Pipeline Processing Only First Two Samples in Metadata

[achisha21]

Hi,

I've encountered an issue with the ENCODE ATAC-seq workflow where the pipeline processes only the first two samples listed in the metadata. For example, if I have the following samples in my metadata:

sample_1 rep 1
sample_2 rep 2
sample_3 rep 1
sample_4 rep 2

The pipeline processes only sample_1 rep 1 and sample_2 rep 2, ignoring the rest.

This issue is also present with the original workflow using the ENCSR356KRQ_subsampled.json metadata file. The pipeline processes only the samples ENCFF341MYG (rep 1) and ENCFF641SFZ (rep 2) out of many samples listed in the metadata.

Please find the attached input.json (https://github.com/user-attachments/files/16802459/input.json)

Could you please investigate this issue? Let me know if you need any additional information.

Thank you!