr`` - Standard error from running PeptideProphetParser. Check here for errors.
- ``PeptideProphetParser.stdout`` - Standard out from running PeptideProphetParser. This is what is normally displayed on the console.
- ``PTMProphetParser.stderr`` - Standard error from running PTMProphetParser. Check here for errors.
- ``PTMProphetParser.stdout`` - Standard out from running PTMProphetParser. This is what is normally displayed on the console.
- ``RefreshParser.stderr`` - Standard error from running RefreshParser. Check here for errors.
- ``RefreshParser.stdout`` - Standard out from running RefreshParser. This is what is normally displayed on the console.

``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.