Update shapeit5 phaserare

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

@@ -14,12 +14,12 @@ process SHAPEIT5_PHASERARE {
 
     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_plain), path(input_plain_index), path(pedigree), val(input_region)
-        tuple val(meta2), path(scaffold)   , path(scaffold_index)   , val(scaffold_region)
+        tuple val(meta) , path(input)    , path(input_index)    , path(pedigree), val(input_region)
+        tuple val(meta2), path(scaffold) , path(scaffold_index) , val(scaffold_region)
         tuple val(meta3), path(map)
 
     output:
@@ -34,15 +34,16 @@ process SHAPEIT5_PHASERARE {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def suffix = task.ext.suffix ?: "vcf.gz"
 
-    if ("$input_plain" == "${prefix}.${suffix}") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
+    if ("$input" == "${prefix}.${suffix}") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
+    if ("$scaffold" == "${prefix}.${suffix}") error "Scaffold and output names are the same, set prefix in module configuration to disambiguate!"
 
     def map_command       = map       ? "--map $map"             : ""
     def pedigree_command  = pedigree  ? "--pedigree $pedigree"   : ""
 
     """
     SHAPEIT5_phase_rare \\
         $args \\
-        --input-plain $input_plain \\
+        --input $input \\
         --scaffold $scaffold \\
         $map_command \\
         $pedigree_command \\
@@ -58,11 +59,11 @@ process SHAPEIT5_PHASERARE {
     """
 
     stub:
-    def args   = task.ext.args   ?: ''
     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/phaserare/meta.yml

@@ -23,12 +23,12 @@ input:
         description: |
           Groovy Map containing sample information
           e.g. [ id:'test', single_end:false ]
-    - input_plain:
+    - input:
         type: file
         description: |
           Genotypes to be phased in plain VCF/BCF format.
         pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}"
-    - input_plain_index:
+    - input_index:
         type: file
         description: Index file of the input_plain VCF/BCF file containing genotype
           likelihoods.

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

@@ -0,0 +1,105 @@
+nextflow_process {
+
+    name "Test Process SHAPEIT5_PHASERARE"
+    script "../main.nf"
+    process "SHAPEIT5_PHASERARE"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "shapeit5"
+    tag "shapeit5/phaserare"
+    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] = Channel.of([
+                    [ id:'input', 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),
+                    [],
+                    "chr22:16580000-16600000",
+                ])
+                input[1] = SHAPEIT5_PHASECOMMON.out.phased_variant
+                    .join(BCFTOOLS_INDEX.out.csi)
+                    .combine(Channel.of("chr22:16570000-16610000"))
+                input[2] = Channel.of([[],[]])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.phased_variant.collect { meta, vcf -> [ meta, file(vcf).name ] },
+                    process.out.versions
+                ).match() }
+            )
+        }
+
+    }
+
+    test("homo sapiens - vcf, scaffold, [] - stub") {
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'input', 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),
+                    [],
+                    "chr22:16580000-16600000",
+                ])
+                input[1] = Channel.of([[],[],[],[]])
+                input[2] = Channel.of([[],[]])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}

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

@@ -0,0 +1,58 @@
+{
+    "homo sapiens - vcf, scaffold, [] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "input",
+                            "single_end": false
+                        },
+                        "input.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,c8092f58dd64199400ee9b9bfd96032e"
+                ],
+                "phased_variant": [
+                    [
+                        {
+                            "id": "input",
+                            "single_end": false
+                        },
+                        "input.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,c8092f58dd64199400ee9b9bfd96032e"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-11-22T18:11:56.868657182"
+    },
+    "homo sapiens - vcf, scaffold, []": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "input",
+                        "single_end": false
+                    },
+                    "input.vcf.gz"
+                ]
+            ],
+            [
+                "versions.yml:md5,c8092f58dd64199400ee9b9bfd96032e"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-11-22T18:35:35.056441054"
+    }
+}

modules/nf-core/shapeit5/phaserare/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/ligate:
   - modules/nf-core/shapeit5/ligate/**
   - tests/modules/nf-core/shapeit5/ligate/**
-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/**