add samtools merge (#296)

* add samtools merge

* Update pytest_software.yml

* get it back to 20.11.0-edge

* Update test.yml

* Update test.yml

* Update test.yml

* Update test.yml

software/samtools/merge/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/samtools/merge/main.nf

@@ -0,0 +1,35 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process SAMTOOLS_MERGE {
+    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::samtools=1.10" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
+    } else {
+        container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
+    }
+
+    input:
+    tuple val(meta),path(bams)
+
+    output:
+    tuple val(meta), path("*merged.bam"), emit: merged_bam
+    path  "*.version.txt"              , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    """
+    samtools merge ${prefix}_merged.bam $bams
+    echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt
+    """
+}

tests/config/pytest_software.yml

@@ -295,6 +295,10 @@ samtools_mpileup:
   - software/samtools/mpileup/**
   - tests/software/samtools/mpileup/**
 
+samtools_merge:
+  - software/samtools/merge/**
+  - tests/software/samtools/merge/**
+
 samtools_sort:
   - software/samtools/sort/**
   - tests/software/samtools/sort/**

tests/software/samtools/merge/main.nf

@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SAMTOOLS_MERGE } from '../../../../software/samtools/merge/main.nf' addParams( options: [:] )
+
+workflow test_samtools_merge {
+
+    def input = []
+    input = [ [ id: 'test' ], // meta map 
+              [ file("${launchDir}/tests/data/genomics/sarscov2/bam/test_methylated_paired_end.sorted.bam", checkIfExists: true ),
+                file("${launchDir}/tests/data/genomics/sarscov2/bam/test_paired_end.sorted.bam", checkIfExists: true),
+                file("${launchDir}/tests/data/genomics/sarscov2/bam/test_single_end.sorted.bam", checkIfExists: true) ] ]
+
+    SAMTOOLS_MERGE ( input )
+}

tests/software/samtools/merge/test.yml

@@ -0,0 +1,7 @@
+- name: samtools merge
+  command: nextflow run ./tests/software/samtools/merge -entry test_samtools_merge -c tests/config/nextflow.config
+  tags:
+    - samtools
+    - samtools_merge
+  files:
+    - path: output/samtools/test_merged.bam