added test

nf-core · Sep 27, 2024 · c7fbb67 · c7fbb67
1 parent 43ac414
commit c7fbb67
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Showing 3 changed files with 11 additions and 7 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -182,7 +182,7 @@ process {
             ].join(" ").trim()
         ext.prefix = { "${meta.id}_stardist_mask" }
         publishDir = [
-            path: "${params.outdir}/segmentation/cellpose",
+            path: "${params.outdir}/segmentation/stardist",
             pattern: "*.tif",
             saveAs: { filename -> "${meta.id}_stardist_mask.tif" }
         ]

diff --git a/tests/main.nf.test b/tests/main.nf.test
@@ -6,7 +6,7 @@ nextflow_pipeline {
     tag "pipeline"
     tag "pipeline_molkart"
 
-    test("Nuclear channel, mesmer and cellpose, without clahe") {
+    test("Nuclear channel, stardist, mesmer and cellpose, without clahe") {
 
         when {
             params {
@@ -16,7 +16,7 @@ nextflow_pipeline {
                 mindagap_tilesize = 90
                 mindagap_boxsize = 7
                 mindagap_loopnum = 100
-                segmentation_method = "cellpose,mesmer"
+                segmentation_method = "cellpose,mesmer,stardist"
             }
         }
 
@@ -27,7 +27,9 @@ nextflow_pipeline {
                 path("$outputDir/mindagap/nuc_only_spots_markedDups.txt"),
                 path("$outputDir/segmentation/cellpose/nuc_only_cellpose_mask.tif"),
                 path("$outputDir/segmentation/mesmer/nuc_only_mesmer_mask.tif"),
+                path("$outputDir/segmentation/stardist/nuc_only_stardist_mask.tif"),
                 path("$outputDir/segmentation/filtered_masks/nuc_only_mesmer_filtered.tif"),
+                path("$outputDir/segmentation/filtered_masks/nuc_only_stardist_filtered.tif"),
                 path("$outputDir/segmentation/filtered_masks/nuc_only_cellpose_filtered.tif"),
                 path("$outputDir/spot2cell/cellxgene_nuc_only_cellpose.csv"),
                 path("$outputDir/spot2cell/cellxgene_nuc_only_mesmer.csv"),

diff --git a/tests/main.nf.test.snap b/tests/main.nf.test.snap
@@ -21,13 +21,15 @@
         },
         "timestamp": "2024-06-11T11:48:45.961121703"
     },
-    "Nuclear channel, mesmer and cellpose, without clahe": {
+    "Nuclear channel, stardist, mesmer and cellpose, without clahe": {
         "content": [
             "nuc_only_nuclear_gridfilled.tiff:md5,123763d54f05b2274690b3b84f9690b1",
             "nuc_only_spots_markedDups.txt:md5,4562caad05850d7dd7b6e9235e068a8b",
             "nuc_only_cellpose_mask.tif:md5,29947c9cc51a9dd791452710e00ea6d6",
             "nuc_only_mesmer_mask.tif:md5,e9719f53651b4bf76a37e9374db7f4e4",
+            "nuc_only_stardist_mask.tif:md5,89baf7c188fd640f236dbf8b116664e5",
             "nuc_only_mesmer_filtered.tif:md5,5a6761c80ea65d41ce00d06d3414c96b",
+            "nuc_only_stardist_filtered.tif:md5,bd988411c7c6221d304f4cf398503bf1",
             "nuc_only_cellpose_filtered.tif:md5,29947c9cc51a9dd791452710e00ea6d6",
             "cellxgene_nuc_only_cellpose.csv:md5,87b0816ae6fca91a789d08528d2deb87",
             "cellxgene_nuc_only_mesmer.csv:md5,425cfb90a60b564e4bfff09ac5ea94c7",
@@ -38,9 +40,9 @@
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-06-11T11:47:51.185058276"
+        "timestamp": "2024-09-27T08:46:57.464933353"
     },
     "Skip mindagap - clahe - cellpose": {
         "content": [
@@ -66,4 +68,4 @@
         },
         "timestamp": "2023-11-28T21:40:40.925034909"
     }
-}
+}