From 6e7c0e945b490a7c1e9d2d01cc37e45d581e78bd Mon Sep 17 00:00:00 2001
From: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
Date: Fri, 17 Jun 2022 15:54:02 +0200
Subject: [PATCH] new module vcf2db (#1795)

* added vcf2db

* fix test.yml

* possible fix for failing tests

* fix version number

* fix test.yml

* removed some comments
---
 modules/vcf2db/main.nf               | 37 ++++++++++++++++++++++
 modules/vcf2db/meta.yml              | 47 ++++++++++++++++++++++++++++
 tests/config/pytest_modules.yml      |  4 +++
 tests/modules/vcf2db/main.nf         | 16 ++++++++++
 tests/modules/vcf2db/nextflow.config |  5 +++
 tests/modules/vcf2db/test.yml        |  6 ++++
 6 files changed, 115 insertions(+)
 create mode 100644 modules/vcf2db/main.nf
 create mode 100644 modules/vcf2db/meta.yml
 create mode 100644 tests/modules/vcf2db/main.nf
 create mode 100644 tests/modules/vcf2db/nextflow.config
 create mode 100644 tests/modules/vcf2db/test.yml

diff --git a/modules/vcf2db/main.nf b/modules/vcf2db/main.nf
new file mode 100644
index 00000000..1030c596
--- /dev/null
+++ b/modules/vcf2db/main.nf
@@ -0,0 +1,37 @@
+VERSION = "2020.02.24"
+
+process VCF2DB {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::vcf2db=2020.02.24" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/vcf2db:2020.02.24--hdfd78af_1':
+        'quay.io/biocontainers/vcf2db:2020.02.24--hdfd78af_1' }"
+
+    input:
+    tuple val(meta), path(vcf), path(ped)
+
+    output:
+    tuple val(meta), path("*.db") , emit: db
+    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}"
+    """
+    vcf2db.py \\
+        $vcf \\
+        $ped \\
+        ${prefix}.db \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        vcf2db: $VERSION
+    END_VERSIONS
+    """
+}
diff --git a/modules/vcf2db/meta.yml b/modules/vcf2db/meta.yml
new file mode 100644
index 00000000..65e41113
--- /dev/null
+++ b/modules/vcf2db/meta.yml
@@ -0,0 +1,47 @@
+name: "vcf2db"
+description: A tool to create a Gemini-compatible DB file from an annotated VCF
+keywords:
+  - vcf2db
+  - vcf
+  - gemini
+tools:
+  - "vcf2db":
+      description: "Create a gemini-compatible database from a VCF"
+      homepage: "https://github.com/quinlan-lab/vcf2db"
+      documentation: "https://github.com/quinlan-lab/vcf2db"
+      tool_dev_url: "https://github.com/quinlan-lab/vcf2db"
+      doi: ""
+      licence: "['MIT']"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - vcf:
+      type: file
+      description: VCF file
+      pattern: "*.vcf.gz"
+  - ped:
+      type: file
+      description: PED file
+      pattern: "*.ped"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - db:
+      type: file
+      description: Gemini-compatible database file
+      pattern: "*.db"
+
+authors:
+  - "@nvnieuwk"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index 198785e6..63cd0f39 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -2140,6 +2140,10 @@ variantbam:
   - modules/variantbam/**
   - tests/modules/variantbam/**
 
+vcf2db:
+  - modules/vcf2db/**
+  - tests/modules/vcf2db/**
+
 vcfanno:
   - modules/vcfanno/**
   - tests/modules/vcfanno/**
diff --git a/tests/modules/vcf2db/main.nf b/tests/modules/vcf2db/main.nf
new file mode 100644
index 00000000..0d4be5d2
--- /dev/null
+++ b/tests/modules/vcf2db/main.nf
@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { VCF2DB } from '../../../modules/vcf2db/main.nf'
+
+workflow test_vcf2db {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['genome']['justhusky_minimal_vcf_gz'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['genome']['justhusky_ped'], checkIfExists: true)
+    ]
+
+    VCF2DB ( input )
+}
diff --git a/tests/modules/vcf2db/nextflow.config b/tests/modules/vcf2db/nextflow.config
new file mode 100644
index 00000000..50f50a7a
--- /dev/null
+++ b/tests/modules/vcf2db/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    
+}
\ No newline at end of file
diff --git a/tests/modules/vcf2db/test.yml b/tests/modules/vcf2db/test.yml
new file mode 100644
index 00000000..df276b1c
--- /dev/null
+++ b/tests/modules/vcf2db/test.yml
@@ -0,0 +1,6 @@
+- name: vcf2db test_vcf2db
+  command: nextflow run ./tests/modules/vcf2db -entry test_vcf2db -c ./tests/config/nextflow.config -c ./tests/modules/vcf2db/nextflow.config
+  tags:
+    - vcf2db
+  files:
+    - path: output/vcf2db/test.db