contigs_input(wildcards)

assembly.smk

@@ -93,3 +93,9 @@ rule metaspades:
 		"-i work/metaSPADES/{wildcards.reads}/contigs.fasta "
 		"-o {output.contigs} "
 		"--min-length {params.min_len} "
+
+def contigs_input(wildcards):
+	if config["ASSEMBLER"] == "megahit":
+		return ["work/megahit/{wildcards.sample}/{wildcards.sample}.contigs.fa".format(wildcards=wildcards)]
+	elif config["ASSEMBLER"] == "metaspades":
+		return ["work/metaSPADES/{wildcards.sample}/{wildcards.sample}.contigs.fasta".format(wildcards=wildcards)]

global.smk

@@ -8,6 +8,7 @@ rule all:
 	input:
 		"report/multiqc_report.html",
 		expand("report/reads_{sample}-krona.html", sample=config["SAMPLES"]),
+		"report/contigs_coassembly-taxNames.tsv",
 
 include: "../workflow_metagenomics/quality.smk"
 include: "../workflow_metagenomics/preprocess.smk"