Commit be068df3 authored by khalid's avatar khalid
Browse files

put stats output in outputdir

parent a7d8c416
......@@ -15,7 +15,7 @@ rule <step_name>__FROGS_affiliation:
taxfile = config["<step_name>__FROGS_affiliation_reference_fasta"]+"/train_set.fasta",
yamlfile = config["<step_name>__FROGS_affiliation_reference_fasta"]+"/info.yaml",
# taxonomic_ranks = "-t Domain Phylum Class Order Family Genus Species",
# rdp = "--rdp "+config["<step_name>__FROGS_affiliation_rdp"] if config["<step_name>__FROGS_affiliation_rdp"] else "",
#rdp = "--rdp "+config["<step_name>__FROGS_affiliation_rdp"] if config["<step_name>__FROGS_affiliation_rdp"] else "",
threads:
config["<step_name>__FROGS_affiliation_threads"],
shell: """
......@@ -36,7 +36,7 @@ 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' ;
{params.cmdStat} -i {output.abundance_file} --tax-consensus-tag 'blast_taxonomy' --multiple-tag 'blast_affiliations' -o {params.outDir}/affiliations_stat.html ;
echo \"2\t./{params.stepDir}/affiliations_stat.html\" >> {params.outDir}/text.generic.tsv
"""
# {params.rdp} \
......
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