How to enable DRAGEN to process multiple FASTQ files for the same subject?

How to enable DRAGEN to process multiple FASTQ files, produced by the Illumina bcl2fastq or BCL Convert programs, for the same subject?

The command line options, combine-samples-by-name or fastq-list, can be used for this purpose. Both options are specified in the User Guide. The fastq-list is the preferred option, which will let you specify all FASTQ files for a sample along with read group IDs. The fastq-list is in CSV format and can include all the samples in a flowcell/run (See the FASTQ List documentation for more information about FASTQ List format).

To process a specific sample from the CSV file, use the --fastq-list-sample-id {SampleID} option. Only the entries in the fastq-list file with an RGSM value matching the specified SampleID are processed. If using DRAGEN BCL conversion, then the conversion process will also generate these fastq-list CSV for you.

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