Commit b06eb584 authored by khalid's avatar khalid
Browse files

Add affiliations stats

parent d89527b6
......@@ -7,6 +7,8 @@ rule <step_name>__FROGS_affiliation:
log: config["results_dir"]+'/logs/' + config["<step_name>__FROGS_affiliation_output_dir"] + '/FROGS_affiliation_log.txt',
params:
command = config["<step_name>__FROGS_affiliation_command"],
cmdStat = os.path.dirname(config["<step_name>__FROGS_cluster_command"])+"/affiliations_stat.py",
outDir = config["results_dir"]+'/'+config["<step_name>__FROGS_affiliation_output_dir"],
stepDir = config["<step_name>__FROGS_affiliation_output_dir"],
taxonomypath = config["<step_name>__FROGS_affiliation_reference_fasta"],
......@@ -34,7 +36,8 @@ rule <step_name>__FROGS_affiliation:
--nb-cpus {threads} \
--java-mem 20;
echo \"1\t./{params.stepDir}/affi_report.html\" > {params.outDir}/text.generic.tsv
{params.cmdStat} -i {output.abundance_file} --tax-consensus-tag 'blast_taxonomy' --multiple-tag 'blast_affiliations' ;
echo \"2\t./{params.stepDir}/affiliations_stat.html\" > {params.outDir}/text.generic.tsv
"""
# {params.rdp} \
#{params.taxonomic_ranks} \
\ No newline at end of file
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