From f44e6c74b4c51c5e49bc91e3d9d225544b5c1685 Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Fri, 4 Feb 2022 15:29:44 +0100
Subject: [PATCH] Add svdb/merge (#1233)

* nf-core create

* svdb merge module and test

* remove to-do from test.yml

* version

* update meta.yml

* add stub

* add when
---
 modules/svdb/merge/main.nf               | 52 ++++++++++++++++++++++++
 modules/svdb/merge/meta.yml              | 39 ++++++++++++++++++
 tests/config/pytest_modules.yml          |  4 ++
 tests/modules/svdb/merge/main.nf         | 16 ++++++++
 tests/modules/svdb/merge/nextflow.config |  5 +++
 tests/modules/svdb/merge/test.yml        |  7 ++++
 6 files changed, 123 insertions(+)
 create mode 100644 modules/svdb/merge/main.nf
 create mode 100644 modules/svdb/merge/meta.yml
 create mode 100644 tests/modules/svdb/merge/main.nf
 create mode 100644 tests/modules/svdb/merge/nextflow.config
 create mode 100644 tests/modules/svdb/merge/test.yml

diff --git a/modules/svdb/merge/main.nf b/modules/svdb/merge/main.nf
new file mode 100644
index 00000000..1f479ea4
--- /dev/null
+++ b/modules/svdb/merge/main.nf
@@ -0,0 +1,52 @@
+process SVDB_MERGE {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::svdb=2.5.0" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/svdb:2.5.0--py39hcbe4a3b_0':
+        'quay.io/biocontainers/svdb:2.5.0--py39hcbe4a3b_0' }"
+
+    input:
+    tuple val(meta), path(vcfs)
+    val (priority)
+
+    output:
+    tuple val(meta), path("*_sv_merge.vcf"), emit: vcf
+    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 input  = ""
+    for (int index = 0; index < vcfs.size(); index++) {
+        input += " ${vcfs[index]}:${priority[index]}"
+    }
+    """
+    svdb \\
+        --merge \\
+        $args \\
+        --priority ${priority.join(',')} \\
+        --vcf $input \\
+        > ${prefix}_sv_merge.vcf
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        svdb: \$( echo \$(svdb) | head -1 | sed 's/usage: SVDB-\\([0-9]\\.[0-9]\\.[0-9]\\).*/\\1/' )
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_sv_merge.vcf
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        svdb: \$( echo \$(svdb) | head -1 | sed 's/usage: SVDB-\\([0-9]\\.[0-9]\\.[0-9]\\).*/\\1/' )
+    END_VERSIONS
+    """
+}
diff --git a/modules/svdb/merge/meta.yml b/modules/svdb/merge/meta.yml
new file mode 100644
index 00000000..2092ddd9
--- /dev/null
+++ b/modules/svdb/merge/meta.yml
@@ -0,0 +1,39 @@
+name: svdb_merge
+description: The merge module merges structural variants within one or more vcf files.
+keywords:
+  - structural variants
+tools:
+  - svdb:
+      description: structural variant database software
+      homepage: https://github.com/J35P312/SVDB
+      documentation: https://github.com/J35P312/SVDB/blob/master/README.md
+      licence: ['MIT']
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test' ]
+  - priority:
+      type: list
+      description: prioritise the input vcf files according to this list, e.g ['tiddit','cnvnator']
+  - vcfs:
+      type: list
+      description: Two or more VCF files. Order of files should correspond to the order of tags used for priority.
+      pattern: "*.{vcf,vcf.gz}"
+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"
+  - vcf:
+      type: file
+      description: merged VCF file
+      pattern: "*_sv_merge.vcf"
+authors:
+  - "@ramprasadn"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index b6b906f4..203005da 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -1445,6 +1445,10 @@ subread/featurecounts:
   - modules/subread/featurecounts/**
   - tests/modules/subread/featurecounts/**
 
+svdb/merge:
+  - modules/svdb/merge/**
+  - tests/modules/svdb/merge/**
+
 svdb/query:
   - modules/svdb/query/**
   - tests/modules/svdb/query/**
diff --git a/tests/modules/svdb/merge/main.nf b/tests/modules/svdb/merge/main.nf
new file mode 100644
index 00000000..f417c3f7
--- /dev/null
+++ b/tests/modules/svdb/merge/main.nf
@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SVDB_MERGE } from '../../../../modules/svdb/merge/main.nf'
+
+workflow test_svdb_merge {
+
+    input = [ [ id:'test' ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test2_vcf'], checkIfExists: true) ]
+            ]
+    priority = [ 'tiddit', 'cnvnator']
+
+    SVDB_MERGE ( input, priority )
+}
diff --git a/tests/modules/svdb/merge/nextflow.config b/tests/modules/svdb/merge/nextflow.config
new file mode 100644
index 00000000..50f50a7a
--- /dev/null
+++ b/tests/modules/svdb/merge/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/svdb/merge/test.yml b/tests/modules/svdb/merge/test.yml
new file mode 100644
index 00000000..8d16562f
--- /dev/null
+++ b/tests/modules/svdb/merge/test.yml
@@ -0,0 +1,7 @@
+- name: svdb merge
+  command: nextflow run ./tests/modules/svdb/merge -entry test_svdb_merge -c ./tests/config/nextflow.config -c ./tests/modules/svdb/merge/nextflow.config
+  tags:
+    - svdb
+    - svdb/merge
+  files:
+    - path: output/svdb/test_sv_merge.vcf