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Implement Wes Output Bam file into data model #110

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merged 3 commits into from Aug 2, 2019

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@dnunes88
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commented Jul 30, 2019

Implemented BAM files for Wes Output data model

@dnunes88 dnunes88 requested review from jim-bo and priti88 Jul 30, 2019

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commented Jul 30, 2019

I'm not sure if a Wes_Export schema is necessary, but wanted to mimic the Wes_input model as much as possible. I was also unable to get the test_prism to pass when "experiment" was required within wes_assay, but not sure if that is even necessary either. It passed test_assays.

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Great start. I would just take a look at these comments, should be a quick update. Maybe next you can ask Priti to review so she is up to speed?

"capture_date": "01/02/2001",
"output_files": {
"tumor": {
"fastq_1_alignment": [

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jim-bo Jul 30, 2019

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@dnunes88 think we just need one copy of these per "tumor" and "normal" since the alignment is done using each "fastq_1 and fastq_2" at the same time.

@@ -106,11 +107,58 @@ def test_wes():
}
}

experiment = {

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I think this is an OK placeholder... Next sprint I'm going to propose a formal metadata template we define for Shirley's team that they can fill out and transfer the results to us (same process we use for getting the input data)

"fastq_1_alignment":{
"type":"array",
"properties":{
"align_sorted": {

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As mentioned below I don't think we need to duplicate all these properties per fastq_1/fastq_2 since hte alignment uses both files. I would just have one per tumor/normal.

@@ -0,0 +1,22 @@
{

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jim-bo Jul 30, 2019

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Is this called export but referred to as "experiement" or am I missing something?

@jim-bo jim-bo self-requested a review Aug 1, 2019

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jim-bo approved these changes Aug 1, 2019

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Updated changes look good.

@dnunes88 dnunes88 merged commit faaff71 into master Aug 2, 2019

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@dnunes88 dnunes88 deleted the wes_output_proposal_2 branch Aug 7, 2019

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