Add nftests custom modules

.github/workflows/pytest-workflow.yml

@@ -117,6 +117,12 @@ jobs:
             tags: controlfreec/makegraph2
           - profile: conda
             tags: coreograph
+          - profile: conda
+            tags: custom/matrixfilter
+          - profile: conda
+            tags: custom/tabulartogseacls
+          - profile: conda
+            tags: custom/tabulartogseagct
           - profile: conda
             tags: deepcell/mesmer
           - profile: conda

modules/nf-core/custom/matrixfilter/main.nf

@@ -2,9 +2,7 @@ process CUSTOM_MATRIXFILTER {
     tag "$meta"
     label 'process_single'
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/r-base:4.2.1' :
-        'biocontainers/r-base:4.2.1' }"
+    container "community.wave.seqera.io/library/r-base:4.2.1--b0b5476e2e7a0872"
 
     input:
     tuple val(meta), path(abundance)
@@ -27,4 +25,12 @@ process CUSTOM_MATRIXFILTER {
     // (new variables defined here don't seem to be available in templates, so
     // we have to access $task directly)
     template 'matrixfilter.R'
+
+    stub:
+    """
+    touch mock.filtered.tsv
+    touch mock.tests.tsv
+    touch R_sessionInfo.log
+    touch versions.yml
+    """
 }

modules/nf-core/custom/matrixfilter/tests/main.nf.test

@@ -0,0 +1,57 @@
+nextflow_process {
+
+    name "Test Process CUSTOM_MATRIXFILTER"
+    script "../main.nf"
+    process "CUSTOM_MATRIXFILTER"
+    config "./nextflow.config"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "custom_matrixfilter"
+    tag "custom"
+    tag "custom/matrixfilter"
+
+    test("test_custom_matrixfilter") {
+
+        when {
+            process {
+                """
+                input[0] = [ [id:"test"], file("https://github.com/nf-core/test-datasets/raw/refs/heads/differentialabundance/modules_testdata/SRP254919.salmon.merged.gene_counts.top1000cov.assay.tsv",checkIfExists: true) ]
+                input[1] = [ [id:"test"], file("https://github.com/nf-core/test-datasets/raw/refs/heads/differentialabundance/modules_testdata/SRP254919.samplesheet.sample_metadata.tsv",checkIfExists: true) ]
+                """
+
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out.filtered).match("filtered") },
+                { assert snapshot(process.out.tests).match("tests") },
+                { assert snapshot(process.out.versions).match("versions") }
+            )
+        }
+    }
+
+    test("test_custom_matrixfilter - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [ [id:"test"], file("https://github.com/nf-core/test-datasets/raw/refs/heads/differentialabundance/modules_testdata/SRP254919.salmon.merged.gene_counts.top1000cov.assay.tsv",checkIfExists: true) ]
+                input[1] = [ [id:"test"], file("https://github.com/nf-core/test-datasets/raw/refs/heads/differentialabundance/modules_testdata/SRP254919.samplesheet.sample_metadata.tsv",checkIfExists: true) ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out.filtered).match("filtered_stub") },
+                { assert snapshot(process.out.tests).match("tests_stub") },
+                { assert snapshot(process.out.versions).match("versions_stub") }
+            )
+        }
+    }
+}

modules/nf-core/custom/matrixfilter/tests/main.nf.test.snap

@@ -0,0 +1,94 @@
+{
+    "filtered_stub": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "mock.filtered.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-11T20:24:23.270885558"
+    },
+    "versions_stub": {
+        "content": [
+            [
+                "versions.yml:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-11T20:24:23.286233277"
+    },
+    "tests": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.tests.tsv:md5,9a0f14988df8c1b8975039eed91b85e2"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-11T20:24:15.105582542"
+    },
+    "tests_stub": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "mock.tests.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-11T20:24:23.278625607"
+    },
+    "filtered": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.filtered.tsv:md5,ecc3ca4c6538f9248dce844108474a66"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-11T20:24:15.091697173"
+    },
+    "versions": {
+        "content": [
+            [
+                "versions.yml:md5,275e382be9ca5bdd30ff5d6fc4340616"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-11T20:24:15.113337441"
+    }
+}

modules/nf-core/custom/matrixfilter/tests/nextflow.config

@@ -0,0 +1,21 @@
+params {
+    observations_id_col             = 'sample'
+    filtering_min_samples           = 1.0
+    filtering_min_abundance         = 10
+    filtering_min_proportion        = null
+    filtering_grouping_var          = null
+    filtering_min_proportion_not_na = 0.5
+    filtering_min_samples_not_na    = null
+}
+process {
+    ext.prefix = { "${meta.id}" }
+    ext.args   = [
+        "--sample_id_col \"${params.observations_id_col}\"",
+        "--minimum_samples ${params.filtering_min_samples}",
+        "--minimum_abundance ${params.filtering_min_abundance}",
+        (params.filtering_min_proportion ? "--minimum_proportion ${params.filtering_min_proportion}" : ''),
+        (params.filtering_grouping_var ? "--grouping_variable \"${params.filtering_grouping_var}\"" : ''),
+        (params.filtering_min_proportion_not_na ? "--minimum_proportion_not_na \"${params.filtering_min_proportion_not_na}\"" : ''),
+        (params.filtering_min_samples_not_na ? "--minimum_samples_not_na \"${params.filtering_min_samples_not_na}\"" : '')
+    ].join(' ').trim()
+    }

modules/nf-core/custom/tabulartogseacls/main.nf

@@ -3,9 +3,7 @@ process CUSTOM_TABULARTOGSEACLS {
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-        'nf-core/ubuntu:20.04' }"
+    container "community.wave.seqera.io/library/coreutils:8.30--b947da103164f84b"
 
     input:
     tuple val(meta), path(samples)
@@ -38,7 +36,17 @@ process CUSTOM_TABULARTOGSEACLS {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        bash: \$(echo \$(bash --version | grep -Eo 'version [[:alnum:].]+' | sed 's/version //'))
+        awk: \$(mawk -W version | head -n 1 | awk '{print  \$2}')
     END_VERSIONS
     """
+
+    stub:
+    """
+    touch mock.cls
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        awk: \$(mawk -W version | head -n 1 | awk '{print  \$2}')
+    END_VERSIONS
+    """
+
 }

modules/nf-core/custom/tabulartogseacls/tests/main.nf.test

@@ -0,0 +1,51 @@
+nextflow_process {
+
+    name "Test Process CUSTOM_TABULARTOGSEACLS"
+    script "../main.nf"
+    process "CUSTOM_TABULARTOGSEACLS"
+    config "./nextflow.config"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "custom_tabulartogseacls"
+    tag "custom"
+    tag "custom/tabulartogseacls"
+
+    test("test_custom_tabulartogseacls") {
+
+        when {
+            process {
+                """
+                input[0] = [ [id:'treatment_mCherry_hND6_sample_number', variable:'treatment', reference:'mCherry', target:'hND6', blocking:'sample_number'], file("https://github.com/nf-core/test-datasets/raw/refs/heads/differentialabundance/modules_testdata/SRP254919.samplesheet.sample_metadata.tsv",checkIfExists: true) ]
+                """
+
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test_custom_tabulartogseacls - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [ [id:'treatment_mCherry_hND6_sample_number', variable:'treatment', reference:'mCherry', target:'hND6', blocking:'sample_number'], file("https://github.com/nf-core/test-datasets/raw/refs/heads/differentialabundance/modules_testdata/SRP254919.samplesheet.sample_metadata.tsv",checkIfExists: true) ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}

modules/nf-core/custom/tabulartogseacls/tests/main.nf.test.snap

@@ -0,0 +1,84 @@
+{
+    "test_custom_tabulartogseacls - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "treatment_mCherry_hND6_sample_number",
+                            "variable": "treatment",
+                            "reference": "mCherry",
+                            "target": "hND6",
+                            "blocking": "sample_number"
+                        },
+                        "mock.cls:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,bdeacaf3413865c27625dce2b7adcd9e"
+                ],
+                "cls": [
+                    [
+                        {
+                            "id": "treatment_mCherry_hND6_sample_number",
+                            "variable": "treatment",
+                            "reference": "mCherry",
+                            "target": "hND6",
+                            "blocking": "sample_number"
+                        },
+                        "mock.cls:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,bdeacaf3413865c27625dce2b7adcd9e"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-12T18:12:13.838536831"
+    },
+    "test_custom_tabulartogseacls": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "treatment_mCherry_hND6_sample_number",
+                            "variable": "treatment",
+                            "reference": "mCherry",
+                            "target": "hND6",
+                            "blocking": "sample_number"
+                        },
+                        "treatment_mCherry_hND6_sample_number.cls:md5,7b887159417842b1fe87afebe4f8c2b7"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,bdeacaf3413865c27625dce2b7adcd9e"
+                ],
+                "cls": [
+                    [
+                        {
+                            "id": "treatment_mCherry_hND6_sample_number",
+                            "variable": "treatment",
+                            "reference": "mCherry",
+                            "target": "hND6",
+                            "blocking": "sample_number"
+                        },
+                        "treatment_mCherry_hND6_sample_number.cls:md5,7b887159417842b1fe87afebe4f8c2b7"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,bdeacaf3413865c27625dce2b7adcd9e"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-12T18:12:07.37704262"
+    }
+}

modules/nf-core/custom/tabulartogseacls/tests/nextflow.config

@@ -0,0 +1,3 @@
+process {
+    ext.args = { [ "separator": "\t", "variable": "$meta.variable" ] }
+}