Commit c33b9280 authored by khalid's avatar khalid
Browse files

Using frogs databases

parent c1993558
......@@ -7,12 +7,12 @@ rule <step_name>__dada2_assign_taxonomy:
params:
output_dir = config["results_dir"] + "/" + config["<step_name>__dada2_assign_taxonomy_output_dir"],
step_dir = config["<step_name>__dada2_assign_taxonomy_output_dir"],
script = config["<step_name>__dada2_assign_taxonomy_script"]
script = config["<step_name>__dada2_assign_taxonomy_script"],
#taxonomypath = config["<step_name>__dada2_assign_taxonomy_taxonomypath"],
taxonomypath = config["<step_name>__dada2_assign_taxonomy_reference_fasta"],
taxfile = config["<step_name>__dada2_assign_taxonomy_reference_fasta"]+"/train_set.fasta",
yamlfile = config["<step_name>__FROGS_assign_taxonomy_reference_fasta"]+"/info.yaml",
yamlfile = config["<step_name>__dada2_assign_taxonomy_reference_fasta"]+"/info.yaml",
#OTUabundance = config["<step_name>__dada2_assign_taxonomy_abundance"],
richness = config["results_dir"] + "/" + config["<step_name>__dada2_assign_taxonomy_output_dir"] + "/richness_mqc.png",
......@@ -25,5 +25,5 @@ rule <step_name>__dada2_assign_taxonomy:
config["results_dir"]+'/logs/' + config["<step_name>__dada2_assign_taxonomy_output_dir"] + '/dada2_assign_taxonomy_log.txt'
script:
config["<step_name>__dada2_assign_taxonomy_script"]
\ No newline at end of file
......@@ -66,24 +66,6 @@
value: "/FROGS_taxonomy/SILVA/16S",
label: "Taxonomy source"
},
{
name: dada2_assign_taxonomy_taxonomypath,
type: select,
choices: [
silva138 (16S): "/taxonomy/silva138",
silva132 (16S): "/taxonomy/silva132",
silva128 (16S): "/taxonomy/silva128",
rdp16 (16S): "/taxonomy/rdp16",
greengenes13.8 (16S): "/taxonomy/gg13_8",
unite_8.2 (ITS): "/taxonomy/unite_8.2",
unite_2_2_2019 (ITS): "/taxonomy/unite_2_2_2019",
midori_COI (COI): "/taxonomy/midori_coi",
midori_COI_Without_Terrestrial (COI): "/taxonomy/midori_coi_wo_terrestrial",
refseq-rdp16s (16S): "/taxonomy/refseq-rdp16s"
],
value: "silva138 (16S)",
label: "Taxonomy source"
},
{
name: dada2_assign_taxonomy_tryRC,
prefix: ,
......@@ -154,6 +136,9 @@
krona: [
"Ondov BD, Bergman NH, and Phillippy AM. Interactive metagenomic visualization in a Web browser. BMC Bioinformatics. 2011 Sep 30; 12(1):385"
],
frogs: [
"Maria Bernard, Olivier Rué, Mahendra Mariadassou and Géraldine Pascal; FROGS: a powerful tool to analyse the diversity of fungi with special management of internal transcribed spacers, Briefings in Bioinformatics 2021, 10.1093/bib/bbab318 "
]
}
}
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