From bad2110a3f1ef3fbe2232517fb908a371d445909 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Theresa=20St=C3=B6riko?=
 <73145457+tstoeriko@users.noreply.github.com>
Date: Wed, 20 Mar 2024 13:49:19 +0100
Subject: [PATCH] New module svtypersso (#5311)

* Add module svtypersso

* Adjust formatting

- align equal signs
---
 .../svtyper/svtypersso/environment.yml        |   7 +
 modules/nf-core/svtyper/svtypersso/main.nf    |  57 +++++++
 modules/nf-core/svtyper/svtypersso/meta.yml   |  68 +++++++++
 .../svtyper/svtypersso/tests/main.nf.test     | 129 ++++++++++++++++
 .../svtypersso/tests/main.nf.test.snap        | 140 ++++++++++++++++++
 .../nf-core/svtyper/svtypersso/tests/tags.yml |   2 +
 6 files changed, 403 insertions(+)
 create mode 100644 modules/nf-core/svtyper/svtypersso/environment.yml
 create mode 100644 modules/nf-core/svtyper/svtypersso/main.nf
 create mode 100644 modules/nf-core/svtyper/svtypersso/meta.yml
 create mode 100644 modules/nf-core/svtyper/svtypersso/tests/main.nf.test
 create mode 100644 modules/nf-core/svtyper/svtypersso/tests/main.nf.test.snap
 create mode 100644 modules/nf-core/svtyper/svtypersso/tests/tags.yml

diff --git a/modules/nf-core/svtyper/svtypersso/environment.yml b/modules/nf-core/svtyper/svtypersso/environment.yml
new file mode 100644
index 00000000000..b00cc4338ba
--- /dev/null
+++ b/modules/nf-core/svtyper/svtypersso/environment.yml
@@ -0,0 +1,7 @@
+name: "svtyper_svtypersso"
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - "bioconda::svtyper=0.7.1"
diff --git a/modules/nf-core/svtyper/svtypersso/main.nf b/modules/nf-core/svtyper/svtypersso/main.nf
new file mode 100644
index 00000000000..123a12495b9
--- /dev/null
+++ b/modules/nf-core/svtyper/svtypersso/main.nf
@@ -0,0 +1,57 @@
+process SVTYPER_SVTYPERSSO {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/svtyper:0.7.1--py_0':
+        'biocontainers/svtyper:0.7.1--py_0' }"
+
+    input:
+    tuple val(meta), path(bam), path(bam_index), path(vcf)
+    tuple val(meta2), path(fasta)
+
+    output:
+    tuple val(meta), path("*.vcf") , emit: gt_vcf
+    tuple val(meta), path("*.json"), emit: json
+    path "versions.yml"            , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args   = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def vcf    = vcf ? "--input_vcf ${vcf}" : ""
+    def fasta  = fasta ? "--ref_fasta ${fasta}" : ""
+    if ("$vcf" == "${prefix}.vcf") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
+    if ("$bam" == "${prefix}.bam") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
+    """
+    svtyper-sso \\
+        --bam $bam \\
+        $vcf \\
+        $fasta \\
+        --output_vcf ${prefix}.vcf \\
+        --lib_info ${prefix}.json \\
+        --cores $task.cpus \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        svtyper: \$(echo \$(svtyper-sso -h 2>&1 | grep "version:" | sed 's/^version: v//'))
+    END_VERSIONS
+    """
+
+    stub:
+    def args   = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.json
+    touch ${prefix}.vcf
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        svtyper: \$(echo \$(svtyper-sso -h 2>&1 | grep "version:" | sed 's/^version: v//'))
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/svtyper/svtypersso/meta.yml b/modules/nf-core/svtyper/svtypersso/meta.yml
new file mode 100644
index 00000000000..edbf8e3ce5c
--- /dev/null
+++ b/modules/nf-core/svtyper/svtypersso/meta.yml
@@ -0,0 +1,68 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "svtyper_svtypersso"
+description: SVTyper-sso computes structural variant (SV) genotypes based on breakpoint depth on a SINGLE sample
+keywords:
+  - sv
+  - structural variants
+  - genotyping
+  - Bayesian
+tools:
+  - "svtyper":
+      description: "Bayesian genotyper for structural variants"
+      homepage: "https://github.com/hall-lab/svtyper"
+      documentation: "https://github.com/hall-lab/svtyper"
+      tool_dev_url: "https://github.com/hall-lab/svtyper"
+      doi: "10.1038/nmeth.3505"
+      licence: ["MIT"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test']
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing sample information for reference FASTA file
+        e.g. [ id:'fasta']
+  - bam:
+      type: file
+      description: BAM or CRAM file with alignments
+      pattern: "*.{bam,cram}"
+  - bam_index:
+      type: file
+      description: BAI file matching the BAM file
+      pattern: "*.{bai}"
+  - vcf:
+      type: file
+      description: Matching VCF of alignments
+      pattern: "*.vcf"
+  - fasta:
+      type: file
+      description: indexed reference FASTA file (recommended for reading CRAM files)
+      pattern: "*.{fa,fasta}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test' ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - json:
+      type: file
+      description: JSON file including library information
+      pattern: "*.json"
+  - gt_vcf:
+      type: file
+      description: Genotyped SVs
+      pattern: "*.vcf"
+authors:
+  - "@tstoeriko"
+maintainers:
+  - "@tstoeriko"
diff --git a/modules/nf-core/svtyper/svtypersso/tests/main.nf.test b/modules/nf-core/svtyper/svtypersso/tests/main.nf.test
new file mode 100644
index 00000000000..b263f3be7f0
--- /dev/null
+++ b/modules/nf-core/svtyper/svtypersso/tests/main.nf.test
@@ -0,0 +1,129 @@
+nextflow_process {
+
+    name "Test Process SVTYPER_SVTYPERSSO"
+    script "../main.nf"
+    process "SVTYPER_SVTYPERSSO"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "svtyper"
+    tag "svtyper/svtypersso"
+
+    test("homo_sapiens - bam - vcf - fasta") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true)
+                ]
+                input[1] = [
+                     [ id:'reference' ], // meta map
+                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.gt_vcf,
+                                    process.out.versions).match("bam_vcf_fasta") },
+                { assert file(process.out.json.get(0).get(1)).exists() }
+            )
+        }
+    }
+
+    test("homo_sapiens - bam - vcf - fasta - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true)
+                ]
+                input[1] = [
+                     [ id:'reference' ], // meta map
+                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match("bam_vcf_fasta_stub") }
+            )
+        }
+    }
+
+    test("homo_sapiens - bam") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+                    []
+                ]
+                input[1] = [
+                     [ id:'reference' ], // meta map
+                     []
+                ]
+                """
+            }
+        }
+
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.gt_vcf,
+                                    process.out.versions).match("bam") },
+                { assert file(process.out.json.get(0).get(1)).exists() }
+            )
+        }
+    }
+
+    test("homo_sapiens - bam - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+                    []
+                ]
+                input[1] = [
+                     [ id:'reference' ], // meta map
+                     []
+                ]
+                """
+            }
+        }
+
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match("bam_stub") }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/svtyper/svtypersso/tests/main.nf.test.snap b/modules/nf-core/svtyper/svtypersso/tests/main.nf.test.snap
new file mode 100644
index 00000000000..e83a9345e89
--- /dev/null
+++ b/modules/nf-core/svtyper/svtypersso/tests/main.nf.test.snap
@@ -0,0 +1,140 @@
+{
+    "bam_vcf_fasta_stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,5fae80f0d38e21c8f42733cf3ef61665"
+                ],
+                "gt_vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "json": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,5fae80f0d38e21c8f42733cf3ef61665"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-20T08:49:25.044877605"
+    },
+    "bam_vcf_fasta": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.vcf:md5,aee556ba714a2a3d64fb4fc9f2753cea"
+                ]
+            ],
+            [
+                "versions.yml:md5,5fae80f0d38e21c8f42733cf3ef61665"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-20T08:30:52.404061568"
+    },
+    "bam": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.vcf:md5,b4a4e316e8524535ca1d3f26ad39ac78"
+                ]
+            ],
+            [
+                "versions.yml:md5,5fae80f0d38e21c8f42733cf3ef61665"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-20T08:31:15.057840812"
+    },
+    "bam_stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,5fae80f0d38e21c8f42733cf3ef61665"
+                ],
+                "gt_vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "json": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,5fae80f0d38e21c8f42733cf3ef61665"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-20T08:49:53.327743119"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/svtyper/svtypersso/tests/tags.yml b/modules/nf-core/svtyper/svtypersso/tests/tags.yml
new file mode 100644
index 00000000000..da061baf163
--- /dev/null
+++ b/modules/nf-core/svtyper/svtypersso/tests/tags.yml
@@ -0,0 +1,2 @@
+svtyper/svtypersso:
+  - "modules/nf-core/svtyper/svtypersso/**"