snakefile assign taxon

cebd17f5 · peguerin · 307968ce · cebd17f5
Commit cebd17f5 authored Dec 02, 2019 by peguerin
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03-filtered/Snakefile 03-filtered/Snakefile +21 -0

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--- a/03-filtered/Snakefile
+++ b/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"
+