Add bamutil/trimbam (#1060)

* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* feat: add megahit module, currently decompressed output

* Update main.nf

* Update tests/modules/megahit/test.yml

Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>

* Apply suggestions from code review

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

* feat: compress all outputs, remove md5sums due to gz stochasicity

* fix: wrong conda channel for pigz

* fix: broken singleend tests and update meta.yml

* Missed one

* Apply suggestions from code review

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

* fix: pigz formatting

* Apply suggestions from code review

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

* Apply suggestions from code review

* Add bamUtil trimBam

* Update modules/bamutil/trimbam/main.nf

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

* Update modules/bamutil/trimbam/main.nf

* Changes after code-review

* YAML lint

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

modules/bamutil/trimbam/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/bamutil/trimbam/main.nf

@@ -0,0 +1,44 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process BAMUTIL_TRIMBAM {
+    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::bamutil=1.0.15" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/bamutil:1.0.15--h2e03b76_1"
+    } else {
+        container "quay.io/biocontainers/bamutil:1.0.15--h2e03b76_1"
+    }
+
+    input:
+    tuple val(meta), path(bam), val(trim_left), val(trim_right)
+
+    output:
+    tuple val(meta), path("*.bam"), emit: bam
+    path "versions.yml"           , emit: versions
+
+    script:
+    def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    """
+    bam \\
+        trimBam \\
+        $bam \\
+        ${prefix}.bam \\
+        $options.args \\
+        -L $trim_left \\
+        -R $trim_right
+
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$( echo \$( bam trimBam 2>&1 ) | sed 's/^Version: //;s/;.*//' )
+    END_VERSIONS
+    """
+}

modules/bamutil/trimbam/meta.yml

@@ -0,0 +1,51 @@
+name: bamutil_trimbam
+description: trims the end of reads in a SAM/BAM file, changing read ends to ‘N’ and quality to ‘!’, or by soft clipping
+keywords:
+  - bam
+  - trim
+  - clipping
+  - bamUtil
+  - trimBam
+tools:
+  - bamutil:
+      description: Programs that perform operations on SAM/BAM files, all built into a single executable, bam.
+      homepage: https://genome.sph.umich.edu/wiki/BamUtil
+      documentation: https://genome.sph.umich.edu/wiki/BamUtil:_trimBam
+      tool_dev_url: https://github.com/statgen/bamUtil
+      doi: "10.1101/gr.176552.114"
+      licence: ['GPL v3']
+
+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"
+  - trim_left:
+      type: integer
+      description: Number of bases to trim off the right-hand side of a read. Reverse strands are reversed before trimming.
+  - trim_right:
+      type: integer
+      description: Number of bases to trim off the right-hand side of a read. Reverse strands are reversed before trimming.
+
+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: Trimmed but unsorted BAM file
+      pattern: "*.bam"
+
+authors:
+  - "@jfy133"

tests/config/pytest_modules.yml

@@ -46,6 +46,10 @@ bamtools/split:
   - modules/bamtools/split/**
   - tests/modules/bamtools/split/**
 
+bamutil/trimbam:
+  - modules/bamutil/trimbam/**
+  - tests/modules/bamutil/trimbam/**
+
 bandage/image:
   - modules/bandage/image/**
   - tests/modules/bandage/image/**

tests/modules/bamutil/trimbam/main.nf

@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BAMUTIL_TRIMBAM } from '../../../../modules/bamutil/trimbam/main.nf' addParams( options: [:] )
+
+workflow test_bamutil_trimbam {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true),
+              2,
+              2 ]
+
+    BAMUTIL_TRIMBAM ( input )
+}

tests/modules/bamutil/trimbam/test.yml

@@ -0,0 +1,8 @@
+- name: bamutil trimbam test_bamutil_trimbam
+  command: nextflow run tests/modules/bamutil/trimbam -entry test_bamutil_trimbam -c tests/config/nextflow.config
+  tags:
+    - bamutil/trimbam
+    - bamutil
+  files:
+    - path: output/bamutil/test.bam
+      md5sum: 9ddd0ecca82f7f3433383f3d1308970e