=================================== Output & Results =================================== Command Line Output =================== When running the workflow in the default combined mode (``process_separately = false``), 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-comet` [ridiculous_mahavira] DSL2 - revision: 39f01e6119 [main] executor > awsbatch (22) [skipped ] process > wf_comet_combined_percolator:MSCONVERT (7) [100%] 9 of 9, stored: 9 ✔ [e8/bb3aec] process > wf_comet_combined_percolator:COMET (6) [100%] 9 of 9 ✔ [5e/24ea8a] process > wf_comet_combined_percolator:FILTER_PIN (1) [100%] 9 of 9 ✔ [53/bba634] process > wf_comet_combined_percolator:COMBINE_PIN_FILES [100%] 1 of 1 ✔ [ae/3899ff] process > wf_comet_combined_percolator:PERCOLATOR [100%] 1 of 1 ✔ [d4/d2c311] process > wf_comet_combined_percolator:CONVERT_TO_LIMELIGHT_XML_COM [100%] 1 of 1 ✔ [7e/9530ea] process > wf_comet_combined_percolator:UPLOAD_TO_LIMELIGHT_COM [100%] 1 of 1 ✔ Completed at: 14-Jun-2023 13:39:38 Duration : 18m 53s CPU hours : 3.9 Succeeded : 22 When running with ``process_separately = true``, the parent sub-workflow name will be ``wf_comet_separate_percolator``, the ``COMBINE_PIN_FILES`` step will not appear, ``PERCOLATOR`` will run once per input scan file, and the Limelight steps will be named ``CONVERT_TO_LIMELIGHT_XML_SEP`` / ``UPLOAD_TO_LIMELIGHT_SEP``. 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 *AWS Batch* executor was used. The next several lines show the actual steps of the workflow as they are running. If a particular step is run multiple times (e.g., converting many RAW files to mzML using msconvert), the percent complete shows the percentage of the RAW files that have been converted. 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 ================ All results will be output to the ``results/nf-ms-dda-comet`` 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-comet`` and a description of files that will be found in those directories. ``comet`` Subdirectory ^^^^^^^^^^^^^^^^^^^^^^^^^ This directory holds logs and output related to running Comet. 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 generated 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. - ``scan_file_base.pin`` - The Percolator input file generated by Comet for this scan file. ``percolator`` Subdirectory ^^^^^^^^^^^^^^^^^^^^^^^^^^^ This directory holds logs and output related to filtering Percolator input files and running Percolator. The workflow includes a step where the ``.pin`` files (Percolator input files generated by Comet) are filtered to remove all non-rank-one hits. As a result, the following files will exist for each input scan file regardless of mode: - ``scan_file_base.filtered.pin`` - The filtered ``.pin`` file for this scan file. - ``scan_file_base.filtered.pin.stderr`` - Any error messages output by the filtering process. The remaining contents depend on the value of the ``process_separately`` parameter. **Combined mode (default,** ``process_separately = false`` **)** All filtered ``.pin`` files are concatenated and Percolator is run once on the combined input: - ``combined.filtered.pin`` - The result of combining all the filtered ``.pin`` files for each scan file into a single ``.pin`` file. - ``combine-pin.stderr`` - Any error messages output by the process of combining ``.pin`` files. - ``combined.percolator.stderr`` - Any error messages generated by running Percolator on the combined ``.pin`` file. - ``combined.percolator.stdout`` - The command line output generated by running Percolator on the combined ``.pin`` file. - ``combined.pout.xml`` - The final results in XML format of running Percolator on the combined ``.pin`` file. **Separate mode (** ``process_separately = true`` **)** Percolator is run once per input scan file. The ``.pin`` files are *not* combined. For each scan file, the following additional files will exist: - ``scan_file_base.percolator.stderr`` - Any error messages generated by running Percolator on this scan file. - ``scan_file_base.percolator.stdout`` - The command line output generated by running Percolator on this scan file. - ``scan_file_base.pout.xml`` - The final results in XML format of running Percolator on this scan file. ``limelight`` Subdirectory ^^^^^^^^^^^^^^^^^^^^^^^^^^ This directory holds logs related to Limelight XML conversion and uploading to Limelight. It will only be present if ``limelight_upload`` is set to ``true``. Any configuration files you pass on the command line with ``-c`` are attached to the uploaded search so the exact run configuration is recorded in Limelight. Before upload, ``smtp.user`` and ``smtp.password`` values in these files are redacted, so mail credentials are never sent. The pipeline's bundled ``nextflow.config`` and your ``~/.nextflow/config`` are not uploaded. **Combined mode (default,** ``process_separately = false`` **)** A single Limelight XML file is generated from the combined Percolator results and a single search is uploaded: - ``results.limelight.xml`` - The Limelight XML file generated by converting the combined search results. This format is necessary for uploading data to Limelight. - ``limelight-xml-convert.stderr`` - Any error messages generated by converting the search results to Limelight XML. - ``limelight-xml-convert.stdout`` - The standard command line output generated by the program that converts search results to Limelight XML. - ``limelight-submit-upload.stderr`` - Any error messages generated by uploading the search results to Limelight. - ``limelight-submit-upload.stdout`` - The standard command line output generated by the program that uploads data to Limelight. **Separate mode (** ``process_separately = true`` **)** One Limelight XML file is generated and one search is uploaded per input scan file. For each scan file: - ``scan_file_base.limelight.xml`` - The Limelight XML file for this scan file. - ``scan_file_base.limelight-xml-convert.stderr`` - Any error messages generated by converting this scan file's search results. - ``scan_file_base.limelight-xml-convert.stdout`` - The standard command line output generated for this conversion. - ``scan_file_base.limelight-submit-upload.stderr`` - Any error messages generated by uploading this scan file's search. - ``scan_file_base.limelight-submit-upload.stdout`` - The standard command line output generated for this upload. ``panorama`` Subdirectory ^^^^^^^^^^^^^^^^^^^^^^^^^ This directory is only present if any input (``fasta``, ``comet_params``, or ``spectra_dir``) was specified as a PanoramaWeb WebDAV URL. It contains the standard output and error logs from the Panorama download steps: - ``panorama-get-.stdout`` / ``.stderr`` - Logs from downloading individual files (FASTA, Comet params). - ``panorama-get-files.stdout`` / ``.stderr`` - Logs from listing raw files in a PanoramaWeb directory. - ``*.download`` - Empty placeholder files (one per raw file listed) used to coordinate per-file downloads. The raw files themselves are not published here; they are stored in the cache directory specified by ``panorama_cache_directory``.