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aryeelab / guideseq

Analysis pipeline for the GUIDE-seq assay.
GNU Affero General Public License v3.0
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yaml with multiple controls #65

Open jsacco1 opened 2 years ago

jsacco1 commented 2 years ago

Hi all, how do I create a yaml manifest with multiple controls (specifically, one for the M samples, and one for the P samples), and how would the filtering step know which to use for each sample?

I cannot label a control anything other than "control" in the yaml. I get this error:

[ERROR][validation] A control sample must be specified

Any sample labeled "control_b" or "control_P" just seems to be ignored when generating the "consolidated", "identify", and "visualization" files.

Thank you,

James

martinaryee commented 2 years ago

You’d unfortunately need to make 2 separate manifests since the pipeline currently only allows 1 control per manifest.

Hopefully that will work for your scenario?

Martin.

On Aug 27, 2021, at 3:47 PM, James Sacco @.***> wrote:

Hi all, how do I create a yaml manifest with multiple controls (specifically, one for the M samples, and one for the P samples), and how would the filtering step know which to use for each sample?

I cannot label a control anything other than "control" in the yaml. I get this error:

[ERROR][validation] A control sample must be specified

Any sample labeled "control_b" or "control_P" just seems to be ignored when generating the "consolidated", "identify", and "visualization" files.

Thank you,

James

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jsacco1 commented 2 years ago

Hi Martin,

Thank you for your quick reply! Two manifests will work for me.

Best,

James