Peddy nf core2 2dev0 (#1048)

* Updated module to fit nf-core2.2dev0 templates

* Updated module to fit nf-core2.2dev0 templates

* Linked test files to nf-core/test-dataset branch:raredisease raw files

* Change order of input: vcf and tbi with meta, ped without

* Change order of input: vcf and tbi with meta, ped without/adapt test

* Change order of input: vcf and tbi with meta, ped without/adapt test, bugfix

* Indent and rename files

* Update modules/peddy/main.nf

Removed newline

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>

* Update modules/peddy/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update modules/peddy/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update modules/peddy/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update modules/peddy/meta.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update modules/peddy/meta.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update modules/peddy/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update modules/peddy/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update pytest_modules.yml

* Update main.nf

* Apply suggestions from code review

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

modules/peddy/functions.nf

@@ -0,0 +1,78 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
+    if (ioptions.publish_by_meta) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+        for (key in key_list) {
+            if (args.meta && key instanceof String) {
+                def path = key
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
+            }
+        }
+    }
+    if (ioptions.publish_files instanceof Map) {
+        for (ext in ioptions.publish_files) {
+            if (args.filename.endsWith(ext.key)) {
+                def ext_list = path_list.collect()
+                ext_list.add(ext.value)
+                return "${getPathFromList(ext_list)}/$args.filename"
+            }
+        }
+    } else if (ioptions.publish_files == null) {
+        return "${getPathFromList(path_list)}/$args.filename"
+    }
+}

modules/peddy/main.nf

@@ -0,0 +1,47 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process PEDDY {
+    tag "$meta.id"
+    label 'process_low'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
+
+    conda (params.enable_conda ? "bioconda::peddy=0.4.8" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/peddy:0.4.8--pyh5e36f6f_0"
+    } else {
+        container "quay.io/biocontainers/peddy:0.4.8--pyh5e36f6f_0"
+    }
+
+    input:
+    tuple val(meta), path(vcf), path(vcf_tbi)
+    path ped
+
+    output:
+    tuple val(meta), path("*.html")     , emit: html
+    tuple val(meta), path("*.csv")      , emit: csv
+    tuple val(meta), path("*.peddy.ped"), emit: ped
+    tuple val(meta), path("*.png")      , emit: png
+    path "versions.yml"                 , emit: versions
+
+    script:
+    def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    """
+    peddy \\
+        $options.args \\
+        --plot \\
+        -p $task.cpus \\
+        $vcf \\
+        $ped
+
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$( peddy --version 2>&1 | sed 's/peddy, version //' )
+    END_VERSIONS
+    """
+}

modules/peddy/meta.yml

@@ -0,0 +1,64 @@
+name: peddy
+description: Manipulation, validation and exploration of pedigrees
+keywords:
+  - pedigrees
+  - ped
+  - family
+
+tools:
+  - peddy:
+      description: genotype, ped correspondence check, ancestry check, sex check. directly, quickly on VCF
+      homepage: https://github.com/brentp/peddy
+      documentation: https://peddy.readthedocs.io/en/latest/
+      tool_dev_url: https://github.com/brentp/peddy
+      doi: "https://doi.org/10.1016/j.ajhg.2017.01.017"
+      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/FAM file
+      pattern: "*.{ped,fam}"
+  - vcf_tbi:
+      type: file
+      description: TBI file
+      pattern: "*.{vcf.gz.tbi}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - ped:
+      type: file
+      description: PED/FAM file
+      pattern: "*.peddy.{ped}"
+  - html:
+      type: file
+      description: HTML file
+      pattern: "*.{html}"
+  - csv:
+      type: file
+      description: CSV file
+      pattern: "*.{csv}"
+  - png:
+      type: file
+      description: PNG file
+      pattern: "*.{png}"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@rannick"

tests/config/pytest_modules.yml

@@ -1019,6 +1019,10 @@ picard/collecthsmetrics:
   - modules/picard/collecthsmetrics/**
   - tests/modules/picard/collecthsmetrics/**
 
+peddy:
+  - modules/peddy/**
+  - tests/modules/peddy/**
+
 picard/collectmultiplemetrics:
   - modules/picard/collectmultiplemetrics/**
   - tests/modules/picard/collectmultiplemetrics/**

tests/config/test_data.config

@@ -128,6 +128,10 @@ params {
 
                 index_salmon                                   = "${test_data_dir}/genomics/homo_sapiens/genome/index/salmon"
                 repeat_expansions                              = "${test_data_dir}/genomics/homo_sapiens/genome/loci/repeat_expansions.json"
+                justhusky_ped                                  = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/ped/justhusky.ped"
+                justhusky_minimal_vcf_gz                       = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/ped/justhusky_minimal.vcf.gz"
+                justhusky_minimal_vcf_gz_tbi                   = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/ped/justhusky_minimal.vcf.gz.tbi"
+
             }
             'illumina' {
                 test_paired_end_sorted_bam                              = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam"

tests/modules/peddy/main.nf

@@ -0,0 +1,17 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PEDDY } from '../../../modules/peddy/main.nf' addParams( options: [:] )
+
+workflow test_peddy {
+
+    input = [
+        [ id:'test', single_end:false ],
+        file(params.test_data['homo_sapiens']['genome']['justhusky_minimal_vcf_gz'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['genome']['justhusky_minimal_vcf_gz_tbi'], checkIfExists: true)
+    ]
+    ped = file(params.test_data['homo_sapiens']['genome']['justhusky_ped'], checkIfExists: true)
+
+    PEDDY ( input , ped )
+}

tests/modules/peddy/test.yml

@@ -0,0 +1,17 @@
+- name: peddy test_peddy
+  command: nextflow run tests/modules/peddy -entry test_peddy -c tests/config/nextflow.config
+  tags:
+    - peddy
+  files:
+    - path: output/peddy/justhusky_minimal.het_check.csv
+      md5sum: f4006d47355f2a760e40215b403926c3
+    - path: output/peddy/justhusky_minimal.html
+      md5sum: 4f189cdbe8f03fe5c32d343c183506a5
+    - path: output/peddy/justhusky_minimal.ped_check.csv
+      md5sum: d79a98558e280afe794d1374d2b985d4
+    - path: output/peddy/justhusky_minimal.ped_check.rel-difference.csv
+      md5sum: 9de7e287cb30c742db2ff3622b0e63b1
+    - path: output/peddy/justhusky_minimal.sex_check.csv
+      md5sum: 60848489bc697490da6a53b5170baf3b
+    - path: output/peddy/justhusky_minimal.vs.html
+      md5sum: 20f5f3a97fa781057c876ac79e044010