biom_to_tsv

affiliation.smk

@@ -75,7 +75,7 @@ rule stdBIOM:
 		biom = "work/FROGS/affiliation.biom"
 	output:
 		biom = "work/FROGS/abundance.biom",
-		tsv = "work/FROGS/multihits.tsv"
+		tsv = "work/FROGS/blast_informations.std.tsv"
 	shell:
 		"conda activate frogs-3.2.0 "
 		"&& "
@@ -86,6 +86,24 @@ rule stdBIOM:
 		"&& "
 		"conda deactivate"
 
+rule biom_to_tsv:
+	input:
+		biom = "work/FROGS/affiliation.biom",
+		fasta = "work/dada/seqtab.fasta"
+	output:
+		tsv = "work/FROGS/abundance.tsv",
+		multi = "work/FROGS/multihits.tsv"
+	shell:
+		"conda activate frogs-3.2.0 "
+		"&& "
+		"biom_to_tsv.py "
+		"--input-biom {input.biom} "
+		"--input-fasta {input.fasta} "
+		"--output-tsv {output.tsv} "
+		"--output-multi-affi {output.multi}"
+		"&& "
+		"conda deactivate"
+
 localrules: copy
 rule copy:
 	input:

global.smk

@@ -14,7 +14,8 @@ rule all:
 		"work/FROGS/affiliation.biom",
 		"report/clusters_metrics.html",
 		"report/affiliations_metrics.html",
-		"report/abundance.biom"
+		"report/abundance.biom",
+		"report/abundance.tsv"
 
 include: "quality.smk"
 include: "preprocess.smk"