Commit 0f7ad1ca authored by Cedric Midoux's avatar Cedric Midoux
Browse files

interproscan output

parent 2e801311
......@@ -144,21 +144,17 @@ rule interproscan:
input:
unpack(faa_input)
output:
tsv = "work/interproscan/{sample}.faa.tsv",
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))
"work/interproscan/{sample}/{sample}.{format}"
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 "
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