snakefile assign taxon

03-filtered/Snakefile

+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"
+