adding subworklfow test

Author: CaroAMN

…workflows/local/numorph_preprocessing.nf …lows/local/numorph_preprocessing/main.nfsubworkflows/local/numorph_preprocessing.nf renamed to subworkflows/local/numorph_preprocessing/main.nf subworkflows/local/numorph_preprocessing.nf renamed to subworkflows/local/numorph_preprocessing/main.nf

@@ -1,9 +1,7 @@
 
-
-
-include { NUMORPHINTENSITY   } from '../../modules/local/numorphintensity/'
-include { NUMORPHALIGN       } from '../../modules/local/numorphalign/'
-include { NUMORPHSTITCH      } from '../../modules/local/numorphstitch/'
+include { NUMORPHINTENSITY   } from '../../../modules/local/numorphintensity/'
+include { NUMORPHALIGN       } from '../../../modules/local/numorphalign/'
+include { NUMORPHSTITCH      } from '../../../modules/local/numorphstitch/'
 
 workflow NUMORPH_PREPROCESSING {
 

subworkflows/local/numorph_preprocessing/meta.yml

@@ -0,0 +1,51 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
+name: "numorph_preprocessing"
+## TODO nf-core: Add a description of the subworkflow and list keywords
+description: Sort SAM/BAM/CRAM file
+keywords:
+  - sort
+  - bam
+  - sam
+  - cram
+## TODO nf-core: Add a list of the modules and/or subworkflows used in the subworkflow
+components:
+  - samtools/sort
+  - samtools/index
+## TODO nf-core: List all of the channels used as input with a description and their structure
+input:
+  - ch_bam:
+      type: file
+      description: |
+        The input channel containing the BAM/CRAM/SAM files
+        Structure: [ val(meta), path(bam) ]
+      pattern: "*.{bam/cram/sam}"
+## TODO nf-core: List all of the channels used as output with a descriptions and their structure
+output:
+  - bam:
+      type: file
+      description: |
+        Channel containing BAM files
+        Structure: [ val(meta), path(bam) ]
+      pattern: "*.bam"
+  - bai:
+      type: file
+      description: |
+        Channel containing indexed BAM (BAI) files
+        Structure: [ val(meta), path(bai) ]
+      pattern: "*.bai"
+  - csi:
+      type: file
+      description: |
+        Channel containing CSI files
+        Structure: [ val(meta), path(csi) ]
+      pattern: "*.csi"
+  - versions:
+      type: file
+      description: |
+        File containing software versions
+        Structure: [ path(versions.yml) ]
+      pattern: "versions.yml"
+authors:
+  - "@CaroAMN"
+maintainers:
+  - "@CaroAMN"

subworkflows/local/numorph_preprocessing/tests/main.nf.test

@@ -0,0 +1,39 @@
+nextflow_workflow {
+
+    name "Test Subworkflow NUMORPH_PREPROCESSING"
+    script "../main.nf"
+    workflow "NUMORPH_PREPROCESSING"
+
+    tag "subworkflows"
+    tag "subworkflows_"
+    tag "subworkflows/numorph_preprocessing"
+    tag "numorph"
+    tag "numorph preprocessing"
+    tag "numorph intensity"
+    tag "numorph align"
+    tag "numorph stitch"
+
+
+    test("Numorph Preprocessing") {
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.fromList([
+                    tuple([ id:'TEST1'],
+                    file('/home/schwitalla/Documents/test-datasets/test_data/images'),
+                    file('test-datasets/test_data/parameterfiles/params_TEST1_lsmquant.csv'))
+                    ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(workflow.out).match()}
+            )
+        }
+    }
+}

subworkflows/local/numorph_preprocessing/tests/main.nf.test.snap

@@ -0,0 +1,47 @@
+{
+    "Numorph Preprocessing": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "TEST1"
+                        },
+                        "TEST1_stitched.tif:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "thresholds.mat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "2": [
+                    "NM_variables.mat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "3": [
+                    
+                ],
+                "NM_variables": [
+                    "NM_variables.mat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "intensity_thresholds": [
+                    "thresholds.mat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "stitched": [
+                    [
+                        {
+                            "id": "TEST1"
+                        },
+                        "TEST1_stitched.tif:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-02-21T16:16:38.660022739"
+    }
+}