Pulsar New feature: develop client code for scAtac submission

[twang15]

Currently, there is no submission code for scAtac. Since we no longer use DNANexus for submission, it makes to develop a new API for scAtac or snRNA

[twang15]

Requirements:

1. 3 fastq files that have to be submitted for scATAC: R1, R3 and index (=R2)
2. Files are identified by their barcode and read number (R1 or R2 or R3)

[twang15]

Depends by https://github.com/nathankw/pulsar_lims/issues/104

[twang15]

The implementation has been done. Now it is ready to test its correctness.

[twang15]

Hi Annika and Yunhai,

I’ve been developing new server and client side codes for Pulsar to automate the submission for single-cell Atacseq.

Please help me to verify the correctness of the submission that was done with these codes. https://test.encodedcc.org/experiments/TSTSR086379/

Thanks a lot!

Best, Tao

[twang15]

Hi Tao,

I believe the content error is because the run type should be PE50nt for read 1 and 2 for the first library?

@DCC, correct me if I am wrong :-)

Other than that, I think it looks correct.

Thanks, Annika

[twang15]

Hi Tao,

I believe the content error is because the run type should be PE50nt for read 1 and 2 for the first library?

@dcc, correct me if I am wrong :-)

Other than that, I think it looks correct.

Thanks, Annika

Hi Annika,

Thanks for correcting me. Bug fixed in my code.

Best, Tao

[twang15]

Resolved.

[twang15]

Hi Tao and Annika,

All checks on our side passed. I think https://test.encodedcc.org/experiments/TSTSR086379/ is in good shape now.

Best, Yunhai

[twang15]

For multiome ATAC, the submission is: R1 as read 1 R3 as read 2 R2 as index read I1 not submittable

For multiome RNA:

R1 as read 1 R2 as read 2 I1 not submittable I2 not submittable