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Added Subject Analysis panel to show WGTS results from BYOB by OrcaBus #365

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Added Subject Analysis panel to show WGTS results from BYOB by OrcaBus #365

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4 changes: 3 additions & 1 deletion src/api/subject.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,9 @@ export type SubjectApiRes = {
results: S3Row[];
results_gds: GDSRow[];
results_sash: S3Row[];
results_cttsov2: S3Row[];
results_byob_cttsov2: S3Row[];
results_byob_wgts: S3Row[];
results_byob_sash: S3Row[];
};

export type SubjectListApiRes = DjangoRestApiResponse & { results: string[] };
Expand Down
119 changes: 111 additions & 8 deletions src/containers/subjects/AnalysisResultTable/index.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -361,7 +361,9 @@ function AnalysisResultsTable({ subjectId }: Props) {
results_gds: data.results_gds,
results_s3: data.results,
results_sash: data.results_sash,
results_cttsov2: data.results_cttsov2,
results_byob_cttsov2: data.results_byob_cttsov2,
results_byob_wgts: data.results_byob_wgts,
results_byob_sash: data.results_byob_sash,
});

return (
Expand Down Expand Up @@ -461,6 +463,44 @@ function AnalysisResultsTable({ subjectId }: Props) {
<AnalysisResultGDSTable title='bam' data={groupedData.sash.gdsWgsBams} />
</div>
</TabPanel>
<TabPanel header='WGS (orcabus)'>
<AnalysisResultS3Table title='cancer report' data={groupedData.wgtsByob.wgsCancer} />
<AnalysisResultS3Table title='pcgr' data={groupedData.wgtsByob.wgsPcgr} />
<AnalysisResultS3Table title='cpsr' data={groupedData.wgtsByob.wgsCpsr} />
<AnalysisResultS3Table title='qc report' data={groupedData.wgtsByob.wgsMultiqc} />
<AnalysisResultS3Table title='coverage report' data={groupedData.wgtsByob.wgsCoverage} />
<AnalysisResultS3Table title='vcf' data={groupedData.wgtsByob.wgsVcfs} />
<AnalysisResultS3Table title='circos plot' data={groupedData.wgtsByob.wgsCircos} />
<AnalysisResultS3Table title='bam' data={groupedData.wgtsByob.wgsBams} />
</TabPanel>
<TabPanel header='WTS (orcabus)'>
<AnalysisResultS3Table title='rnasum report' data={groupedData.wgtsByob.wtsRNAsum} />
<AnalysisResultS3Table title='qc report' data={groupedData.wgtsByob.wtsMultiqc} />
<AnalysisResultS3Table title='fusions report' data={groupedData.wgtsByob.wtsFusionsIca} />
<AnalysisResultS3Table title='bam' data={groupedData.wgtsByob.wtsBamsIca} />
</TabPanel>
<TabPanel header='WGS (orcabus-sash)'>
<div className='bg-yellow-100 p-3'>
<Message
className='w-full mb-3 bg-yellow-100'
severity='warn'
text='RESEARCH USE ONLY'
pt={{ text: { className: 'font-bold' } }}
/>
<AnalysisResultS3Table title='cancer report' data={groupedData.sashByob.cancer} />
<AnalysisResultS3Table title='pcgr' data={groupedData.sashByob.pcgr} />
<AnalysisResultS3Table title='cpsr' data={groupedData.sashByob.cpsr} />
<AnalysisResultS3Table title='linx report' data={groupedData.sashByob.linx} />
<AnalysisResultS3Table title='qc report' data={groupedData.sashByob.multiqc} />
<AnalysisResultS3Table
title='vcf'
data={groupedData.sashByob.vcfs}
enforceIgvPresignedMode={true}
isDisableObjectRestore={true}
/>
<AnalysisResultS3Table title='circos plot' data={groupedData.sashByob.circos} />
</div>
</TabPanel>
</TabView>
);
}
Expand All @@ -474,12 +514,16 @@ function groupResultsData({
results_s3,
results_gds,
results_sash,
results_cttsov2,
results_byob_cttsov2,
results_byob_wgts,
results_byob_sash,
}: {
results_s3: S3Row[];
results_gds: GDSRow[];
results_sash: S3Row[];
results_cttsov2: S3Row[];
results_byob_cttsov2: S3Row[];
results_byob_wgts: S3Row[];
results_byob_sash: S3Row[];
}) {
const wgs = results_s3.filter((r) => r.key.includes('WGS/'));
const wts = results_s3.filter((r) => r.key.includes('WTS/'));
Expand Down Expand Up @@ -561,27 +605,80 @@ function groupResultsData({
);

// CTTSOV2 results
const cttsov2Bams = results_cttsov2.filter(
const cttsov2Bams = results_byob_cttsov2.filter(
(r) => r.key.includes('cttsov2') && r.key.endsWith('bam')
);
const cttsov2Vcfs = results_cttsov2.filter(
const cttsov2Vcfs = results_byob_cttsov2.filter(
(r) =>
r.key.includes('cttsov2') &&
(r.key.endsWith('.vcf') ||
r.key.endsWith('.gvcf') ||
r.key.endsWith('.vcf.gz') ||
r.key.endsWith('.gvcf.gz'))
);
const cttsov2Tsv = results_cttsov2.filter(
const cttsov2Tsv = results_byob_cttsov2.filter(
(r) => r.key.includes('cttsov2') && r.key.endsWith('tsv')
);
const cttsov2Csv = results_cttsov2.filter(
const cttsov2Csv = results_byob_cttsov2.filter(
(r) => r.key.includes('cttsov2') && r.key.endsWith('csv')
);
const cttsov2Json = results_cttsov2.filter(
const cttsov2Json = results_byob_cttsov2.filter(
(r) => r.key.includes('cttsov2') && (r.key.endsWith('json') || r.key.endsWith('json.gz'))
);

// WGTS BYOB results from ICA v2
const wgtsByobGrouped = {

wgsBams: results_byob_wgts.filter(
(r) => r.key.includes('tumor') && r.key.includes('normal') && r.key.endsWith('bam')
),
wgsVcfs: results_byob_wgts.filter(
(r) =>
(r.key.includes('umccrise') || r.key.includes('tumor') || r.key.includes('normal')) &&
(r.key.endsWith('vcf.gz') || r.key.endsWith('.maf'))
),
wgsCircos: results_byob_wgts.filter(
(r) => r.key.includes('umccrise') && r.key.endsWith('png')
),
wgsPcgr: results_byob_wgts.filter(
(r) => r.key.includes('umccrise') && r.key.endsWith('pcgr.html')
),
wgsCpsr: results_byob_wgts.filter(
(r) => r.key.includes('umccrise') && r.key.endsWith('cpsr.html')
),
wgsMultiqc: results_byob_wgts.filter(
(r) => r.key.includes('umccrise') && r.key.endsWith('multiqc_report.html')
),
wgsCancer: results_byob_wgts.filter(
(r) => r.key.includes('umccrise') && r.key.endsWith('cancer_report.html')
),
wgsCoverage: results_byob_wgts.filter(
(r) => r.key.includes('cacao') && r.key.endsWith('html')
),
wtsBamsIca: results_byob_wgts.filter(
(r) => r.key.includes('wts') && r.key.endsWith('bam')
),
wtsMultiqc: results_byob_wgts.filter(
(r) => r.key.includes('wts') && r.key.endsWith('multiqc.html')
),
wtsFusionsIca: results_byob_wgts.filter(
(r) => r.key.includes('wts') && r.key.endsWith('fusions.pdf')
),
wtsRNAsum: results_byob_wgts.filter((r) => r.key.endsWith('RNAseq_report.html')),
}

// Sash BYOB results from orcabus
const sashByobGrouped = {
// The rest of the output needed to show
vcfs: results_byob_sash.filter((r) => r.key.endsWith('vcf.gz') || r.key.endsWith('.maf')),
circos: results_byob_sash.filter((r) => r.key.includes('circos') && r.key.endsWith('.png')),
pcgr: results_byob_sash.filter((r) => r.key.endsWith('pcgr.html')),
cpsr: results_byob_sash.filter((r) => r.key.endsWith('cpsr.html')),
multiqc: results_byob_sash.filter((r) => r.key.includes('multiqc') && r.key.endsWith('.html')),
cancer: results_byob_sash.filter((r) => r.key.endsWith('cancer_report.html')),
linx: results_byob_sash.filter((r) => r.key.endsWith('linx.html')),
};

// Sash results
const sashGrouped = {
// The input bam
Expand Down Expand Up @@ -641,5 +738,11 @@ function groupResultsData({

// S3 - Sash
sash: sashGrouped,

// S3 - BYOB from orcabus
wgtsByob: wgtsByobGrouped,

// S3 - BYOB from orcabus sash
sashByob: sashByobGrouped,
};
}