Commit a615a1d5 authored by Midoux Cedric's avatar Midoux Cedric
Browse files

metabat output .fa

parent 0f7ad1ca
......@@ -127,7 +127,6 @@ checkpoint metabat:
"--minContig 5000 "
"--minClsSize {params.clustrsize} "
"--numThreads {threads} "
"--onlyLabel "
"--unbinned "
"--verbose "
" ; "
......@@ -135,15 +134,19 @@ checkpoint metabat:
rule metabat_kaiju:
input:
clustr = "work/metabat/{sample}/{sample}.{num}",
clustr = "work/metabat/{sample}/{sample}.{num}.fa",
kaiju = "report/contigs_{sample}-taxNames.tsv"
output:
"work/metabat/{sample}/{sample}.{num}_kaiju.tsv"
shell:
"grep "
"'>' "
"--file {input.clustr} "
" | "
"grep "
"--no-messages "
"--word-regexp "
"--file {input.clustr} "
"--file - "
"{input.kaiju} "
" > "
"{output} "
......
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