alter extract busco genes to use basal lineages as intended

genomehubs · Dec 13, 2022 · 617a758 · 617a758
1 parent 669867a
commit 617a758
Showing 1 changed file with 1 addition and 3 deletions.
diff --git a/src/pipeline/rules/extract_busco_genes.smk b/src/pipeline/rules/extract_busco_genes.smk
@@ -7,14 +7,12 @@ rule extract_busco_genes:
     output:
         fasta = "{assembly}.busco_genes.fasta"
     params:
-        busco = lambda wc: " --busco ".join(expand("%s/%s.busco.{lineage}/full_table.tsv.gz" % (busco_path, wc.assembly), lineage=config['busco']['lineages'])),
+        busco = lambda wc: " --busco ".join(expand("%s/%s.busco.{lineage}/full_table.tsv.gz" % (busco_path, wc.assembly), lineage=get_basal_lineages(config))),
     threads: 1
     log:
         "logs/{assembly}/extract_busco_genes.log"
     benchmark:
         "logs/{assembly}/extract_busco_genes.benchmark.txt"
-    # script:
-    #     "../lib/extract_busco_genes.py"
 
     shell:
         """(btk pipeline extract-busco-genes \