Merge pull request #23 from mc2-center/openslide-converter

Add openslide converter

main.nf

@@ -4,6 +4,15 @@ nextflow.enable.dsl=2
 
 if (params.input) { params.input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' }
 
+params.convert = false
+
+if (params.convert) {
+    if (!params.mag || !params.mpp) {
+        error "Both nominal magnification ('mag') and microns per pixel ('mpp' parameters must be provided when 'params.convert' is set to true."
+    }
+}
+
+
 // Set parameters and defaults
 params.outDir = './outputs'
 params.config = 'default'

modules/convert_to_openslide.nf

@@ -0,0 +1,17 @@
+process CONVERT {
+
+    container 'ghcr.io/mc2-center/histoqc-openslide-converter:latest'
+
+    input:
+    tuple val(meta), path(images)
+
+    output:
+    tuple val(meta), path("${images.simpleName}_openslide.tiff")
+
+    script:
+
+    """
+    vips im_vips2tiff $images ${images.simpleName}_openslide.tiff:jpeg:75,tile:512x512,pyramid
+    tifftools set -y -s ImageDescription  "Aperio nf-histoqc |AppMag = $params.mag|MPP = $params.mpp" ${images.simpleName}_openslide.tiff
+    """
+}

nextflow_schema.json

@@ -38,6 +38,29 @@
           "enum": ["default", "ihc", "clinical", "first", "light", "v2.1"]
         }
       }
+    },
+    "conversion_options": {
+      "title": "Conversion options",
+      "type": "object",
+      "fa_icon": "fas fa-solid fa-magic",
+      "description": "Define parameters used during conversion to openslide compatible tiff",
+      "properties": {
+        "convert": {
+            "type": "boolean",
+            "description": "Should images be converted to an openslide compatible tiff",
+            "hidden": true
+        },
+        "mag": {
+            "type": "integer",
+            "description": "Nominal magnification to inject into openslide compatible tiff",
+            "hidden": true
+        },
+        "mpp": {
+          "type": "number",
+          "description": "Image resolution (microns per pixel) to inject into openslide compatible tiff",
+          "hidden": true
+        }
+      }
     }
   },
   "allOf": [

subworkflows/run_histoqc.nf

@@ -1,12 +1,14 @@
 include { HISTOQC } from "../modules/histoqc.nf"
+include { CONVERT } from "../modules/convert_to_openslide.nf"
 
 workflow RUN {
 
     take:
     images
 
     main:
-    HISTOQC ( images ) 
+
+    params.convert ? CONVERT(images) | HISTOQC : HISTOQC(images)
 
     emit:
     output = HISTOQC.out.masks