nf-test migration: plink/indeppairwise

.pre-commit-config.yaml

@@ -9,13 +9,13 @@ repos:
         types: [yaml]
         additional_dependencies: ["ruamel.yaml"]
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: "v3.1.0"
+    rev: "v4.0.0-alpha.8"
     hooks:
       - id: prettier
         additional_dependencies:
           - [email protected]
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.29.4
+    rev: 0.32.1
     hooks:
       - id: check-jsonschema
         name: "Match meta.ymls in one of the subdirectories of modules/nf-core"
@@ -36,20 +36,20 @@ repos:
 
   # use ruff for python files
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.7.3
+    rev: v0.11.2
     hooks:
       - id: ruff
         files: \.py$
         args: [--fix, --exit-non-zero-on-fix, "--select", "I,E1,E4,E7,E9,F,UP,N"] # sort imports and fix (rules taken from nf-core/tools)
       - id: ruff-format # formatter
   - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
-    rev: "3.0.3"
+    rev: "3.2.0"
     hooks:
       - id: editorconfig-checker
         alias: ec
     # NOTE This runs with Docker instead of the binary. Hoping anyone messing with Dockerfiles has Docker installed
   - repo: https://github.com/hadolint/hadolint
-    rev: v2.12.0
+    rev: v2.13.1-beta
     hooks:
       - id: hadolint-docker
   - repo: https://github.com/nf-core/tools

modules/nf-core/plink/indeppairwise/main.nf

@@ -1,4 +1,3 @@
-
 process PLINK_INDEPPAIRWISE {
     tag "$meta.id"
     label 'process_low'
@@ -31,10 +30,23 @@ process PLINK_INDEPPAIRWISE {
         --bed ${bed}  \\
         --bim ${bim}  \\
         --fam ${fam}  \\
-        --threads $task.cpus \\
+        --threads ${task.cpus} \\
         --indep-pairwise ${window_size} ${variant_count} ${r2_threshold} \\
-        $args \\
-        --out $prefix
+        ${args} \\
+        --out ${prefix}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        plink: \$(echo \$(plink --version) | sed 's/^PLINK v//;s/64.*//')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    touch ${meta.id}.prune.in
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         plink: \$(echo \$(plink --version) | sed 's/^PLINK v//;s/64.*//')

modules/nf-core/plink/indeppairwise/tests/main.nf.test

@@ -0,0 +1,78 @@
+nextflow_process {
+
+    name "Test Process PLINK_INDEPPAIRWISE"
+    script "../main.nf"
+    process "PLINK_INDEPPAIRWISE"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "plink"
+    tag "plink/indeppairwise"
+    tag "plink/vcf"
+
+    test("test_plink_indeppairwise") {
+
+        config "./nextflow.config"
+
+        setup {
+
+            params.module_args = '--make-bed --biallelic-only strict --vcf-half-call haploid --allow-extra-chr'
+
+            run("PLINK_VCF") {
+                script "../../vcf/main.nf"
+
+                process {
+                    """
+                    input[0] = [
+                        [id:'test',single_end:false],// meta map
+                        file("https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/genome/vcf/ped/justhusky_minimal.vcf.gz", checkIfExists:true)
+                        ]
+                    """
+                }
+            }
+        }
+        when {
+            process {
+                """
+                input[0] = PLINK_VCF.out.bed.join(PLINK_VCF.out.bim).join(PLINK_VCF.out.fam)
+                input[1] = Channel.value(50)
+                input[2] = Channel.value(5)
+                input[3] = Channel.value(0.2)
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test_plink_indeppairwise - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file("test.bed"),
+                    file("test.bim"),
+                    file("test.fam")
+                    ]
+                input[1] = Channel.value(50)
+                input[2] = Channel.value(5)
+                input[3] = Channel.value(0.2)
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}

modules/nf-core/plink/indeppairwise/tests/main.nf.test.snap

@@ -0,0 +1,96 @@
+{
+    "test_plink_indeppairwise": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.prune.in:md5,dce7ba75405107468f2ce18fc95a9786"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.prune.out:md5,1f65f71308f2c4a03b9a4a98bbfb11e9"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,dd52fb8375a5ba36e766f25e9028d128"
+                ],
+                "prunein": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.prune.in:md5,dce7ba75405107468f2ce18fc95a9786"
+                    ]
+                ],
+                "pruneout": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.prune.out:md5,1f65f71308f2c4a03b9a4a98bbfb11e9"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,dd52fb8375a5ba36e766f25e9028d128"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-03-26T14:55:08.717872783"
+    },
+    "test_plink_indeppairwise - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.prune.in:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+
+                ],
+                "2": [
+                    "versions.yml:md5,dd52fb8375a5ba36e766f25e9028d128"
+                ],
+                "prunein": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.prune.in:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "pruneout": [
+
+                ],
+                "versions": [
+                    "versions.yml:md5,dd52fb8375a5ba36e766f25e9028d128"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-03-26T15:26:32.033778403"
+    }
+}

modules/nf-core/plink/indeppairwise/tests/nextflow.config

@@ -0,0 +1,5 @@
+process {
+    withName: "PLINK_VCF" {
+        ext.args = params.module_args
+    }
+}

tests/config/pytest_modules.yml

@@ -176,9 +176,6 @@ phyloflash:
 plink/indep:
   - modules/nf-core/plink/indep/**
   - tests/modules/nf-core/plink/indep/**
-plink/indeppairwise:
-  - modules/nf-core/plink/indeppairwise/**
-  - tests/modules/nf-core/plink/indeppairwise/**
 pneumocat:
   - modules/nf-core/pneumocat/**
   - tests/modules/nf-core/pneumocat/**