Merge pull request #7 from CaroAMN/dev

nf-tests for modules

.gitignore

@@ -7,3 +7,4 @@ testing/
 testing*
 *.pyc
 null/
+.nf-test

conf/test.config

@@ -25,6 +25,6 @@ params {
     // 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
-    input  = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv'// Genome references
-    genome = 'R64-1-1'
+    input  = 'https://raw.githubusercontent.com/CaroAMN/test-datasets/lsmquant/test_data/samplesheets/sample_sheet.csv'
+    stage  = 'full'
 }

main.nf

@@ -14,8 +14,6 @@
     IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
-
-//include { NUMORPH_PREPROCESSING } from './subworkflows/local/numorph_preprocessing'
 include { PIPELINE_INITIALISATION       } from './subworkflows/local/utils_nfcore_lsmquant_pipeline'
 include { PIPELINE_COMPLETION           } from './subworkflows/local/utils_nfcore_lsmquant_pipeline'
 include { LSMQUANT                      } from './workflows/lsmquant'
@@ -31,24 +29,11 @@ include { LSMQUANT                      } from './workflows/lsmquant'
 //
 workflow NFCORE_LSMQUANT {
     take:
-    ch_input // the sample sheet
+    samplesheet // channel: samplesheet read in from --input
 
     main:
-    Channel
-        .fromPath(ch_input)
-        .splitCsv(header: true)
-        .map { row ->
-            def meta = [id: row.sample_id]
-            tuple(meta, file(row.img_directory), file(row.parameter_file))
-        }
-        .set { sample_data }
-
-    LSMQUANT(sample_data)
-
-
-
-
 
+    LSMQUANT(samplesheet)
 
 }
 /*
@@ -76,7 +61,7 @@ workflow {
     // WORKFLOW: Run main workflow
     //
     NFCORE_LSMQUANT (
-        params.input
+        PIPELINE_INITIALISATION.out.samplesheet
     )
     //
     // SUBWORKFLOW: Run completion tasks

modules/local/numorphalign.nf → modules/local/numorphalign/main.nf

@@ -50,24 +50,28 @@ process NUMORPHALIGN {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        numorph: 1.0
+        numorphalign: 1.0
     END_VERSIONS
 
     """
 
     stub:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    // TODO nf-core: A stub section should mimic the execution of the original module as best as possible
-    //               Have a look at the following examples:
-    //               Simple example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bcftools/annotate/main.nf#L47-L63
-    //               Complex example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bedtools/split/main.nf#L38-L54
+
     """
-    touch ${prefix}.bam
+    mkdir -p results/samples/alignment
+    mkdir -p results/variables
+
+    touch results/variables/path_table.mat
+    touch results/variables/alignment_table.mat
+    touch results/variables/z_displacement_align.mat
+    touch results/NM_variables.mat
+    touch results/samples/alignment/${meta.id}_full.tif
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        numorphalign: \$(samtools --version |& sed '1!d ; s/samtools //')
+        numorphalign: 1.0
     END_VERSIONS
     """
 }

modules/local/numorphalign/tests/main.nf.test

@@ -0,0 +1,48 @@
+nextflow_process {
+    name "Test Process Numorphalign"
+    script "../main.nf"
+    process "NUMORPHALIGN"
+
+    test("Numorphalign stub test") {
+        options '-stub'
+        setup {
+            run ("NUMORPHINTENSITY") {
+                script "../../numorphintensity/main.nf"
+                options '-stub'
+                process {
+                    """
+                    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'))
+                    ])
+                """
+                }
+            }
+
+
+        }
+
+        when {
+            process {
+                """
+                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'))
+                    ])
+                input[1] = NUMORPHINTENSITY.out.adj_params_mat
+                input[2] = NUMORPHINTENSITY.out.path_table_mat
+                input[3] = NUMORPHINTENSITY.out.thresholds_mat
+                input[4] = NUMORPHINTENSITY.out.NM_variables
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}

modules/local/numorphalign/tests/main.nf.test.snap

@@ -0,0 +1,49 @@
+{
+    "Numorphalign stub test": {
+        "content": [
+            {
+                "0": [
+                    "TEST1_full.tif:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "1": [
+                    "path_table.mat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "2": [
+                    "alignment_table.mat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "3": [
+                    "z_displacement_align.mat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "4": [
+                    "NM_variables.mat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "5": [
+                    "versions.yml:md5,c413276640fb035336c7c5bc450abde3"
+                ],
+                "NM_variables": [
+                    "NM_variables.mat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "alignment_table_mat": [
+                    "alignment_table.mat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "path_table_mat": [
+                    "path_table.mat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "samples": [
+                    "TEST1_full.tif:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "versions": [
+                    "versions.yml:md5,c413276640fb035336c7c5bc450abde3"
+                ],
+                "z_displacement_align_mat": [
+                    "z_displacement_align.mat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-02-19T13:04:16.238937653"
+    }
+}

modules/local/numorphintensity.nf → modules/local/numorphintensity/main.nf

@@ -7,14 +7,8 @@ process NUMORPHINTENSITY {
 
 
     input:
-    // TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
-    //               MUST be provided as an input via a Groovy Map called "meta".
-    //               This information may not be required in some instances e.g. indexing reference genome files:
-    //               https://github.com/nf-core/modules/blob/master/modules/nf-core/bwa/index/main.nf
-
     tuple val(meta), path(img_directory), path(parameter_file)
 
-
     output:
     path "results/samples/intensity_adjustment/*"            , emit: samples
     path "results/variables/adj_params.mat"                  , emit: adj_params_mat
@@ -23,8 +17,6 @@ process NUMORPHINTENSITY {
     path "results/NM_variables.mat"                          , emit: NM_variables
     path "versions.yml"                                      , emit: versions
 
-
-
     when:
     task.ext.when == null || task.ext.when
 
@@ -43,24 +35,28 @@ process NUMORPHINTENSITY {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        numorph: 1.0
+        numorphintensity : 1.0
     END_VERSIONS
 
     """
 
     stub:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    // TODO nf-core: A stub section should mimic the execution of the original module as best as possible
-    //               Have a look at the following examples:
-    //               Simple example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bcftools/annotate/main.nf#L47-L63
-    //               Complex example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bedtools/split/main.nf#L38-L54
+
     """
-    touch ${prefix}.bam
+    mkdir -p results/samples/intensity_adjustment
+    mkdir -p results/variables
+
+    touch results/variables/adj_params.mat
+    touch results/variables/path_table.mat
+    touch results/variables/thresholds.mat
+    touch results/NM_variables.mat
+    touch results/samples/intensity_adjustment/${meta.id}.png
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        numorph: 1.0
+        numorphintensity : 1.0
     END_VERSIONS
     """
 }

modules/local/numorphintensity/tests/main.nf.test

@@ -0,0 +1,33 @@
+nextflow_process {
+
+    name "Test Process Numorphintensity"
+    script "../main.nf"
+    process "NUMORPHINTENSITY"
+
+    tag "lsmquant"
+    tag "stub"
+
+    test("Numorphintensity stub test") {
+
+        options '-stub'
+
+        when {
+            process {
+                """
+                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 process.success },
+                { assert snapshot(process.out).match() }
+
+            )
+        }
+    }
+}

modules/local/numorphintensity/tests/main.nf.test.snap

@@ -0,0 +1,49 @@
+{
+    "Numorphintensity stub test": {
+        "content": [
+            {
+                "0": [
+                    "TEST1.png:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "1": [
+                    "adj_params.mat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "2": [
+                    "path_table.mat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "3": [
+                    "thresholds.mat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "4": [
+                    "NM_variables.mat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "5": [
+                    "versions.yml:md5,885c43b8dff8c26d121a817887a07702"
+                ],
+                "NM_variables": [
+                    "NM_variables.mat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "adj_params_mat": [
+                    "adj_params.mat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "path_table_mat": [
+                    "path_table.mat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "samples": [
+                    "TEST1.png:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "thresholds_mat": [
+                    "thresholds.mat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "versions": [
+                    "versions.yml:md5,885c43b8dff8c26d121a817887a07702"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-02-20T14:54:29.642551731"
+    }
+}

modules/local/numorphregister.nf → modules/local/numorphregister/main.nf

@@ -5,10 +5,6 @@ process NUMORPHREGISTER {
     container "carolinschwitalla/numorph_analyze:latest"
 
     input:
-    // TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
-    //               MUST be provided as an input via a Groovy Map called "meta".
-    //               This information may not be required in some instances e.g. indexing reference genome files:
-    //               https://github.com/nf-core/modules/blob/master/modules/nf-core/bwa/index/main.nf
     tuple val(meta), path(resampled_directory), path(parameter_file)
     path NM_variables
 
@@ -21,10 +17,6 @@ process NUMORPHREGISTER {
     path "versions.yml"                         , emit: versions
 
 
-
-            //errorStrategy { task.exitStatus == 249 ? 'ignore' : 'terminate' }
-
-
     when:
     task.ext.when == null || task.ext.when
 
@@ -46,23 +38,26 @@ process NUMORPHREGISTER {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        numorph: 1.0
+        numoprhregister: 1.0
     END_VERSIONS
     """
 
     stub:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    // TODO nf-core: A stub section should mimic the execution of the original module as best as possible
-    //               Have a look at the following examples:
-    //               Simple example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bcftools/annotate/main.nf#L47-L63
-    //               Complex example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bedtools/split/main.nf#L38-L54
+
     """
-    touch ${prefix}.bam
+    mkdir -p results/registered
+    mkdir -p results/variables
+
+    touch results/variables/reg_params.mat
+    touch results/variables/${meta.id}_mask.mat
+    touch results/NM_variables.mat
+    touch results/registered/${meta.id}_registered.tif
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        numoprhregister: \$(samtools --version |& sed '1!d ; s/samtools //')
+        numoprhregister: 1.0
     END_VERSIONS
     """
 }