Merge pull request #55 from RobJY/mesmer_mpp_mod

updated mesmer image-mpp to use pixel_size if available
nf-core · Aug 19, 2024 · 86e4f50 · 86e4f50
2 parents 561d2b3 + 344dfd6
commit 86e4f50
Show file tree

Hide file tree

Showing 3 changed files with 224 additions and 63 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -46,7 +46,7 @@ process {
 
     withName: "DEEPCELL_MESMER" {
         ext.prefix = { "mask_${meta.id}" }
-        ext.args = '--image-mpp=0.215 --nuclear-channel 0 --compartment nuclear'
+        ext.args = {"--image-mpp=${params.pixel_size ?: 0.65} --nuclear-channel 0 --compartment nuclear"}
         ext.when = {params.segmentation && params.segmentation.split(',').contains('mesmer')}
         publishDir = [
             path: { "${params.outdir}/segmentation/deepcell_mesmer" },

diff --git a/tests/main.nf.test b/tests/main.nf.test
@@ -40,7 +40,7 @@ nextflow_workflow {
                         assert snapshot (
                             path("$outputDir/registration/ashlar/TEST1.ome.tif"),
                             path("$outputDir/segmentation/deepcell_mesmer/mask_TEST1.tif"),
-                            CsvUtils.roundAndHashCsv("$outputDir/quantification/mcquant/mesmer/TEST1_mask_TEST1.csv"),
+                            CsvUtils.summarizeCsv("$outputDir/quantification/mcquant/mesmer/TEST1_mask_TEST1.csv"),
                         ).match()
                     },
                     { assert workflow.success }
@@ -129,7 +129,7 @@ nextflow_workflow {
                         assert snapshot (
                             path("$outputDir/registration/ashlar/TEST1.ome.tif"),
                             path("$outputDir/segmentation/deepcell_mesmer/mask_TEST1.tif"),
-                            CsvUtils.roundAndHashCsv("$outputDir/quantification/mcquant/mesmer/TEST1_mask_TEST1.csv")
+                            CsvUtils.summarizeCsv("$outputDir/quantification/mcquant/mesmer/TEST1_mask_TEST1.csv")
                         ).match()
                     },
                     { assert workflow.success }
@@ -191,7 +191,7 @@ nextflow_workflow {
                         assert snapshot (
                             path("$outputDir/registration/ashlar/cycif-tonsil.ome.tif"),
                             path("$outputDir/segmentation/deepcell_mesmer/mask_cycif-tonsil.tif"),
-                            CsvUtils.roundAndHashCsv("$outputDir/quantification/mcquant/mesmer/cycif-tonsil_mask_cycif-tonsil.csv")
+                            CsvUtils.summarizeCsv("$outputDir/quantification/mcquant/mesmer/cycif-tonsil_mask_cycif-tonsil.csv")
                         ).match()
                     },
                     { assert workflow.success }
@@ -257,8 +257,8 @@ nextflow_workflow {
                             path("$outputDir/registration/ashlar/cycif-tonsil2.ome.tif"),
                             path("$outputDir/segmentation/deepcell_mesmer/mask_cycif-tonsil.tif"),
                             path("$outputDir/segmentation/deepcell_mesmer/mask_cycif-tonsil2.tif"),
-                            CsvUtils.roundAndHashCsv("$outputDir/quantification/mcquant/mesmer/cycif-tonsil_mask_cycif-tonsil.csv"),
-                            CsvUtils.roundAndHashCsv("$outputDir/quantification/mcquant/mesmer/cycif-tonsil2_mask_cycif-tonsil2.csv"),
+                            CsvUtils.summarizeCsv("$outputDir/quantification/mcquant/mesmer/cycif-tonsil_mask_cycif-tonsil.csv"),
+                            CsvUtils.summarizeCsv("$outputDir/quantification/mcquant/mesmer/cycif-tonsil2_mask_cycif-tonsil2.csv"),
                         ).match()
                     },
                     { assert workflow.success }
@@ -326,8 +326,8 @@ nextflow_workflow {
                             path("$outputDir/segmentation/deepcell_mesmer/mask_cycif-tonsil2.tif"),
                             path("$outputDir/segmentation/cellpose/cycif-tonsil.ome_cp_masks.tif"),
                             path("$outputDir/segmentation/cellpose/cycif-tonsil2.ome_cp_masks.tif"),
-                            CsvUtils.roundAndHashCsv("$outputDir/quantification/mcquant/mesmer/cycif-tonsil_mask_cycif-tonsil.csv"),
-                            CsvUtils.roundAndHashCsv("$outputDir/quantification/mcquant/mesmer/cycif-tonsil2_mask_cycif-tonsil2.csv"),
+                            CsvUtils.summarizeCsv("$outputDir/quantification/mcquant/mesmer/cycif-tonsil_mask_cycif-tonsil.csv"),
+                            CsvUtils.summarizeCsv("$outputDir/quantification/mcquant/mesmer/cycif-tonsil2_mask_cycif-tonsil2.csv"),
                             CsvUtils.roundAndHashCsv("$outputDir/quantification/mcquant/cellpose/cycif-tonsil_cycif-tonsil.csv"),
                             CsvUtils.roundAndHashCsv("$outputDir/quantification/mcquant/cellpose/cycif-tonsil2_cycif-tonsil2.csv"),
                         ).match()
@@ -464,7 +464,7 @@ nextflow_workflow {
                             ImageUtils.getImageMetadata("$outputDir/registration/ashlar/cycif-tonsil.ome.tif"),
                             ImageUtils.getImageMetadata("$outputDir/registration/ashlar/cycif-tonsil2.ome.tif"),
                             ImageUtils.getImageMetadata("$outputDir/segmentation/deepcell_mesmer/mask_cycif-tonsil.tif"),
-                            path("$outputDir/segmentation/deepcell_mesmer/mask_cycif-tonsil2.tif"),
+                            ImageUtils.getImageMetadata("$outputDir/segmentation/deepcell_mesmer/mask_cycif-tonsil2.tif"),
                             CsvUtils.summarizeCsv("$outputDir/quantification/mcquant/mesmer/cycif-tonsil_mask_cycif-tonsil.csv"),
                             CsvUtils.summarizeCsv("$outputDir/quantification/mcquant/mesmer/cycif-tonsil2_mask_cycif-tonsil2.csv"),
                             ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil-cycle1.ome-dfp.tiff"),