Add bwa index

software/bwa/index/functions.nf

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

software/bwa/index/main.nf

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+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+process BWA_INDEX {
+    tag "$fasta"
+    label 'process_high'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:'') }
+
+    container "biocontainers/bwa:v0.7.17_cv1"
+    //container "https://depot.galaxyproject.org/singularity/bwa:0.7.17--hed695b0_7"
+
+    conda (params.conda ? "bioconda::bwa=0.7.17" : null)
+
+    input:
+    path fasta
+    val options
+
+    output:
+    path "${fasta}.*", emit: index
+    path "*.version.txt", emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def ioptions = initOptions(options)
+    """
+    bwa index $ioptions.args $fasta
+    echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//' > ${software}.version.txt
+    """
+}