QC dir

FrancisCrickInstitute · Oct 26, 2023 · e85ac90 · e85ac90
1 parent 5b5cb50
commit e85ac90
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Showing 5 changed files with 16 additions and 13 deletions.
diff --git a/bin/plot_overlays.R b/bin/plot_overlays.R
@@ -62,21 +62,24 @@ legend("left", fill = cellTypeColors, legend = names(cellTypeColors),
 			pch = 21, box.lty = 0, title = "Cell subtypes", cex = 1)
 dev.off()
 
+
+maskDirs=Sys.glob(args$maskDir)
+
 for(imagename in imagenames) {
 
 	print(imagename)
 	dataFlt = data[data$imagename == imagename, ]
 
 	if(args$mccs) {
-		if(dir.exists(file.path(args$maskDir, "consensus_cell_segmentation"))) {
-			outlineImg = list.files(file.path(args$maskDir, "consensus_cell_segmentation"), 
+		if(any(dir.exists(file.path(maskDirs, "consensus_cell_segmentation")))) {
+			outlineImg = list.files(file.path(maskDirs, "consensus_cell_segmentation"), 
 	  					pattern = "total_cells_mask.tiff", recursive = T, full.name = T)		
 		} else {
-			outlineImg = list.files(file.path(args$maskDir, "segmentation"), 
+			outlineImg = list.files(file.path(maskDirs, "segmentation"), 
 	  					pattern = "total_cells_mask.tiff", recursive = T, full.name = T)
 		}
 	} else {
-		outlineImg = list.files(file.path(args$maskDir, "simple_segmentation/"), 
+		outlineImg = list.files(file.path(maskDirs, "simple_segmentation/"), 
 						pattern = '.*nuclear_mask_nuclear_dilation.tiff', 
 						full.name = T, recursive = T)
 	}
@@ -128,15 +131,15 @@ if(file.size(args$posFile)) {
 		dataFlt = data[data$imagename == imagename, ]
 
 		if(args$mccs) {
-			if(dir.exists(file.path(args$maskDir, "consensus_cell_segmentation"))) {
-				outlineImg = list.files(file.path(args$maskDir, "consensus_cell_segmentation"), 
+			if(any(dir.exists(file.path(maskDirs, "consensus_cell_segmentation")))) {
+				outlineImg = list.files(file.path(maskDirs, "consensus_cell_segmentation"), 
 		  					pattern = "total_cells_mask.tiff", recursive = T, full.name = T)		
 			} else {
-				outlineImg = list.files(file.path(args$maskDir, "segmentation"), 
+				outlineImg = list.files(file.path(maskDirs, "segmentation"), 
 		  					pattern = "total_cells_mask.tiff", recursive = T, full.name = T)
 			}			
 		} else {
-			outlineImg = list.files(file.path(args$maskDir, "simple_segmentation/"), 
+			outlineImg = list.files(file.path(maskDirs, "simple_segmentation/"), 
 				pattern = '.*nuclear_mask_nuclear_dilation.tiff',
 				full.name = T, recursive = T)
 		}

diff --git a/modules/qc.nf b/modules/qc.nf
@@ -69,7 +69,7 @@ process qc_overlay {
 			
 			plot_overlays.R \
 				--rawDir ${params.output_dir}/summary/${subset}_${ref_markers}_${method}/overlays/ \
-				--maskDir ${params.input_dir} --mccs ${params.cellprofiler}	 \
+				--maskDir \"${params.input_dir}\" --mccs ${params.cellprofiler}	 \
 				--inDir ${params.output_dir}/summary/${subset}_${ref_markers}_${method}/tables/ \
 				--outDir "${params.output_dir}/summary/${subset}_${ref_markers}_${method}/" \
 				--posFile ${params.output_dir}/summary/${subset}_${ref_markers}_${method}/overlays/overlay_examples.txt \

diff --git a/nextflow.config b/nextflow.config
@@ -39,7 +39,7 @@ params {
 	input_table = '${baseDir}/data/cell_objects.tracerx.txt' // input when deep-imcyto has not been used
 	output_dir = "$baseDir/results/TYPEx/${params.release}/"
 	params_config = "${baseDir}/conf/typing_params.json"
-	annotation_config = "${baseDir}/conf/cell_type_annotation.p1.json"
+	annotation_config = "${baseDir}/data/cell_type_annotation.testdata.json"
 	color_config = "${baseDir}/conf/celltype_colors.json"
 
 	// TISSUE SEGMENTATION

diff --git a/test.config b/test.config
@@ -38,7 +38,7 @@ params {
 	input_table = '${baseDir}/data/cell_objects.tracerx.txt' // input when deep-imcyto has not been used
 	output_dir = "$baseDir/results/TYPEx/${params.release}/"
 	params_config = "${baseDir}/conf/typing_params.json"
-	annotation_config = "${baseDir}/conf/cell_type_annotation.p1.json"
+	annotation_config = "${baseDir}/conf/cell_type_annotation.testdata.json"
 	color_config = "${baseDir}/conf/celltype_colors.json"
 
 	// TISSUE SEGMENTATION

diff --git a/workflows/qcw.nf b/workflows/qcw.nf
@@ -9,7 +9,7 @@ workflow QC {
 		  method
 	main:
 
-		if(file(params.image_dir).isDirectory())	{
+		//if(file(params.image_dir).isDirectory())	{
 				qc_select_images(
 					markers, 
 					subset,
@@ -28,7 +28,7 @@ workflow QC {
 					method,
 					qc_create_single_channel_images.out
 			)
-		}
+		//}
 		qc_intensity_heatmap(
 			markers,
 			subset,