As the fasta contigs are always stored in the database, a reprocessing pipeline can be used to re-run the processing for a large number of existing samples. This can be useful when new task templates are added to an existing project (e.g., a cgMLST that was turned from local to stable and public status), or if the settings of a target scan process were changed.

• Step 1: Create a new pipeline script. Leave the general settings to default and press Next.

• Step 2: In step Define Input Sources choose as Input Source Type the option From Samples in database. Then press Next.

• Step 3: In step Define Projects choose the project that should be reprocessed. In the Task Templates row below press the Choose... button, and choose only the task templates that should be processed (e.g., the ones that were newly added to the project). Then press Next.

• Step 4: In step Define Submission the submission can normally be disabled. If the new task templates are from a newly established stable public cgMLST that replaces the local one it makes sense to enable submission here. Then press Next.

• Step 5: In step Define File Management" everything is disabled. Just press Finish.

• Step 6: Start the newly created pipeline script to invoke the reprocessing for the samples.