Biosample unrecognized in Analysis Workflow App launch

[Tyler K]

Hello, 

I'm trying to set up an analysis workflow using both the DNA amplicon (-i 90090) and RNA amplicon (-i 430430) apps. After uploading the Biosample Workflow file on bs, an app session starts but aborts with the following error:

[ERROR] - Errors found while validating input form: Please select at least one sample.

It looks like the Biosamples are not being imported properly into the inputs for the app session. All other parameters from my workflow are correct. I get the same error for both Apps I've tried. I've only tested on existing biosamples but nothing I've found in the documentation suggests this should be the problem. 

Any advice would be appreciated.

thanks. 

[Nick Vinckier]

Hi Tyler,

What does your Biosample Workflow manifest look like and what did the command look like that was used to create the workflow?

Best,

Nick

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[Tyler K]

Hi Nick,

The command used to create the workflow was just:

bs workflow create -n DNACOMP --appsession-id 2802211

I didn't set any dependencies for this test. 

I downloaded the the biosample workflow template from bs and only filled the BioSample Name, Analysis Workflow, and Analysis Group fields as below. I tried with and without Analysis Groups and get the same error both ways. 

[Header]

FileVersion,1

[Data]

BioSample Name,Default Project,Container Name,Container Position,Prep Request,Required Yield Gbp,Analysis Workflow,Analysis Group,Sample Label,Delivery Mode

Sample1,,,,,,(DNACOMP),GROUP1,,

Sample2,,,,,,(DNACOMP),GROUP1,,

thanks, 

Tyler

[Nick Vinckier]

I would try adding some dependencies, the biosample yield can be set to essentially wait for 1 base pair of yield. I know you mentioned these are existing samples so you can just see what the lowest yield is for those and set the dependency a bit below that. That way all will meet the yield threshold. If you do not want to do that, I think it should be ok, for existing samples. But, for samples awaiting datasets (i.e. a run is ongoing and FASTQ Generation has not yet created the FASTQ datasets) I think it may try to kick off analysis, even if the Biosample exists without any datasets.

I think the error you're hitting can be resolved by adding the --can-use-primary-biosample dependency shown below.

bs workflows dependency add biosample-yield --id=<workflowId> --can-use-primary-biosample

I hope that helps!

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[Nick Vinckier]

Actually, in looking at the docs, it looks like some type of yield may be explicitly required: https://developer.basespace.illumina.com/docs/content/documentation/cli/cli-examples#SetDependencies
"In order to launch the analysis workflow with a biosample input, we must add a "BioSample Yield" dependency:"

[Tyler K]

I think you're right. The dependency is required, but I haven't been able to get it working. I tried running the command you suggested and was prompted that the chooser-id flag wasn't entered. I confirmed with bs launch application -i 90090 --list that the sample chooser is called 'sample-id' and used the command below to add the dependency

bs workflow dependency add biosample-yield --chooser-id=sample-id --can-use-primary-biosample --required-yield 10000 -i <workflow id>

After uploading the biosample workflow manifest the error I now see is:

>> 2021-11-03 17:55:41Z [ERROR] - Scheduling application for auto-launch failed while resolving dependencies: Workflow failed. Unable to resolve dependency during scheduling: sample-id.

To troubleshoot I cleared the dependency and tried again with the chooser-id argument left blank using this command:

bs workflow dependency add biosample-yield --chooser-id= --can-use-primary-biosample --required-yield 10000 -i <workflow id>

The log for the analysis now reads:

>> 2021-11-03 17:58:24Z [INFO] - Required yield dependency for biosample 'Sample1'; Output project 'Project1'

>> 2021-11-03 17:58:25Z [INFO] - Met yield dependency for biosample 'Sample1' of any library type  for field '' - Required=100.00 Kbp, Actual=2.49 Gbp

>> 2021-11-03 17:58:26Z [ERROR] - Errors found while validating input form: Please select at least one sample.

So it looks to me like the biosample is being recognized in the dependency but I can't figure out the correct argument to use for the chooser-id parameter. 

[Nick Vinckier]

Hi Tyler,

I just tested this with the RNA Amplicon app and it's moving along. The chooser-id for that should be set to rna-sample-id. I am guessing the above is an attempt with the DNA Amplicon app? For that app, the chooser-id should indeed be sample-id. I also tested that and it's working as expected.

Just curious, does the name of your workflow actually have the parentheses in it? If so, that could be confounding things as those characters have special meanings/uses in Linux and may not be getting properly handled.

The one difference I have in my manifest, is I put the same thing in the Sample Label columns as is in the BioSample Name column. I'm not sure, but that could be where things are breaking down.

Best,

Nick

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[Tyler K]

The workflow was in parentheses because when launching the this app via the browser I can select multiple biosamples in a single analyses. I interpreted the CLI documentation's description of the Analysis Group field as being the equivalent to this. I found elsewhere in the documentation that this feature is for apps requiring multiple biosamples as input (tumor-normal). Not applicable to this app and apparently what was throwing my workflow off because removing the Analysis Group worked. I'd have preferred 1 appsession instead of 16 to be launched for a run, but that's just for aesthetics and not a big deal. 

The Sample Label column didn't matter. I left it blank and it still worked for me. Adding the dependency was definitely the solution to my original problem because after getting things working I cleared the dependency and re-tried the workflow and I got the original error again. 

Thanks for the help Nick!

[Nick Vinckier]

Right on, glad that worked out and you were able to narrow it down. I also tested without Sample Label and got the same result as you, not needed for these apps. I hope all is smooth sailing from here.

Cheers,

Nick

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