Commit 49e50524 authored by Cedric Midoux's avatar Cedric Midoux
Browse files

checkm

parent a615a1d5
......@@ -162,3 +162,25 @@ rule resume_metabat:
done = temp("work/metabat/{sample}.done")
shell:
"touch {output.done} "
rule checkm:
input:
"work/metabat/{sample}/{sample}.unbinned.fa"
output:
"work/checkm/{sample}/checkm.log"
threads:
8
params:
input = lambda wildcards, input: os.path.dirname(str(input)),
output = lambda wildcards, output: os.path.dirname(str(output))
shell:
"conda activate checkm-genome-1.0.18 "
" ; "
"checkm "
"lineage_wf "
"-t {threads} "
"-x fa "
"{params.output} "
"{params.input} "
" ; "
"conda deactivate"
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