Commit cebd17f5 authored by peguerin's avatar peguerin
Browse files

snakefile assign taxon

parent 307968ce
configfile: "config.yaml"
RUNS, = glob_wildcards('01-runs/{run}_run.fasta')
rule all:
input:
expand('01-runs/{run}_run.fasta',run=RUNS),
expand('02-dereplicated/{run}_run.uniq.fasta', run=RUNS),
expand('03-assigned/{run}_run.tag.u.fasta', run=RUNS),
expand('04-formated/{run}_run.a.t.u.fasta', run=RUNS),
expand('04-formated/{run}_run.s.a.t.u.fasta', run=RUNS),
expand('../04-final_tables/{run}.csv', run=RUNS),
expand('../99-log/09-dereplicate_runs/{run}.log', run=RUNS),
expand('../99-log/10-assign_taxon/{run}.log', run=RUNS),
expand('../99-log/11-rm_attributes/{run}.log', run=RUNS),
expand('../99-log/12-sort_runs/{run}.log', run=RUNS),
expand('../99-log/13-table_runs/{run}.log',run=RUNS)
include: "../00-rules/dereplicate_runs.smk"
include: "../00-rules/assign_taxon.smk"
include: "../00-rules/format_fas2tab.smk"
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment