How do I manage multiline fastq?

Healthcare & Life Sciences Parabricks
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How do I manage multiline fastq?
Hi, I have for each sample coming from different lines, so I have named fast as:

sample_L001.R1.fastq 
sample_L001.R2.fastq
sample_L002.R1.fastq 
sample_L002.R2.fastq 
sample_L003.R1.fastq 
sample_L003.R2.fastq

I want to run clara-parabricks_4.2.1-1.sif pbrun deepvariant_germline workflow, how can I manage these files?
Is there a best practice to avoid losing information about read groups?
Thanks

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You can pass in multiple FASTQ pairs and associated read group lines to deepvariant_germline. See the documentation here regarding --in-fq (I linked to that part of the page): deepvariant_germline - NVIDIA Docs.

Also, we recommend using the newest version of Parabricks, v4.4.0. You can get the container from NGC: NVIDIA Parabricks | NVIDIA NGC.

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