Merge pull request #8 from CaroAMN/dev

new module and subworkflow test
qbic-pipelines · Feb 21, 2025 · 2af8f46 · 2af8f46
2 parents 971a211 + 6e93cc7
commit 2af8f46
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Showing 10 changed files with 384 additions and 9 deletions.
diff --git a/conf/test.config b/conf/test.config
@@ -21,10 +21,7 @@ process {
 params {
     config_profile_name        = 'Test profile'
     config_profile_description = 'Minimal test dataset to check pipeline function'
-
-    // Input data
-    // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
-    // TODO nf-core: Give any required params for the test so that command line flags are not needed
+    // Define the input data
     input  = 'https://raw.githubusercontent.com/CaroAMN/test-datasets/lsmquant/test_data/samplesheets/sample_sheet.csv'
     stage  = 'full'
 }
diff --git a/modules/local/mat2json/environment.yml b/modules/local/mat2json/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "YOUR-TOOL-HERE"
diff --git a/modules/local/mat2json/main.nf b/modules/local/mat2json/main.nf
@@ -0,0 +1,43 @@
+
+process MAT2JSON {
+    tag "$meta.id"
+    label 'process_single'
+
+    container 'carolinschwitalla/mat2json:latest'
+
+    input:
+    tuple val(meta), path(matfile)
+
+    output:
+    tuple val(meta), path("*.*"),     emit: converted_file
+    path "versions.yml"              ,     emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    /usr/bin/mlrtapp/mat2json $matfile
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        mat2json: 1.0
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    touch ${prefix}.json
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        mat2json: 1.0
+    END_VERSIONS
+    """
+}
diff --git a/modules/local/mat2json/meta.yml b/modules/local/mat2json/meta.yml
@@ -0,0 +1,55 @@
+---
+name: "mat2json"
+description: converst matlab .mat files into json or csv files.
+keywords:
+  - file conversion
+  - matlab
+  - json
+  - csv
+tools:
+  - "mat2json":
+      description: "converst matlab .mat files into json or csv files."
+      homepage: ""
+      documentation: ""
+      tool_dev_url: ""
+      doi: ""
+      licence:
+      identifier:
+
+input:
+  # Only when we have meta
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1']`
+
+    - mat_file:
+        type: file
+        description: matlab file
+        pattern: "*.{mat}"
+
+output:
+  - converted_file:
+      #Only when we have meta
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+
+      - "*_conv.*":
+          type: file
+          description: JSON or CSV file containing the the data from the input .mat file
+          pattern: "*.{json,csv}"
+
+  - versions:
+      - "versions.yml":
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+
+authors:
+  - "@CaroAMN"
+maintainers:
+  - "@CaroAMN"
diff --git a/modules/local/mat2json/tests/main.nf.test b/modules/local/mat2json/tests/main.nf.test
@@ -0,0 +1,58 @@
+nextflow_process {
+
+    name "Test Process MAT2JSON"
+    script "../main.nf"
+    process "MAT2JSON"
+
+    tag "modules"
+    tag "modules_"
+    tag "mat2json"
+
+    test("matlab file conversion to json") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test'], // meta map
+                    file('/mnt/ssd/numorph_testdata_s/module_testrun/output_nextflow/intensity/results/variables/thresholds.mat', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+
+            )
+        }
+
+    }
+
+    test("matlab file conversion to json - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test'], // meta map
+                    file('/mnt/ssd/numorph_testdata_s/module_testrun/output_nextflow/intensity/results/variables/thresholds.mat', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/local/mat2json/tests/main.nf.test.snap b/modules/local/mat2json/tests/main.nf.test.snap
@@ -0,0 +1,80 @@
+{
+    "matlab file conversion to json": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "thresholds.json:md5,88adeb36bb657798c80085b6a58ac58b",
+                            "versions.yml:md5,d8fdb19b7f6440f3644b923cf0bf7eee"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,d8fdb19b7f6440f3644b923cf0bf7eee"
+                ],
+                "converted_file": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "thresholds.json:md5,88adeb36bb657798c80085b6a58ac58b",
+                            "versions.yml:md5,d8fdb19b7f6440f3644b923cf0bf7eee"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,d8fdb19b7f6440f3644b923cf0bf7eee"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-02-21T15:36:22.030027548"
+    },
+    "matlab file conversion to json - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test.json:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "versions.yml:md5,d8fdb19b7f6440f3644b923cf0bf7eee"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,d8fdb19b7f6440f3644b923cf0bf7eee"
+                ],
+                "converted_file": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test.json:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "versions.yml:md5,d8fdb19b7f6440f3644b923cf0bf7eee"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,d8fdb19b7f6440f3644b923cf0bf7eee"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-02-21T15:36:26.450520824"
+    }
+}
diff --git a/subworkflows/local/numorph_preprocessing.nf → ...flows/local/numorph_preprocessing/main.nf b/subworkflows/local/numorph_preprocessing.nf → ...flows/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 {
 

diff --git a/subworkflows/local/numorph_preprocessing/meta.yml b/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"
diff --git a/subworkflows/local/numorph_preprocessing/tests/main.nf.test b/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()}
+            )
+        }
+    }
+}