output interproscan

0a6b2da8 · Midoux Cedric · 313f2381 · 0a6b2da8
Commit 0a6b2da8 authored 5 years ago by Midoux Cedric
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with 5 additions and 9 deletions
+5 -9
--- a/annotation.smk
+++ b/annotation.smk
@@ -144,21 +144,17 @@ rule interproscan:
 	input:
 		unpack(faa_input)
 	output:
-		tsv = "work/interproscan/{sample}.faa.tsv",
+		"work/interproscan/{sample}/{sample}.{format}"
-		gff3 = "work/interproscan/{sample}.faa.gff3",
-		html = "work/interproscan/{sample}.faa.html.tar.gz"
-	params:
-		output = lambda wildcards, output: os.path.dirname(str(output.tsv))
 	threads:
 		8
 	shell:
 		"interproscan.sh "
 		"--cpu {threads} "
+		"--formats {wildcards.format} "
+		"--goterms "
 		"--highmem "
 		"--input {input.faa} "
-		"--seqtype p "
-		"--output-dir {params.output} "
-		"--formats tsv,gff3,html "
 		"--iprlookup "
-		"--goterms "
+		"--outfile {output} "
 		"--pathways "
+		"--seqtype p "