SHAPEIT5_SWITCH Migrate to nf-test

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

@@ -4,8 +4,8 @@ process SHAPEIT5_SWITCH {
 
     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(estimate), path(estimate_index), val(region), path(pedigree)
@@ -43,18 +43,18 @@ process SHAPEIT5_SWITCH {
     """
 
     stub:
-    def args         = task.ext.args   ?: ''
     def prefix       = task.ext.prefix ?: "${meta.id}"
+    def create_cmd   = "echo '' | gzip >"
     """
-    touch ${prefix}.block.switch.txt.gz
-    touch ${prefix}.calibration.switch.txt.gz
-    touch ${prefix}.flipsAndSwitches.txt.gz
-    touch ${prefix}.frequency.switch.txt.gz
-    touch ${prefix}.sample.switch.txt.gz
-    touch ${prefix}.sample.typing.txt.gz
-    touch ${prefix}.type.switch.txt.gz
-    touch ${prefix}.variant.switch.txt.gz
-    touch ${prefix}.variant.typing.txt.gz
+    ${create_cmd} ${prefix}.block.switch.txt.gz
+    ${create_cmd} ${prefix}.calibration.switch.txt.gz
+    ${create_cmd} ${prefix}.flipsAndSwitches.txt.gz
+    ${create_cmd} ${prefix}.frequency.switch.txt.gz
+    ${create_cmd} ${prefix}.sample.switch.txt.gz
+    ${create_cmd} ${prefix}.sample.typing.txt.gz
+    ${create_cmd} ${prefix}.type.switch.txt.gz
+    ${create_cmd} ${prefix}.variant.switch.txt.gz
+    ${create_cmd} ${prefix}.variant.typing.txt.gz
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

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

@@ -0,0 +1,105 @@
+nextflow_process {
+
+    name "Test Process SHAPEIT5_SWITCH"
+    script "../main.nf"
+    process "SHAPEIT5_SWITCH"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "shapeit5"
+    tag "shapeit5/switch"
+    tag "shapeit5/phasecommon"
+    tag "bcftools/index"
+
+    test("homo sapiens - vcf, scaffold, []") {
+        config "./nextflow.config"
+        setup {
+            run("SHAPEIT5_PHASECOMMON") {
+                script "../../../shapeit5/phasecommon"
+                params {
+                    shapeit5_phasecommon_args = "--filter-maf 0.001"
+                }
+                process {
+                    """
+                    input[0] = Channel.of([
+                        [ id:'scaffold', single_end:false ], // meta map
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr22.vcf.gz", checkIfExists: true),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr22.vcf.gz.csi", checkIfExists: true),
+                        [],
+                        "chr22",
+                    ])
+                    input[1] = Channel.of([[],[],[]])
+                    input[2] = Channel.of([[],[],[]])
+                    input[3] = Channel.of([[],[]])
+                    """
+                }
+            }
+            run("BCFTOOLS_INDEX") {
+                script "../../../bcftools/index"
+                process {
+                    """
+                    input[0] = SHAPEIT5_PHASECOMMON.out.phased_variant
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = SHAPEIT5_PHASECOMMON.out.phased_variant
+                    .join(BCFTOOLS_INDEX.out.csi)
+                    .combine(Channel.of("chr22"))
+                    .combine(Channel.of([[]]))
+                input[1] = Channel.of([[ id:'truth_panel'],
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr22.vcf.gz",checkIfExists:true),
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr22.vcf.gz.csi",checkIfExists:true)
+                ])
+                input[2] = Channel.of([[ id:'freq_file'],
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr22.sites.vcf.gz",checkIfExists:true),
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr22.sites.vcf.gz.csi",checkIfExists:true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.errors.collect { meta, txt -> [ meta, txt.collect{ file(it).name } ] },
+                    process.out.versions
+                ).match() }
+            )
+        }
+
+    }
+
+    test("homo sapiens - vcf, scaffold, [] - stub") {
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [id:'truth_panel'],
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr22.vcf.gz",checkIfExists:true),
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr22.vcf.gz.csi",checkIfExists:true),
+                    "chr21",
+                    []
+                ])
+                input[1] = [[], [], []]
+                input[2] = [[], [], []]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}

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

@@ -0,0 +1,86 @@
+{
+    "homo sapiens - vcf, scaffold, [] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "truth_panel"
+                        },
+                        [
+                            "truth_panel.block.switch.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "truth_panel.calibration.switch.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "truth_panel.flipsAndSwitches.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "truth_panel.frequency.switch.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "truth_panel.sample.switch.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "truth_panel.sample.typing.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "truth_panel.type.switch.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "truth_panel.variant.switch.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "truth_panel.variant.typing.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,95238962a141557f464b8e22c8057211"
+                ],
+                "errors": [
+                    [
+                        {
+                            "id": "truth_panel"
+                        },
+                        [
+                            "truth_panel.block.switch.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "truth_panel.calibration.switch.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "truth_panel.flipsAndSwitches.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "truth_panel.frequency.switch.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "truth_panel.sample.switch.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "truth_panel.sample.typing.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "truth_panel.type.switch.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "truth_panel.variant.switch.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "truth_panel.variant.typing.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,95238962a141557f464b8e22c8057211"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-11-22T19:04:42.303883153"
+    },
+    "homo sapiens - vcf, scaffold, []": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "scaffold",
+                        "single_end": false
+                    },
+                    [
+                        "scaffold.block.switch.txt.gz",
+                        "scaffold.calibration.switch.txt.gz",
+                        "scaffold.flipsAndSwitches.txt.gz",
+                        "scaffold.frequency.switch.txt.gz",
+                        "scaffold.sample.switch.txt.gz",
+                        "scaffold.sample.typing.txt.gz",
+                        "scaffold.type.switch.txt.gz",
+                        "scaffold.variant.switch.txt.gz",
+                        "scaffold.variant.typing.txt.gz"
+                    ]
+                ]
+            ],
+            [
+                "versions.yml:md5,95238962a141557f464b8e22c8057211"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-11-22T19:13:32.038870261"
+    }
+}

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

@@ -0,0 +1,5 @@
+process {
+    withName: SHAPEIT5_PHASECOMMON {
+        ext.args = params.shapeit5_phasecommon_args
+    }
+}

tests/config/pytest_modules.yml

@@ -510,9 +510,6 @@ sgdemux:
 shapeit5/phaserare:
   - modules/nf-core/shapeit5/phaserare/**
   - tests/modules/nf-core/shapeit5/phaserare/**
-shapeit5/switch:
-  - modules/nf-core/shapeit5/switch/**
-  - tests/modules/nf-core/shapeit5/switch/**
 shigeifinder:
   - modules/nf-core/shigeifinder/**
   - tests/modules/nf-core/shigeifinder/**