added pilon process as of issue #5, and moved quast analysis to end

Author: hkaspersen

workflows/ASSEMBLY.nf

@@ -1,8 +1,9 @@
-include { UNICYCLER } from "${params.module_dir}/UNICYCLER.nf"
-include { QUAST } from "${params.module_dir}/QUAST.nf"
-include { BWA } from "${params.module_dir}/BWA.nf"
-include { SAMTOOLS } from "${params.module_dir}/SAMTOOLS.nf"
-include { BEDTOOLS } from "${params.module_dir}/BEDTOOLS.nf"
+include { UNICYCLER }	from "${params.module_dir}/UNICYCLER.nf"
+include { QUAST }	from "${params.module_dir}/QUAST.nf"
+include { BWA }		from "${params.module_dir}/BWA.nf"
+include { SAMTOOLS }	from "${params.module_dir}/SAMTOOLS.nf"
+include { BEDTOOLS }	from "${params.module_dir}/BEDTOOLS.nf"
+include { PILON }	from "${params.module_dir}/PILON.nf"
 
 workflow ASSEMBLY {
         // Channel
@@ -12,7 +13,6 @@ workflow ASSEMBLY {
 
 	// Assembly
 	UNICYCLER(reads_ch)
-	QUAST(UNICYCLER.out.quast_ch.collect())
 
 	// Generate channel
 	reads_ch.join(UNICYCLER.out.assembly_ch, by: 0)
@@ -22,4 +22,11 @@ workflow ASSEMBLY {
 	BWA(mapping_ch)
 	SAMTOOLS(BWA.out.samtools_ch)
 	BEDTOOLS(SAMTOOLS.out.bam_ch)
+
+	UNICYCLER.out.assembly_ch.join(SAMTOOLS.out.bam_ch, by: 0)
+		.set { pilon_ch }
+	
+	// Polishing and QC
+	PILON(pilon_ch)
+	QUAST(PILON.out.quast_ch.collect())
 }