added pilon process, as of issue #5

Author: hkaspersen

modules/PILON.nf

@@ -0,0 +1,16 @@
+process PILON {
+	publishDir "${params.out_dir}/02_ASSEMBLY/05_polished_genomes", pattern: "${datasetID}_pilon.fasta", mode: "copy"
+
+        tag "$datasetID"
+
+        input:
+        tuple val(datasetID), file(fasta), file(bam)
+
+        output:
+	file("${datasetID}_pilon.fasta")
+
+        """
+	export _JAVA_OPTIONS="-Xms512M -Xmx2G"
+	pilon --threads $task.cpus --genome $fasta --bam $bam --output ${datasetID}_pilon --changes --vcfqe
+        """
+}