Update basicpy (#9630)

* Update basicpy

The latest version of the tool works properly under Singularity and also
offers control over the output filenames so we can use the standard ext.prefix
or meta.id as the base name.

* Update basicpy meta.yml

* Round ffp file size in snapshot

This is needed to account for normal output variation.

Author: jmuhlich

modules/nf-core/basicpy/main.nf

@@ -2,14 +2,14 @@ process BASICPY {
     tag "$meta.id"
     label 'process_single'
 
-    container "docker.io/labsyspharm/basicpy-docker-mcmicro:1.2.0-patch3"
+    container "docker.io/labsyspharm/basicpy-docker-mcmicro:1.2.0-patch5"
 
     input:
     tuple val(meta), path(image)
 
     output:
-    tuple val(meta), path("*-dfp.tiff"), path("*-ffp.tiff"), emit: profiles
-    path "versions.yml"                                    , emit: versions
+    tuple val(meta), path("*-dfp.ome.tif"), path("*-ffp.ome.tif"), emit: profiles
+    path "versions.yml"                                          , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -20,9 +20,10 @@ process BASICPY {
         error "Basicpy module does not support Conda. Please use Docker / Singularity instead."
     }
     def args    = task.ext.args   ?: ''
+    def prefix  = task.ext.prefix ?: "${meta.id}"
     def VERSION = "1.2.0" // WARN: Version information not provided by tool on CLI. Please update this string when bumping
     """
-    /opt/main.py -i $image -o . $args
+    /opt/main.py -i $image -o . --output-flatfield $prefix --output-darkfield $prefix $args
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -38,8 +39,8 @@ process BASICPY {
     def prefix  = task.ext.prefix ?: "${meta.id}"
     def VERSION = "1.2.0" // WARN: Version information not provided by tool on CLI. Please update this string when bumping
     """
-    touch ${prefix}.-dfp.tiff
-    touch ${prefix}.-ffp.tiff
+    touch ${prefix}-dfp.ome.tif
+    touch ${prefix}-ffp.ome.tif
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/nf-core/basicpy/meta.yml

@@ -26,8 +26,8 @@ input:
           e.g. [ id:'test' ]
     - image:
         type: file
-        description: Tiff file to be used for dark and flat field illumination correction
-        pattern: "*.{tiff,tif}"
+        description: BioFormats-compatible image file to be used for dark and flat field illumination correction
+        pattern: "*.{ome.tiff,ome.tif,rcpnl,btf,nd2,tiff,tif,czi}"
         ontologies: []
 output:
   profiles:
@@ -36,15 +36,15 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test' ]
-      - "*-dfp.tiff":
+      - "*-dfp.ome.tif":
           type: file
-          description: Tiff fields for dark field illumination correction
-          pattern: "*.{tiff}"
+          description: OME-TIFF fields for dark field illumination correction
+          pattern: "*.{ome.tif}"
           ontologies: []
-      - "*-ffp.tiff":
+      - "*-ffp.ome.tif":
           type: file
-          description: Tiff fields for flat field illumination correction
-          pattern: "*.{tiff}"
+          description: OME-TIFF fields for flat field illumination correction
+          pattern: "*.{ome.tif}"
           ontologies: []
   versions:
     - versions.yml:

modules/nf-core/basicpy/tests/main.nf.test

@@ -29,7 +29,7 @@ nextflow_process {
                     file(process.out.profiles.get(0).get(1)).exists(),
                     file(process.out.profiles.get(0).get(2)).exists(),
                     file(process.out.profiles.get(0).get(1)).size(),
-                    file(process.out.profiles.get(0).get(2)).size()
+                    Math.round(file(process.out.profiles.get(0).get(2)).size() / 1000) * 1000
                     ).match()
                 },
             )

modules/nf-core/basicpy/tests/main.nf.test.snap

@@ -6,14 +6,14 @@
             ],
             true,
             true,
-            633904,
-            633904
+            2684,
+            352000
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.7"
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-25T17:40:59.731127948"
+        "timestamp": "2026-01-08T11:57:42.610834295"
     },
     "basicpy - OME-TIFF - stub": {
         "content": [
@@ -23,8 +23,8 @@
                         {
                             "id": "test"
                         },
-                        "test.-dfp.tiff:md5,d41d8cd98f00b204e9800998ecf8427e",
-                        "test.-ffp.tiff:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test-dfp.ome.tif:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "test-ffp.ome.tif:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "1": [
@@ -35,8 +35,8 @@
                         {
                             "id": "test"
                         },
-                        "test.-dfp.tiff:md5,d41d8cd98f00b204e9800998ecf8427e",
-                        "test.-ffp.tiff:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test-dfp.ome.tif:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "test-ffp.ome.tif:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "versions": [
@@ -46,8 +46,8 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.7"
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-25T17:41:02.991040243"
+        "timestamp": "2026-01-08T10:42:02.992888504"
     }
 }