New module: pbbam/pbmerge (#752)

* 👌 IMPROVE: Add some pacbio test files

* 📦 NEW: Add pbbam/pbmerge module

* 🐛 FIX: Add optional arguments to command line

* 👌 IMPROVE: Update to last templates version

* 👌 IMPROVE: Update module to last template version

* 👌 IMPROVE: Update test data config and test script

* 👌 IMPROVE: Remove useless index + Fix Typos

* 👌 IMPROVE: Add some pacbio test files

* 📦 NEW: Add pbbam/pbmerge module

* 🐛 FIX: Add optional arguments to command line

* 👌 IMPROVE: Update to last templates version

* 👌 IMPROVE: Update module to last template version

* 👌 IMPROVE: Update test data config and test script

* 👌 IMPROVE: Remove useless index + Fix Typos

* 👌 IMPROVE: Update and clean code

* 🐛 FIX: Update module path in test

* 🐛 FIX: Add missing () + correct module path in test

* 👌 IMPROVE: Update pbmerge from version 1.6.0 to 1.7.0

* 👌 IMPROVE: Change output filename suffix for something more generic

* 🐛 Update test.yml

* Apply suggestions from code review

* Update tests/modules/pbbam/pbmerge/test.yml

* Update tests/modules/pbbam/pbmerge/main.nf

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

modules/pbbam/pbmerge/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/pbbam/pbmerge/main.nf

@@ -0,0 +1,42 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process PBBAM_PBMERGE {
+    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::pbbam=1.7.0" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/pbbam:1.7.0--h058f120_1"
+    } else {
+        container "quay.io/biocontainers/pbbam:1.7.0--h058f120_1"
+    }
+
+    input:
+    tuple val(meta), path(bam)
+
+    output:
+    tuple val(meta), path("*.bam"), emit: bam
+    tuple val(meta), path("*.pbi"), emit: pbi
+    path "versions.yml"           , emit: versions
+
+    script:
+    def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    """
+    pbmerge \\
+        -o ${prefix}.bam \\
+        $options.args \\
+        *.bam
+
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        pbbam/pbmerge: \$( pbmerge --version|sed 's/pbmerge //' )
+    END_VERSIONS
+    """
+}

modules/pbbam/pbmerge/meta.yml

@@ -0,0 +1,46 @@
+name: pbbam_pbmerge
+description: The pbbam software package provides components to create, query, & edit PacBio BAM files and associated indices. These components include a core C++ library, bindings for additional languages, and command-line utilities.
+keywords:
+  - pbbam
+  - pbbam/pbmerge
+tools:
+  - pbbam:
+      description: PacBio BAM C++ library
+      homepage: https://github.com/PacificBiosciences/pbbioconda
+      documentation: https://pbbam.readthedocs.io/en/latest/tools/pbmerge.html
+      tool_dev_url: https://github.com/pacificbiosciences/pbbam/
+      doi: ""
+      licence: ['BSD-3-clause-Clear']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: BAM files to merge
+      pattern: "*.bam"
+
+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"
+  - bam:
+      type: file
+      description: The merged bam file
+      pattern: "*.bam"
+  - pbi:
+      type: file
+      description: BAM Pacbio index file
+      pattern: "*.bam.pbi"
+
+authors:
+  - "@sguizard"

tests/config/pytest_modules.yml

@@ -731,6 +731,10 @@ pangolin:
   - modules/pangolin/**
   - tests/modules/pangolin/**
 
+pbbam/pbmerge:
+  - modules/pbbam/pbmerge/**
+  - tests/modules/pbbam/pbmerge/**
+
 pbccs:
   - modules/pbccs/**
   - tests/modules/pbccs/**

tests/modules/pbbam/pbmerge/main.nf

@@ -0,0 +1,18 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PBBAM_PBMERGE } from '../../../../modules/pbbam/pbmerge/main.nf' addParams( options: [suffix: '.merged'] )
+
+workflow test_pbbam_pbmerge {
+
+    input = [
+        [ id:'test' ], // meta map
+        [
+            file(params.test_data['homo_sapiens']['pacbio']['cluster']   , checkIfExists: true),
+            file(params.test_data['homo_sapiens']['pacbio']['singletons'], checkIfExists: true)
+        ]
+    ]
+
+    PBBAM_PBMERGE ( input )
+}

tests/modules/pbbam/pbmerge/test.yml

@@ -0,0 +1,10 @@
+- name: pbbam pbmerge test_pbbam_pbmerge
+  command: nextflow run tests/modules/pbbam/pbmerge -entry test_pbbam_pbmerge -c tests/config/nextflow.config
+  tags:
+    - pbbam/pbmerge
+    - pbbam
+  files:
+    - path: output/pbbam/test.merged.bam
+      md5sum: 727c7ba1289192085c06890dda70f973
+    - path: output/pbbam/test.merged.bam.pbi
+      md5sum: edfadd3a81c598d1ee051899792db75d