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empty input array

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    Jason Cerrato

    Hi Haley,

    Thank you, we've received your inquiry. As previously mentioned, I will be following up with our engineers to take a closer look at this and we will get back to you as soon as we can.

    Kind regards,

    Jason

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    Jason Cerrato

    Hi Haley,

    We see in the method configuration that the manta_input_vcfs and smoove_input_vcfs variables are given this.samples.manta_vcfs and this.samples.smoove_vcfs respectively.

    However, it does not appear that the samples table has a column for manta_vcfs nor smoove_vcfs. These columns do exist in the sample_set table, though. Can you confirm whether you experience the same issue if you use this this.manta_vcfs and this.smoove_vcfs instead? Or if there is a column you intend to reference from the sample table, that you use the correct column name for the this.samples.<column> attribute?

    Kind regards,

    Jason

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    Haley Abel

    Thank you--that works, though I find it rather confusing.

    Best,

    Haley

     

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    Jason Cerrato

    Hi Haley,

    The this.samples.<column> notation allows one to access attributes of the samples within the sample_set. As it appears these manta_vcfs and smoove_vcfs were not generated as attributes on a per-sample level, using this notation did not work. It appears these attributes were created on the sample_set level, and since the sv-merge1 workflow uses sample_set as its data entity, you only need to use this.<column> to access them.

    I hope this makes sense. If you have any further questions please let me know and I'll be happy to clarify.

    Kind regards,

    Jason

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