ucsc_bed12tobigbed (previous pull request had conflicts) (#302)

* Add files via upload

* Add files via upload

* Add files via upload

* Add files via upload

* Update pytest_software.yml

* Update main.nf

* fix linting error

* Delete test.yml

* Create functions.nf

* Update main.nf

* change test data

* revert to !>=20.11.0-edge

software/ucsc/bed12tobigbed/functions.nf

@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/ucsc/bed12tobigbed/main.nf

@@ -0,0 +1,41 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+def options    = initOptions(params.options)
+
+def VERSION = '377'
+
+process UCSC_BED12TOBIGBED {
+    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::ucsc-bedtobigbed=377" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/ucsc-bedtobigbed:377--h446ed27_1"
+    } else {
+        container "quay.io/biocontainers/ucsc-bedtobigbed:377--h446ed27_1"
+    }
+
+    input:
+    tuple val(meta), path(bed)
+    path  sizes
+
+    output:
+    tuple val(meta), path("*.bigBed"), emit: bigbed
+    path "*.version.txt"             , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    """
+    bedToBigBed \\
+        $bed \\
+        $sizes \\
+        ${prefix}.bigBed
+    echo $VERSION > ${software}.version.txt
+    """
+}

tests/config/pytest_software.yml

@@ -415,6 +415,10 @@ trimgalore:
   - software/trimgalore/**
   - tests/software/trimgalore/**
 
+ucsc_bed12tobigbed:
+  - software/ucsc/bed12tobigbed/**
+  - tests/software/ucsc/bed12tobigbed/**
+
 ucsc_bedgraphtobigwig:
   - software/ucsc/bedgraphtobigwig/**
   - tests/software/ucsc/bedgraphtobigwig/**

tests/data/generic/sizes/test.sizes

@@ -0,0 +1 @@
+chr7	159138663

tests/data/genomics/sarscov2/bed/test.bed12

@@ -0,0 +1,4 @@
+MT192765.1	1242	1264	nCoV-2019_5_LEFT	1	+	1242	1264	0	2	10,12,	0,10,
+MT192765.1	1573	1595	nCoV-2019_6_LEFT	2	+	1573	1595	0	2	7,15,	0,7,
+MT192765.1	1623	1651	nCoV-2019_5_RIGHT	1	-	1623	1651	0	2	14,14,	0,14,
+MT192765.1	1942	1964	nCoV-2019_6_RIGHT	2	-	1942	1964	0	2	11,11	0,11,

tests/software/ucsc/bed12tobigbed/main.nf

@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { UCSC_BED12TOBIGBED } from '../../../../software/ucsc/bed12tobigbed/main.nf' addParams( options: [:] )
+
+workflow test_ucsc_bed12tobigbed {
+
+    def input = []
+    input = [ [ id: 'test' ], // meta map 
+              [ file("${launchDir}/tests/data/genomics/sarscov2/bed/test.bed12", checkIfExists: true )] ]
+    sizes = file("${launchDir}/tests/data/genomics/sarscov2/general/test.genome.sizes", checkIfExists: true)
+
+    UCSC_BED12TOBIGBED ( input, sizes )
+}

tests/software/ucsc/bed12tobigbed/test.yml

@@ -0,0 +1,7 @@
+- name: ucsc bed12tobigbed
+  command: nextflow run ./tests/software/ucsc/bed12tobigbed -entry test_ucsc_bed12tobigbed -c tests/config/nextflow.config
+  tags:
+    - ucsc_bed12tobigbed
+  files:
+    - path: output/ucsc/test.bigBed
+      md5sum: 98cf0d0baa3ae5a330c80afbb8bc2b18