assembly done

assembly.smk

@@ -49,7 +49,8 @@ rule megahit:
 	input:
 		unpack(assembly_input)
 	output:
-		contigs = "work/megahit/{reads}/{reads}.contigs.fa"
+		contigs = "work/megahit/{reads}/{reads}.contigs.fa",
+		done = "work/megahit/{reads}/done"
 	threads:
 		20
 	params:
@@ -74,7 +75,8 @@ rule metaspades:
 	input:
 		unpack(assembly_input)
 	output:
-		contigs = "work/metaSPADES/{reads}/{reads}.contigs.fasta"
+		contigs = "work/metaSPADES/{reads}/{reads}.contigs.fasta",
+		done = "work/metaSPADES/{reads}/done"
 	threads:
 		20
 	params:
@@ -91,6 +93,8 @@ rule metaspades:
 		"{params.input} "
 		"-o {params.output} "
 		" ; "
+		" touch {output.done} "
+		" ; "
 		"conda activate seqkit-0.10.1 "
 		" ; "
 		"seqkit "