Commit 30fbb95f authored by Cedric Midoux's avatar Cedric Midoux
Browse files

kronaHTMLall

parent ce0824f3
......@@ -7,7 +7,7 @@ configfile: "./config.json"
rule all:
input:
"report/multiqc_report.html",
expand("report/reads_{sample}-krona.html", sample=config["SAMPLES"]),
"report/reads_krona_all.html",
#coassembly
"report/quast_coassembly/report.html",
expand("report/count-contigs-coassembly-{sample}.tsv", sample=config["SAMPLES"]),
......
......@@ -58,6 +58,20 @@ rule kronaHTML:
"&& "
"conda deactivate "
rule kronaHTMLall:
input:
expand("work/kaiju/{{focus}}_{sample}.krona", sample=config["SAMPLES"])
output:
"report/{focus}_krona_all.html"
shell:
"conda activate kaiju-1.7.3 "
"&& "
"ktImportText "
"-o {output} "
"{input} "
"&& "
"conda deactivate "
rule kronaNames:
input:
"work/kaiju/{sample}.kaijuNR"
......
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