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

biom_to_tsv

parent be5578e2
...@@ -75,7 +75,7 @@ rule stdBIOM: ...@@ -75,7 +75,7 @@ rule stdBIOM:
biom = "work/FROGS/affiliation.biom" biom = "work/FROGS/affiliation.biom"
output: output:
biom = "work/FROGS/abundance.biom", biom = "work/FROGS/abundance.biom",
tsv = "work/FROGS/multihits.tsv" tsv = "work/FROGS/blast_informations.std.tsv"
shell: shell:
"conda activate frogs-3.2.0 " "conda activate frogs-3.2.0 "
"&& " "&& "
...@@ -86,6 +86,24 @@ rule stdBIOM: ...@@ -86,6 +86,24 @@ rule stdBIOM:
"&& " "&& "
"conda deactivate" "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 localrules: copy
rule copy: rule copy:
input: input:
......
...@@ -14,7 +14,8 @@ rule all: ...@@ -14,7 +14,8 @@ rule all:
"work/FROGS/affiliation.biom", "work/FROGS/affiliation.biom",
"report/clusters_metrics.html", "report/clusters_metrics.html",
"report/affiliations_metrics.html", "report/affiliations_metrics.html",
"report/abundance.biom" "report/abundance.biom",
"report/abundance.tsv"
include: "quality.smk" include: "quality.smk"
include: "preprocess.smk" include: "preprocess.smk"
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment