From 1a4ab76618a2269ee653aefff8a5ee1f855e5f83 Mon Sep 17 00:00:00 2001
From: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
Date: Tue, 14 Jun 2022 16:02:18 +0200
Subject: [PATCH] new module rtgtools/pedfilter (#1777)

* new module rtgtools/pedfilter

* removed checksum due to the presence of a date in the file
---
 modules/rtgtools/pedfilter/main.nf            | 37 +++++++++++++++
 modules/rtgtools/pedfilter/meta.yml           | 45 +++++++++++++++++++
 tests/config/pytest_modules.yml               |  4 ++
 tests/modules/rtgtools/pedfilter/main.nf      | 15 +++++++
 .../rtgtools/pedfilter/nextflow.config        |  5 +++
 tests/modules/rtgtools/pedfilter/test.yml     |  7 +++
 6 files changed, 113 insertions(+)
 create mode 100644 modules/rtgtools/pedfilter/main.nf
 create mode 100644 modules/rtgtools/pedfilter/meta.yml
 create mode 100644 tests/modules/rtgtools/pedfilter/main.nf
 create mode 100644 tests/modules/rtgtools/pedfilter/nextflow.config
 create mode 100644 tests/modules/rtgtools/pedfilter/test.yml

diff --git a/modules/rtgtools/pedfilter/main.nf b/modules/rtgtools/pedfilter/main.nf
new file mode 100644
index 00000000..9045b5b8
--- /dev/null
+++ b/modules/rtgtools/pedfilter/main.nf
@@ -0,0 +1,37 @@
+process RTGTOOLS_PEDFILTER {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::rtg-tools=3.12.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/rtg-tools:3.12.1--hdfd78af_0':
+        'quay.io/biocontainers/rtg-tools:3.12.1--hdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(ped)
+
+    output:
+    tuple val(meta), path("*.vcf.gz"), 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}"
+
+    """
+    rtg pedfilter \\
+        $ped \\
+        --vcf \\
+        > ${prefix}.vcf
+
+    gzip ${prefix}.vcf
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        rtgtools: \$(echo \$(rtg version | head -n 1 | awk '{print \$4}'))
+    END_VERSIONS
+    """
+}
diff --git a/modules/rtgtools/pedfilter/meta.yml b/modules/rtgtools/pedfilter/meta.yml
new file mode 100644
index 00000000..826f8558
--- /dev/null
+++ b/modules/rtgtools/pedfilter/meta.yml
@@ -0,0 +1,45 @@
+name: "rtgtools_pedfilter"
+description: Converts a PED file to VCF headers
+keywords:
+  - rtgtools
+  - pedfilter
+  - vcf
+tools:
+  - "rtgtools":
+      description: "RealTimeGenomics Tools -- Utilities for accurate VCF comparison and manipulation"
+      homepage: "https://www.realtimegenomics.com/products/rtg-tools"
+      documentation: "https://github.com/RealTimeGenomics/rtg-tools"
+      tool_dev_url: "https://github.com/RealTimeGenomics/rtg-tools"
+      doi: ""
+      licence: "['BSD']"
+
+input:
+  # Only when we have meta
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - ped:
+      type: file
+      description: PED file
+      pattern: "*.ped"
+
+output:
+  #Only when we have meta
+  - 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"
+  - vcf:
+      type: file
+      description: VCF file containing only headers fetched from the PED file
+      pattern: "*.vcf.gz"
+
+authors:
+  - "@nvnieuwk"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index c136b58c..0e82d01a 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -1739,6 +1739,10 @@ rseqc/tin:
   - modules/rseqc/tin/**
   - tests/modules/rseqc/tin/**
 
+rtgtools/pedfilter:
+  - modules/rtgtools/pedfilter/**
+  - tests/modules/rtgtools/pedfilter/**
+
 rtgtools/vcfeval:
   - modules/rtgtools/vcfeval/**
   - tests/modules/rtgtools/vcfeval/**
diff --git a/tests/modules/rtgtools/pedfilter/main.nf b/tests/modules/rtgtools/pedfilter/main.nf
new file mode 100644
index 00000000..a8361e6d
--- /dev/null
+++ b/tests/modules/rtgtools/pedfilter/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { RTGTOOLS_PEDFILTER } from '../../../../modules/rtgtools/pedfilter/main.nf'
+
+workflow test_rtgtools_pedfilter {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['genome']['justhusky_ped'], checkIfExists: true)
+    ]
+
+    RTGTOOLS_PEDFILTER ( input )
+}
diff --git a/tests/modules/rtgtools/pedfilter/nextflow.config b/tests/modules/rtgtools/pedfilter/nextflow.config
new file mode 100644
index 00000000..50f50a7a
--- /dev/null
+++ b/tests/modules/rtgtools/pedfilter/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/rtgtools/pedfilter/test.yml b/tests/modules/rtgtools/pedfilter/test.yml
new file mode 100644
index 00000000..cb0c29a3
--- /dev/null
+++ b/tests/modules/rtgtools/pedfilter/test.yml
@@ -0,0 +1,7 @@
+- name: rtgtools pedfilter test_rtgtools_pedfilter
+  command: nextflow run ./tests/modules/rtgtools/pedfilter -entry test_rtgtools_pedfilter -c ./tests/config/nextflow.config  -c ./tests/modules/rtgtools/pedfilter/nextflow.config
+  tags:
+    - rtgtools/pedfilter
+    - rtgtools
+  files:
+    - path: output/rtgtools/test.vcf.gz