Regarding of paired-reads filename

[aws-hyunmin]

Input S3 bucket (s3://bucket-name/inputs/)

In this case, it looks not work normally.

[nbulsara]

Yes there is a known limitation where the reads have to be named a certain way. It's in the documentation too:

Note that in this solution, the FASTQ files need to be named in the following manner:

_R1.fastq.gz _R2.fastq.gz This can be updated to your needs by updating the Python regex in start_workflow_lambda.py You can also use example FASTQs provided here to test: s3://aws-genomics-static-us-east-1/omics-e2e/test_fastqs/NA1287820K_R1.fastq.gz s3://aws-genomics-static-us-east-1/omics-e2e/test_fastqs/NA1287820K_R2.fastq.gz