Output & Results

Command Line Output

When running the workflow you should see output similar to:

N E X T F L O W  ~  version 22.10.5
Launching `https://github.com/mriffle/nf-skyline-targeted-import` [nasty_kalam] DSL2 - revision: 9e44bb5c46 [import-raw]
executor >  slurm (24)
[6b/81d78d] process > SAVE_RUN_DETAILS                           [100%] 1 of 1 ✔
[44/c6432e] process > skyline_import:SKYLINE_IMPORT_SPECTRA (16) [100%] 16 of 16 ✔
[c8/de923f] process > skyline_import:SKYLINE_MERGE_RESULTS       [100%] 1 of 1 ✔
[dc/5c807b] process > skyline_reports:SKYLINE_RUN_REPORTS        [100%] 1 of 1 ✔
[ee/ee3dfc] process > panorama_upload_results:UPLOAD_FILE (5)    [100%] 5 of 5 ✔
Completed at: 17-Nov-2023 13:58:42
Duration    : 1m 37s
CPU hours   : 1.0
Succeeded   : 24

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 computer cluster executor was used. The next several lines show spectra being loaded into the Skyline template document and reports being run. In this example, 16 RAW files were imported into the Skyline document. The next line shows that 5 files were uploaded to PanoramaWeb. 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-skyline-targeted-import 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. By default, the final Skyline document called final.sky.zip will be present in the skyline/import-spectra directory (this file name can be customized). A full description of output files can be found below.

Output Files

Below are each subdirectory created in results/nf-skyline-targeted-import and a description of files that will be found in those directories.

panorama Subdirectory

This directory contains logs for file transfers from PanoramaWeb. There will be a *.stderr and *.stdout for each file that was transferred. Any errors encountered transferring that file will be present in the stderr file. And the command line output of the transfer program can be found in the stdout file.

skyline/import-spectra Subdirectory

Skyline imports scan data in parallel for each scan file and merges those results into a single, final Skyline document. For each scan file, these files will be present:

  • my_scan_file.mzML.skyd - The intermediate skyd file generated by Skyline when importing this scan file.

  • my_scan_file.log - The log output generated by Skyline for this step.

Then for the merge step, these files will be present:

  • final.sky.zip - The final Skyline document containing all scan data for the targets. This file name can be customized using the skyline_document_name parameter.

  • skyline-merge.log - The log output generated by Skyline for the merge step.

skyline/reports Subdirectory

If .skyr files are specified in the parameters, all reports defined in those files will be run after the Skyline document is populated. The files generated are:

  • report_name.report.tsv - The output of the report_name report in TSV format. report_name is the name of the reported defined in the .skyr file.

  • report_name.report-generation.log - The log generated by Skyline when generating the report for report_name.

  • skyline-import-skyr_file_name.log - The log generated by Skyline when importing the skyr_file_name .skyr file.