From 4e8ff8caa8dab19868a08821956f7e15fe44920a Mon Sep 17 00:00:00 2001 From: Ryan Routsong Date: Tue, 30 Jul 2024 10:22:06 -0400 Subject: [PATCH] fix: align gunc with new drep outputs --- workflow/rules/DNA.smk | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/workflow/rules/DNA.smk b/workflow/rules/DNA.smk index 26f4034..51f0f85 100644 --- a/workflow/rules/DNA.smk +++ b/workflow/rules/DNA.smk @@ -746,15 +746,14 @@ rule gtdbtk_classify: rule gunc_detection: input: - derep_genome_info = join(top_refine_dir, "{name}", "dRep", "data_tables", "Widb.csv"), - derep_winning_figure = join(top_refine_dir, "{name}", "dRep", "figures", "Winning_genomes.pdf"), - derep_args = join(top_refine_dir, "{name}", "dRep", "log", "cluster_arguments.json"), - drep_genomes = join(top_refine_dir, "{name}", "dRep", "dereplicated_genomes"), + derep_genome_info = join(top_refine_dir, "dRep", "data_tables", "Widb.csv"), + derep_winning_figure = join(top_refine_dir, "dRep", "figures", "Winning_genomes.pdf"), + derep_args = join(top_refine_dir, "dRep", "log", "cluster_arguments.json"), + drep_genomes = join(top_refine_dir, "dRep", "dereplicated_genomes"), output: - GUNC_detect_out = directory(join(top_tax_dir, "{name}", "GUNC_detect")) + GUNC_detect_out = directory(join(top_tax_dir,"GUNC_detect")) params: rname = "gunc_detection", - sid = "{name}", gunc_db = "/data2/GUNC_DB/gunc_db_progenomes2.1.dmnd", # from /config/resourcs.json tmp_safe_dir = join(config['options']['tmp_dir'], 'gunc_detect'), singularity: metawrap_container,