From 617a7581474f969bc6568711547f9825e065bb7e Mon Sep 17 00:00:00 2001 From: Richard Challis Date: Tue, 13 Dec 2022 14:23:01 +0000 Subject: [PATCH] alter extract busco genes to use basal lineages as intended --- src/pipeline/rules/extract_busco_genes.smk | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/src/pipeline/rules/extract_busco_genes.smk b/src/pipeline/rules/extract_busco_genes.smk index 9d64ea93..392367ae 100644 --- 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 \