Merge pull request #178 from biomage-ltd/add-prefiltered-property

[BIOMAGE-1494] - Add prefiltered flag to classifier
hms-dbmi-cellenics · Oct 8, 2021 · 1c02f3c · 1c02f3c
2 parents d1d1ed1 + 0728317
commit 1c02f3c
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Showing 3 changed files with 4 additions and 1 deletion.
diff --git a/pipeline-runner/R/gem2s-6-construct_qc_config.R b/pipeline-runner/R/gem2s-6-construct_qc_config.R
@@ -6,6 +6,7 @@ construct_qc_config <- function(scdata, any_filtered) {
     # classifier
     config.classifier <- list(
         enabled = !any_filtered,
+        prefiltered = any_filtered,
         auto = TRUE,
         filterSettings = list(FDR = 0.01))
 

diff --git a/pipeline-runner/tests/testthat/test-gem2s-6-construct_qc_config.R b/pipeline-runner/tests/testthat/test-gem2s-6-construct_qc_config.R
@@ -20,8 +20,10 @@ test_that("cellsize filter is disabled by default and classifier if pre-filtered
     scdata <- mock_scdata()
 
     qc_config <- construct_qc_config(scdata, any_filtered = TRUE)
-    expect_false(qc_config$cellSizeDistribution$enabled)
+
     expect_false(qc_config$classifier$enabled)
+    expect_true(qc_config$classifier$prefiltered)
+    expect_false(qc_config$cellSizeDistribution$enabled)
 })
 
 

diff --git a/pipeline-runner/tests/testthat/testthat-problems.rds b/pipeline-runner/tests/testthat/testthat-problems.rds