6. Test files

To verify the pipeline functionality, execute the following command:

path_to/bin/trigger.sh defaultlab test path_to/assets file_type

Here, file_type specifies the type of test file to be used and determines the corresponding pipeline and search engine. Available options include:

• BSA: A small DDA Bovine QC file processed using the FragPipe search engine.
• HELA: A medium-sized DDA Human QC file processed using the FragPipe search engine.
• DIANN_SMALL: A small DIA mzML test file processed using DIA-NN.
• MZML: A DDA mzML input file processed using the FragPipe search engine.
• EMPTY: An empty test file for debugging error scenarios.
• STY_BIG: A large phosphoproteome file processed using the Comet search engine.
• STY_SMALL: A small phosphoproteome file processed using the Comet search engine.
• TMT: A TMT-labeled test file processed using the Comet search engine.
• SILAC: A SILAC-labeled test file processed using the Comet search engine.

For rapid testing of the pipeline, use the BSA option for DDA workflows and DIANN_SMALL for DIA workflows.