Commit c5c14cfb authored by Cedric Midoux's avatar Cedric Midoux
Browse files

kaiju nr_euk

parent 7963bb36
......@@ -19,8 +19,8 @@ rule kaiju:
"conda activate kaiju-1.7.3 "
"&& "
"kaiju "
"-t /db/outils/kaiju-2020-05-25/nr/nodes.dmp "
"-f /db/outils/kaiju-2020-05-25/nr/kaiju_db_nr.fmi "
"-t /db/outils/kaiju-2020-05-25/nr_euk/nodes.dmp "
"-f /db/outils/kaiju-2020-05-25/nr_euk/kaiju_db_nr_euk.fmi "
"{params.input} "
"-o {output} "
"-z {threads} "
......@@ -36,8 +36,8 @@ rule krona:
"conda activate kaiju-1.7.3 "
"&& "
"kaiju2krona "
"-t /db/outils/kaiju-2020-05-25/nr/nodes.dmp "
"-n /db/outils/kaiju-2020-05-25/nr/names.dmp "
"-t /db/outils/kaiju-2020-05-25/nr_euk/nodes.dmp "
"-n /db/outils/kaiju-2020-05-25/nr_euk/names.dmp "
"-i {input} "
"-o {output} "
"-u "
......@@ -67,8 +67,8 @@ rule kronaNames:
"conda activate kaiju-1.7.3 "
"&& "
"kaiju-addTaxonNames "
"-t /db/outils/kaiju-2020-05-25/nr/nodes.dmp "
"-n /db/outils/kaiju-2020-05-25/nr/names.dmp "
"-t /db/outils/kaiju-2020-05-25/nr_euk/nodes.dmp "
"-n /db/outils/kaiju-2020-05-25/nr_euk/names.dmp "
"-i {input} "
"-o {output} "
"-r superkingdom,phylum,order,class,family,genus,species "
......
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