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Np add testing for atac lib metrics #1385

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Np add testing for atac lib metrics #1385

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2510aae
pin all latest docker version
nikellepetrillo Aug 1, 2024
87b4b46
Merge remote-tracking branch 'origin/develop' into develop
nikellepetrillo Aug 9, 2024
52b66aa
Merge remote-tracking branch 'origin/develop' into develop
nikellepetrillo Aug 16, 2024
fe45047
Merge remote-tracking branch 'origin/develop' into develop
nikellepetrillo Sep 12, 2024
b01d672
Merge remote-tracking branch 'origin/develop' into develop
nikellepetrillo Oct 15, 2024
ef64035
add test for atac lib metrics
nikellepetrillo Oct 15, 2024
38f6000
add metrics to truth
nikellepetrillo Oct 15, 2024
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8 changes: 8 additions & 0 deletions verification/VerifyMultiome.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -29,6 +29,9 @@ workflow VerifyMultiome {
File test_library_metrics
File truth_library_metrics

File test_atac_library_metrics
File truth_atac_library_metrics

Boolean? done
}

Expand Down Expand Up @@ -77,4 +80,9 @@ workflow VerifyMultiome {
test_text_files = select_all([test_library_metrics]),
truth_text_files = select_all([truth_library_metrics])
}
call VerifyTasks.CompareTextFiles as CompareAtacLibraryMetrics {
input:
test_text_files = select_all([test_atac_library_metrics]),
truth_text_files = select_all([truth_atac_library_metrics])
}
}
12 changes: 11 additions & 1 deletion verification/test-wdls/TestMultiome.wdl
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Expand Up @@ -114,7 +114,8 @@ workflow TestMultiome {
Array[String] pipeline_metrics = flatten([
[ # File outputs
Multiome.gene_metrics_gex,
Multiome.cell_metrics_gex
Multiome.cell_metrics_gex,
Multiome.atac_library_metrics
],
# File? outputs
select_all([Multiome.library_metrics]),
Expand Down Expand Up @@ -194,6 +195,13 @@ workflow TestMultiome {
}
}

call Utilities.GetValidationInputs as GetAtacLibraryMetrics {
input:
input_file = Multiome.atac_library_metrics,
results_path = results_path,
truth_path = truth_path
}

call VerifyMultiome.VerifyMultiome as Verify {
input:
truth_optimus_h5ad = GetOptimusH5ad.truth_file,
Expand All @@ -212,6 +220,8 @@ workflow TestMultiome {
test_atac_h5ad = GetSnapMetrics.results_file,
test_library_metrics = select_first([GetLibraryMetrics.results_file, ""]),
truth_library_metrics = select_first([GetLibraryMetrics.truth_file, ""]),
test_atac_library_metrics = GetAtacLibraryMetrics.results_file,
truth_atac_library_metrics = GetAtacLibraryMetrics.truth_file,
done = CopyToTestResults.done
}
}
Expand Down
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