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. If wanted, the field below can be used to limit the pipeline to reprocess only samples that do or do not contain specific tags. 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.

Hint: The steps above will create a pipeline that processes only task entries, that do not exist in the samples yet. To reprocess existing task templates, the option Overwrite existing task entries and fields in database must be enabled in the General Settings of the pipeline. Such a pipeline should not be run in parallel, otherwise the samples will be reprocessed once by each pipeline. To overcome this, the selection of samples can be limited to reprocess only samples that do not contain a specific tag, and to let the pipeline assign this tag by setting it in the field Assign Additional Tag(s) in the Advanced Input Source Options.