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bed-version not added to status-db and unable to start cg #815

Closed keyvanelhami closed 3 years ago

keyvanelhami commented 3 years ago

Problem: Unable to start balsamic automatically since bed version is missing. I am unsure if this is cg or status-db related so I also tag @patrikgrenfeldt 

Case justshrew has following BALSAMIC samples:
SAMPLE ID            TISSUE TYPE          APPLICATION          BED VERSION         
ACC7117A17           tumor                wes                  None                

Could not create config: Application type wes requires a bed file to be analyzed!
Aborted!

The samples are provided bait set in LIMS, but this info is missing in status db: https://clinical-lims.scilifelab.se/clarity/work-complete/159444 https://clinical-api.scilifelab.se/admin/sample/?search=ACC7117A17

Steps to reproduce

  1. up
  2. cg workflow balsamic start justshrew

Expected outcome / suggested solution: Start balsamic

Questions: Is this cg, lims, or status-db related?

What needs to be done on the planning meeting:

See https://github.com/Clinical-Genomics/development/blob/master/git/issue-reports.md for more!

Mropat commented 3 years ago

@keyvanelhami what is the bait set called in LIMS? @hassanfa are we missing the panel_bed in the database perhaps?

hassanfa commented 3 years ago

@Mropat Problem is obvious here: Looking into clinical-api, this sample has no panel bed assigned to it. Thus cg fails.

Solution: A process upstream is causing the problem. Talk to someone in lab and ask them to make sure assigned capture kit made it through order process to, and then update clinical-api.

Mropat commented 3 years ago

@hassanfa the panel bed is never set in clinical anyway. We get capture kit from lims (where we know it was it's set) and then we use it look up panel bed in the panel table. So the capture kit in lims isn't asssociated with any bed in clinical.

keyvanelhami commented 3 years ago

Taking @annaengstrom in the conversation. It seems like the "bed version" is missing in the LIMS step (see red circle below). Is the bed-version added manually or is it provided automatically when choosing bait set ?

The analysis didn't start automatically and we need to know if this is a bug or human error related.

Screen Shot 2020-11-04 at 8 42 13 AM

annaengstrom commented 3 years ago

No bug, no human error in this step. Screenshot 2020-11-04 at 08 57 29

We set the UDF "Bait set" manually, and this step is "required" meaning we cannot go forward without setting it. The field missing is UDF "Capture Library version". What is this UDF used for in the analysis? As I remember for MIP, it should not be used. How is it set? Previously via order, but this will no longer be correct for analysis. Information about bait set should be picked up from UDF bait set, not capture library version.

annaengstrom commented 3 years ago

As we set it, UDF "Capture library version" is set by customer in order, for us to know for PAN app tags which panel to use. It should ideally only be information from customer to the lab staff, but should not involve analysis. It seems orderportal somehow is updated... @patrikgrenfeldt @elevu is UDF Capture library version in orderportal free text? This is not set by orderform as drop down list, and only gives reference to website.

annaengstrom commented 3 years ago

@Mropat Problem is obvious here: Looking into clinical-api, this sample has no panel bed assigned to it. Thus cg fails.

Solution: A process upstream is causing the problem. Talk to someone in lab and ask them to make sure assigned capture kit made it through order process to, and then update clinical-api.

bait set cannot be set via order, as customer does not know which version we use. The UDF is required in LIMS and we cannot proceed without filling it out

keyvanelhami commented 3 years ago

I added the capture kit manually cg set sample ACC7117A17 -kv capture_kit exome_comp_10.1 but still I am unable to start the analysis. @Mropat Any ideas why?

SAMPLE ID            TISSUE TYPE          APPLICATION          BED VERSION         
ACC7117A17           tumor                wes                  None                

Could not create config: Application type wes requires a bed file to be analyzed!
Screen Shot 2020-11-04 at 9 32 34 AM
Mropat commented 3 years ago

I added the capture kit manually cg set sample ACC7117A17 -kv capture_kit exome_comp_10.1 but still I am unable to start the analysis. @Mropat Any ideas why?

SAMPLE ID            TISSUE TYPE          APPLICATION          BED VERSION         
ACC7117A17           tumor                wes                  None                

Could not create config: Application type wes requires a bed file to be analyzed!
Screen Shot 2020-11-04 at 9 32 34 AM

Unfortunately the cg code is not looking at capture kit field and is always fetching it from LIMS. A suggestion to solve this temporarily for the samples where it is a problem: provide panel bed name as an argument to cg workflow balsamic run for cases where error occurred. This bypasses lims and gets panel path from CG instead

keyvanelhami commented 3 years ago

Thanks Maria. I have now started the affected cases manually

annaengstrom commented 3 years ago

Do you know what the initial problem was?

keyvanelhami commented 3 years ago

I have only started the analysis manually while we are investigating the root of this problem. So no, I don't know why this problem happened

mayabrandi commented 3 years ago

The problem is that then new twist v3 workflow has not been updated in the lims config file in cg. This PR will fix that problem. It is my fault. I forgot to update the config in cg when creating the new workflow.