Commit d7c2d7c7 authored by Midoux Cedric's avatar Midoux Cedric
Browse files

biom_to_tsv

parent be5578e2
......@@ -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:
......
......@@ -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"
......
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