Commit 3ac80428 authored by Midoux Cedric's avatar Midoux Cedric
Browse files

checkm

parent 49e50524
...@@ -167,9 +167,9 @@ rule checkm: ...@@ -167,9 +167,9 @@ rule checkm:
input: input:
"work/metabat/{sample}/{sample}.unbinned.fa" "work/metabat/{sample}/{sample}.unbinned.fa"
output: output:
"work/checkm/{sample}/checkm.log" "work/checkm/{sample}/lineage.ms"
threads: threads:
8 4
params: params:
input = lambda wildcards, input: os.path.dirname(str(input)), input = lambda wildcards, input: os.path.dirname(str(input)),
output = lambda wildcards, output: os.path.dirname(str(output)) output = lambda wildcards, output: os.path.dirname(str(output))
...@@ -180,7 +180,7 @@ rule checkm: ...@@ -180,7 +180,7 @@ rule checkm:
"lineage_wf " "lineage_wf "
"-t {threads} " "-t {threads} "
"-x fa " "-x fa "
"{params.output} "
"{params.input} " "{params.input} "
"{params.output} "
" ; " " ; "
"conda deactivate" "conda deactivate"
...@@ -17,6 +17,7 @@ rule all: ...@@ -17,6 +17,7 @@ rule all:
"report/contigs_coassembly-taxNames.tsv", "report/contigs_coassembly-taxNames.tsv",
"report/genes_coassembly-taxNames.tsv", "report/genes_coassembly-taxNames.tsv",
"work/metabat/coassembly.done", "work/metabat/coassembly.done",
"work/checkm/coassembly/lineage.ms",
#catalogue #catalogue
"report/quast_results/report.html", "report/quast_results/report.html",
expand("report/count-contigs-catalogue-{sample}.tsv", sample=config["SAMPLES"]), expand("report/count-contigs-catalogue-{sample}.tsv", sample=config["SAMPLES"]),
......
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