add picard_collectwgsmetrics (#304)

* Added new module picard/collectwgsmetrics.

* Removed unused outputs from meta.yml

* Added version.txt file back to meta.yml

* Updated test.yml

* Removed md5sum from test.yaml and added contain tests.

* Update functions.nf

Fixed missing newline formatting.

* Update main.nf

Fixed missing newline formatting.

* style(picard): Remove trailing whitespace

Co-authored-by: Kevin Menden <kevin.menden@t-online.de>
Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com>

software/picard/collectwgsmetrics/functions.nf

@@ -0,0 +1,60 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.args3         = args.args3 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/picard/collectwgsmetrics/main.nf

@@ -0,0 +1,49 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process PICARD_COLLECTWGSMETRICS {
+    tag "$meta.id"
+    label 'process_medium'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+
+    conda (params.enable_conda ? "bioconda::picard=2.25.0" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/picard:2.25.0--0"
+    } else {
+        container "quay.io/biocontainers/picard:2.25.0--0"
+    }
+
+    input:
+    tuple val(meta), path(bam), path(bai)
+    path  fasta
+
+    output:
+    tuple val(meta), path("*_metrics"), emit: metrics
+    path  "*.version.txt"             , emit: version
+
+    script:
+    def software  = getSoftwareName(task.process)
+    def prefix    = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def avail_mem = 3
+    if (!task.memory) {
+        log.info '[Picard CollectWgsMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = task.memory.giga
+    }
+    """
+    picard \\
+        -Xmx${avail_mem}g \\
+        CollectWgsMetrics \\
+        $options.args \\
+        INPUT=$bam \\
+        OUTPUT=${prefix}.CollectWgsMetrics.coverage_metrics \\
+        REFERENCE_SEQUENCE=$fasta
+
+    echo \$(picard CollectWgsMetrics --version 2>&1) | grep -o 'Version.*' | cut -f2- -d: > ${software}.version.txt
+    """
+}

software/picard/collectwgsmetrics/meta.yml

@@ -0,0 +1,46 @@
+name: picard_collectwgsmetrics
+description: Collect metrics about coverage and performance of whole genome sequencing (WGS) experiments.
+keywords:
+    - alignment
+    - metrics
+    - statistics
+    - quality
+    - bam
+tools:
+    - picard:
+        description: |
+            A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)
+            data and formats such as SAM/BAM/CRAM and VCF.
+        homepage: https://broadinstitute.github.io/picard/
+        documentation: https://broadinstitute.github.io/picard/
+input:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - bam:
+        type: file
+        description: BAM file
+        pattern: "*.{bam}"
+    - fasta:
+        type: file
+        description: Genome fasta file
+output:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - metrics:
+        type: file
+        description: Alignment metrics files generated by picard
+        pattern: "*_{metrics}"
+    - version:
+        type: file
+        description: File containing software version
+        pattern: "*.{version.txt}"
+authors:
+    - "@drpatelh"
+    - "@flowuenne"
+    - "@lassefolkersen"

tests/config/pytest_software.yml

@@ -76,6 +76,11 @@ bismark_methylation_extractor:
   - software/bismark/genome_preparation/**
   - tests/software/bismark/methylation_extractor/**
 
+
+blast_blastn:
+  - software/blast/blastn/**
+  - tests/software/blast/blastn/**
+
 bismark_report:
   - software/bismark/genome_preparation/**
   - software/bismark/align/**
@@ -96,27 +101,23 @@ blast_makeblastdb:
   - software/blast/makeblastdb/**
   - tests/software/blast/makeblastdb/**
 
-blast_blastn:
+bowtie2_align:
-  - software/blast/blastn/**
+  - software/bowtie2/align/**
-  - tests/software/blast/blastn/**
+  - software/bowtie2/build/**
+  - tests/software/bowtie2/align/**
 
-bowtie_build:
+bowtie2_build:
-  - software/bowtie/build/**
+  - software/bowtie2/build/**
-  - tests/software/bowtie/build_test/**
+  - tests/software/bowtie2/build_test/**
 
 bowtie_align:
   - software/bowtie/align/**
   - software/bowtie/build/**
   - tests/software/bowtie/align/**
 
-bowtie2_build:
+bowtie_build:
-  - software/bowtie2/build/**
+  - software/bowtie/build/**
-  - tests/software/bowtie2/build_test/**
+  - tests/software/bowtie/build_test/**
-
-bowtie2_align:
-  - software/bowtie2/align/**
-  - software/bowtie2/build/**
-  - tests/software/bowtie2/align/**
 
 bwa_index:
   - software/bwa/index/**
@@ -255,6 +256,10 @@ picard_collectmultiplemetrics:
   - software/picard/collectmultiplemetrics/**
   - tests/software/picard/collectmultiplemetrics/**
 
+picard_collectwgsmetrics:
+  - software/picard/collectwgsmetrics/**
+  - tests/software/picard/collectwgsmetrics/**
+
 picard_markduplicates:
   - software/picard/markduplicates/**
   - tests/software/picard/markduplicates/**
@@ -370,4 +375,3 @@ ucsc_bedgraphtobigwig:
 untar:
   - software/untar/**
   - tests/software/untar/**
-

tests/software/picard/collectwgsmetrics/main.nf

@@ -0,0 +1,18 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PICARD_COLLECTWGSMETRICS } from '../../../../software/picard/collectwgsmetrics/main.nf' addParams( options: [:] )
+
+workflow test_picard_collectwgsmetrics {
+    
+    def input = []
+    input = [ [ id:'test', single_end:false ], // meta map
+              file("${launchDir}/tests/data/genomics/sarscov2/bam/test_paired_end.sorted.bam", checkIfExists: true),
+            file("${launchDir}/tests/data/genomics/sarscov2/bam/test_paired_end.sorted.bam.bai", checkIfExists: true),]
+
+    PICARD_COLLECTWGSMETRICS ( 
+        input,
+        file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) 
+        )
+}

tests/software/picard/collectwgsmetrics/test.yml

@@ -0,0 +1,11 @@
+- name: picard collectwgsmetrics test_picard_collectwgsmetrics
+  command: nextflow run tests/software/picard/collectwgsmetrics -entry test_picard_collectwgsmetrics -c tests/config/nextflow.config
+  tags:
+    - picard_collectwgsmetrics
+    - picard
+  files:
+    - path: output/picard/test.CollectWgsMetrics.coverage_metrics
+      contains:
+        - "GENOME_TERRITORY"
+        - "29829"
+        - "17554"