Add alleleCounter module (#313)

* Add allelecount module

* Add bed file input

* Added bai file

* Changed conda version

* Update main.nf

* Update pytest_software.yml

* Update pytest_software.yml

* Update pytest_software.yml

* Update pytest_software.yml

* Update pytest_software.yml

* Update pytest_software.yml

* Update pytest_software.yml

* Update pytest_software.yml

* Update pytest_software.yml

* Update pytest_software.yml

* Add allelecount module

* Add bed file input

* Added bai file

* Changed conda version

* Update main.nf

* Update pytest_software.yml

* Update pytest_software.yml

* Update pytest_software.yml

* Update pytest_software.yml

* Update pytest_software.yml

* Update pytest_software.yml

* Remove newline

* Fix pytest_software.yml

* Update pytest_software.yml

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>

software/allelecounter/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/allelecounter/main.nf

@@ -0,0 +1,41 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process ALLELECOUNTER {
+    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), publish_id:meta.id) }
+
+    conda (params.enable_conda ? "bioconda::cancerit-allelecount=4.2.1" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/cancerit-allelecount:4.2.1--h3ecb661_0"
+    } else {
+        container "quay.io/biocontainers/cancerit-allelecount:4.2.1--h3ecb661_0"
+    }
+
+    input:
+    tuple val(meta), path(bam), path(bai)
+    path loci
+
+    output:
+    tuple val(meta), path("*.alleleCount"), emit: allelecount
+    path "*.version.txt"                  , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    """
+    alleleCounter \\
+        $options.args \\
+        -l $loci \\
+        -b $bam \\
+        -o ${prefix}.alleleCount
+
+    alleleCounter --version > ${software}.version.txt
+    """
+}

software/allelecounter/meta.yml

@@ -0,0 +1,52 @@
+name: allelecounter
+
+description: Generates a count of coverage of alleles
+keywords:
+  - allele
+  - count
+tools:
+  - allelecounter:
+      description: Takes a file of locations and a [cr|b]am file and generates a count of coverage of each allele at that location (given any filter settings)
+      homepage: https://github.com/cancerit/alleleCount
+      documentation: https://github.com/cancerit/alleleCount
+      tool_dev_url: https://github.com/cancerit/alleleCount
+      doi: ""
+      licence: A-GPL 3.0
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+  - bai:
+      type: file
+      description: BAM/CRAM/SAM index file
+      pattern: "*.{bai,crai,sai}"
+  - loci:
+      type: file
+      description: loci file <CHR><tab><POS1>
+      pattern: "*.{tsv}"
+
+
+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}"
+  - alleleCount:
+      type: file
+      description: Allele count file
+      pattern: "*.{alleleCount}"
+
+authors:
+  - "@fullama"

tests/config/pytest_software.yml

@@ -2,6 +2,10 @@ adapterremoval:
   - software/adapterremoval/**
   - tests/software/adapterremoval/**
 
+allelecounter:
+  - software/allelecounter/**
+  - tests/software/allelecounter/**
+
 bandage_image:
   - software/bandage/image/**
   - tests/software/bandage/image/**

tests/software/allelecounter/main.nf

@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+nextflow.enable.dsl = 2
+
+include { ALLELECOUNTER } from '../../../software/allelecounter/main.nf' addParams( options: [:] )
+
+workflow test_allelecounter {
+
+    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)]
+    positions = [ file("${launchDir}/tests/data/genomics/sarscov2/bed/test.bed", checkIfExists: true) ]
+    ALLELECOUNTER ( input, positions )
+}

tests/software/allelecounter/test.yml

@@ -0,0 +1,7 @@
+- name: allelecounter test_allelecounter
+  command: nextflow run tests/software/allelecounter -entry test_allelecounter -c tests/config/nextflow.config
+  tags:
+    - allelecounter
+  files:
+    - path: output/allelecounter/test.alleleCount
+      md5sum: 2bbe9d7331b78bdac30fe30dbc5fdaf3