add initial bustools sort module

Fixes #946

Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com>

modules/bustools/sort/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+    // Do not publish versions.yml unless running from pytest workflow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/bustools/sort/main.nf

@@ -0,0 +1,60 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
+
+// TODO nf-core: If in doubt look at other nf-core/modules to see how we are doing things! :)
+//               https://github.com/nf-core/modules/tree/master/software
+//               You can also ask for help via your pull request or on the #modules channel on the nf-core Slack workspace:
+//               https://nf-co.re/join
+
+// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters.
+//               All other parameters MUST be provided as a string i.e. "options.args"
+//               where "params.options" is a Groovy Map that MUST be provided via the addParams section of the including workflow.
+//               Any parameters that need to be evaluated in the context of a particular sample
+//               e.g. single-end/paired-end data MUST also be defined and evaluated appropriately.
+// TODO nf-core: Software that can be piped together SHOULD be added to separate module files
+//               unless there is a run-time, storage advantage in implementing in this way
+//               e.g. it's ok to have a single module for bwa to output BAM instead of SAM:
+//                 bwa mem | samtools view -B -T ref.fasta
+// TODO nf-core: Optional inputs are not currently supported by Nextflow. However, using an empty
+//               list (`[]`) instead of a file can be used to work around this issue.
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process BUSTOOLS_SORT {
+    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::bustools=0.41.0" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/bustools:0.41.0--h60f4f9f_0"
+    } else {
+        container "quay.io/biocontainers/bustools:0.41.0--h60f4f9f_0"
+    }
+
+    input:
+    tuple val(meta), path(bus)
+
+    output:
+    tuple val(meta), path("${prefix}.sorted.bus"), emit: bus
+    path  "versions.yml"          , emit: versions
+
+    script:
+    prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    """
+    bustools sort \\
+        -o ${prefix}.sorted.bus \\
+        -t $task.cpus \\
+        -m ${task.memory.toGiga()}G \\
+        $options.args \\
+        $bus
+
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(bustools version | sed -e "s/bustools, version //g")
+    END_VERSIONS
+    """
+}

modules/bustools/sort/meta.yml

@@ -0,0 +1,48 @@
+name: bustools_sort
+## TODO nf-core: Add a description of the module and list keywords
+description: write your description here
+keywords:
+  - sort
+tools:
+  - bustools:
+      ## TODO nf-core: Add a description and other details for the software below
+      description: bustools is a program for manipulating BUS files for single cell RNA-Seq datasets.
+
+      homepage: None
+      documentation: None
+      tool_dev_url: None
+      doi: ""
+      licence: ['BSD 2-clause "Simplified" License']
+
+## TODO nf-core: Add a description of all of the variables used as input
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  ## TODO nf-core: Delete / customise this example input
+  - bam:
+      type: file
+      description: BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+
+## TODO nf-core: Add a description of all of the variables used as output
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+  ## TODO nf-core: Delete / customise this example output
+  - bam:
+      type: file
+      description: Sorted BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+
+authors:
+  - "@tkhalilullah"

tests/config/pytest_modules.yml

@@ -210,6 +210,10 @@ bowtie2/build:
   - modules/bowtie2/build/**
   - tests/modules/bowtie2/build_test/**
 
+bustools/sort:
+  - modules/bustools/sort/**
+  - tests/modules/bustools/sort/**
+
 bwa/aln:
   - modules/bwa/aln/**
   - tests/modules/bwa/aln/**

tests/modules/bustools/sort/main.nf

@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BUSTOOLS_SORT } from '../../../../modules/bustools/sort/main.nf' addParams( options: [:] )
+
+workflow test_bustools_sort {
+
+    input = [ [ id:'test' ], // meta map
+            file("https://raw.githubusercontent.com/BUStools/bustools/master/test/output.bus", checkIfExists: true) ]
+
+    BUSTOOLS_SORT ( input )
+}

tests/modules/bustools/sort/test.yml

@@ -0,0 +1,8 @@
+- name: bustools sort
+  command: nextflow run ./tests/modules/bustools/sort -entry test_bustools_sort -c tests/config/nextflow.config
+  tags:
+    - bustools
+    - bustools/sort
+  files:
+    - path: output/bustools/test.sorted.bus
+      md5sum: d8ffd0278af7de1c4e1ecafab18cc4d6