Commit 277d26f4 authored by khalid's avatar khalid
Browse files

add a simple OTU abundance count output

parent 5654f689
......@@ -3,10 +3,12 @@ rule <step_name>__FROGS_biom_to_tsv:
**<step_name>__FROGS_biom_to_tsv_inputs(),
output:
abundance_file = config["results_dir"]+'/'+config["<step_name>__FROGS_biom_to_tsv_output_dir"]+'/tax_affiliation.tsv',
lulu_abundance_file = config["results_dir"]+'/'+config["<step_name>__FROGS_biom_to_tsv_output_dir"]+'/simple_OTU_abundance.tsv',
log: config["results_dir"]+'/logs/' + config["<step_name>__FROGS_biom_to_tsv_output_dir"] + '/FROGS_biom_to_tsv_log.txt',
params:
command = config["<step_name>__FROGS_biom_to_tsv_command"],
outDir = config["results_dir"]+'/'+config["<step_name>__FROGS_biom_to_tsv_output_dir"],
shell: """
{params.command} -b {input.biom} -t {output.abundance_file}
{params.command} -b {input.biom} -t {output.abundance_file} ;
cut -f10,12- -d$'\t' {output.abundance_file} > {output.lulu_abundance_file}
"""
\ No newline at end of file
......@@ -23,6 +23,8 @@
outputs:
[
{ name: "abundance_file", file: "tax_affiliation.tsv", type: "tsv", description: "output file with the abundance and metadata (tsv)"},
{ name: "lulu_abundance_file", file: "simple_OTU_abundance.tsv", type: "tsv", description: "OTU abundance with samples as columns and OTUs as rows (for lulu)"},
],
options:
[
......
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