Dummy molecular data for workflow testing

[edsu7]

Determined that DATA-CA program was mainly for clinical. Uploaded molecular data was to help visualization on dashboard. A more comprehensive set is needed for workflow testing.

• [x] Make Seq-CA program on QA
• [x] Make Seq-CA program on dev
• [x] Add Seq-CA with clinical data on QA
• [x] Add Seq-CA with clinical data on dev
• [x] Upload molecular data on QA
• • [x] Normal WGS
• • [x] Tumour WGS
• • [x] Normal WXS
• • [x] Tumour WXS
• • [x] Norma RNASeq
• • [x] Tumour RNASeq
• [x] Upload molecular data on dev
• • [x] Normal WGS
• • [x] Tumour WGS
• • [x] Normal WXS
• • [x] Tumour WXS
• • [x] Norma RNASeq
• • [x] Tumour RNASeq

[lindaxiang]

@edsu7 FYI, the following are some of the test datasets we've used for various workflows:

• DNA-seq alignment: https://github.com/icgc-argo-workflows/dna-seq-processing-wfs/tree/main/dna-seq-alignment/tests
• RNA-seq alignment: https://github.com/icgc-argo-workflows/rna-seq-alignment/tree/main/rna-seq-alignment-wf/tests
• DNA-seq aln + WGS variant calling:
  • Tumour (103 readgroups): https://submission-song.rdpc-dev.cancercollaboratory.org/studies/TEST-PR/analysis/ad6413cd-5987-4682-a413-cd5987f682ca
  • Normal (67 readgroups): https://submission-song.rdpc-dev.cancercollaboratory.org/studies/TEST-PR/analysis/f77ce78b-3366-40c9-bce7-8b336630c9bd
• DNA-Seq aln + WXS variant calling:
  • Normal (67 readgroups): https://submission-song.rdpc-qa.cancercollaboratory.org/studies/TEST-PR/analysis/08e7c5b1-b3af-4e20-a7c5-b1b3af2e206b
  • Tumour (103 readgroups): https://submission-song.rdpc-qa.cancercollaboratory.org/studies/TEST-PR/analysis/c5112600-dfa4-4752-9126-00dfa42752dc

[b-f-chan]

In progress, finishing up QA (RNA-Seq specifically). and then moving onto Dev

[b-f-chan]

RNA-Seq will require more time to implement

Consensus approach with bioinfo --> Suppress incorrect raw reads, then re-submit new dummy data that has the correct relationships so they reflect properly on ARGO platform

[b-f-chan]

In weird state, initial issue was dummy data did not have correct matched normals, so uploaded the fixes and suppressed the old ones. New ones are reflected in QA/Dev yet the old suppressed tumours still showing up as well. May need investigation into the indexing.

As for actual synthetic data, still in progress of getting the RNA Seq data in, doing some debugging!

[puneet-oicr]

To be looked at this week

[b-f-chan]

Gradually coming along, not top priority

[b-f-chan]

Planning to submit this data onto QA sometimes this week

[puneet-oicr]

No updates.

[puneet-oicr]

No updates

[puneet-oicr]

no new updates

[puneet-oicr]

no new updates