SHAPEIT5_LIGATE Migration to nf-test

modules/nf-core/shapeit5/ligate/environment.yml

@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::shapeit5=1.0.0
+  - bioconda::shapeit5=5.1.1

modules/nf-core/shapeit5/ligate/main.nf

@@ -4,11 +4,11 @@ process SHAPEIT5_LIGATE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/shapeit5:1.0.0--h0c8ee15_0':
-        'biocontainers/shapeit5:1.0.0--h0c8ee15_0'}"
+        'https://depot.galaxyproject.org/singularity/shapeit5:5.1.1--hb60d31d_0':
+        'biocontainers/shapeit5:5.1.1--hb60d31d_0'}"
 
     input:
-    tuple val(meta), path(input_list), path (input_list_index)
+    tuple val(meta), path(input_list), path(input_list_index)
 
     output:
     tuple val(meta), path("*.{vcf,bcf,vcf.gz,bcf.gz}"), emit: merged_variants
@@ -37,11 +37,11 @@ process SHAPEIT5_LIGATE {
     """
 
     stub:
-    def args   = task.ext.args   ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    def suffix = task.ext.suffix ?: "vcf.gz"
+    def prefix     = task.ext.prefix        ?: "${meta.id}"
+    def suffix     = task.ext.suffix        ?: "vcf.gz"
+    def create_cmd = suffix.endsWith(".gz") ? "echo '' | gzip >" : "touch"
     """
-    touch ${prefix}.${suffix}
+    ${create_cmd} ${prefix}.${suffix}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/nf-core/shapeit5/ligate/tests/main.nf.test

@@ -0,0 +1,100 @@
+nextflow_process {
+
+    name "Test Process SHAPEIT5_LIGATE"
+    script "../main.nf"
+    process "SHAPEIT5_LIGATE"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "shapeit5"
+    tag "shapeit5/ligate"
+    tag "bcftools/view"
+
+    test("homo sapiens - map, [vcf], [tbi]") {
+            config "./nextflow.config"
+        setup {
+            run("BCFTOOLS_VIEW", alias: "BCFTOOLS_VIEW_1") {
+                script "../../../bcftools/view"
+                params {
+                    bcftools_args = "--regions chr21:16600000-16750000 -Ob --write-index=csi -e 'GT=\"./.\"||GT=\".\"'"
+                }
+                process {
+                    """
+                    input[0] = [
+                        [ id:'NA12878_1X_1' ], // meta map
+                        file(params.modules_testdata_base_path + "delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz", checkIfExists: true),
+                        file(params.modules_testdata_base_path + "delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz.csi", checkIfExists: true),
+                    ]
+                    input[1] = []
+                    input[2] = []
+                    input[3] = []
+                    """
+                }
+            }
+            run("BCFTOOLS_VIEW", alias: "BCFTOOLS_VIEW_2") {
+                script "../../../bcftools/view"
+                params {
+                    bcftools_args = "--regions chr21:16650000-16800000 -Ob --write-index=csi -e 'GT=\"./.\"||GT=\".\"'"
+                }
+                process {
+                    """
+                    input[0] = [
+                        [ id:'NA12878_1X_2' ], // meta map
+                        file(params.modules_testdata_base_path + "delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz", checkIfExists: true),
+                        file(params.modules_testdata_base_path + "delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz.csi", checkIfExists: true),
+                    ]
+                    input[1] = []
+                    input[2] = []
+                    input[3] = []
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = BCFTOOLS_VIEW_1.out.vcf.view().join(BCFTOOLS_VIEW_1.out.csi)
+                    .mix(BCFTOOLS_VIEW_2.out.vcf.join(BCFTOOLS_VIEW_2.out.csi))
+                    .map { meta, vcf, csi -> [ [id : "NA12878"], vcf, csi ] }
+                    .groupTuple()
+                    .view()
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.merged_variants.collect {meta, vcf -> [ meta, path(vcf).vcf.summary ]},
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("homo sapiens - map, [vcf], [tbi] - stub") {
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [id: 'NA12878' ],
+                    [file(params.modules_testdata_base_path + "delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz", checkIfExists: true)],
+                    [file(params.modules_testdata_base_path + "delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz.csi", checkIfExists: true)]
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}

modules/nf-core/shapeit5/ligate/tests/main.nf.test.snap

@@ -0,0 +1,55 @@
+{
+    "homo sapiens - map, [vcf], [tbi] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "NA12878"
+                        },
+                        "NA12878.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,4b66c655a4fd210ca7bc47b6fe35230b"
+                ],
+                "merged_variants": [
+                    [
+                        {
+                            "id": "NA12878"
+                        },
+                        "NA12878.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,4b66c655a4fd210ca7bc47b6fe35230b"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-11-22T17:22:34.235879155"
+    },
+    "homo sapiens - map, [vcf], [tbi]": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "NA12878"
+                    },
+                    "VcfFile [chromosomes=[chr21], sampleCount=1, variantCount=2042, phased=false, phasedAutodetect=false]"
+                ]
+            ],
+            [
+                "versions.yml:md5,4b66c655a4fd210ca7bc47b6fe35230b"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-11-22T17:22:28.218989461"
+    }
+}

modules/nf-core/shapeit5/ligate/tests/nextflow.config

@@ -0,0 +1,6 @@
+process {
+    withName: "BCFTOOLS_VIEW_*" {
+        ext.args = params.bcftools_args
+        ext.prefix = { "${meta.id}" }
+    }
+}

tests/config/pytest_modules.yml

@@ -522,9 +522,6 @@ sgdemux:
   - modules/nf-core/sgdemux/**
   - modules/nf-core/untar/**
   - tests/modules/nf-core/sgdemux/**
-shapeit5/ligate:
-  - modules/nf-core/shapeit5/ligate/**
-  - tests/modules/nf-core/shapeit5/ligate/**
 shapeit5/phasecommon:
   - modules/nf-core/shapeit5/phasecommon/**
   - tests/modules/nf-core/shapeit5/phasecommon/**