Add bwa mem

software/bwa/mem/functions.nf

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+../../lib/functions.nf

software/bwa/mem/main.nf

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+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+process BWA_MEM {
+    tag "$meta.id"
+    label 'process_high'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+
+    container "quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:eabfac3657eda5818bae4090db989e3d41b01542-0"
+    //container "https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:eabfac3657eda5818bae4090db989e3d41b01542-0"
+
+    conda (params.conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.10" : null)
+
+    input:
+    tuple val(meta), path(reads)
+    path index
+    path fasta
+    val options
+
+    output:
+    tuple val(meta), path("*.bam"), emit: bam
+    path "*.version.txt", emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def ioptions = initOptions(options)
+    def prefix   = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
+    def rg       = meta.read_group ? "-R ${meta.read_group}" : ""
+    """
+    bwa mem \\
+        $ioptions.args \\
+        $rg \\
+        -t $task.cpus \\
+        $fasta \\
+        $reads \\
+        | samtools view $ioptions.args2 -@ $task.cpus -bS -o ${prefix}.bam -
+
+    echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//' > ${software}.version.txt
+    """
+}