From 1570aa875e3091a47072e9b3b7993e3c988059c8 Mon Sep 17 00:00:00 2001 From: Lauren Coombe Date: Tue, 3 Dec 2024 08:59:07 -0800 Subject: [PATCH] Make --reads compatible with newer ntEdit (#36) --- ntroot_run_pipeline.smk | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/ntroot_run_pipeline.smk b/ntroot_run_pipeline.smk index 04a3509..7cd9b5d 100644 --- a/ntroot_run_pipeline.smk +++ b/ntroot_run_pipeline.smk @@ -10,7 +10,8 @@ onsuccess: # Read parameters from config or set default values reference=config["reference"] draft_base = os.path.basename(os.path.realpath(reference)) -reads_prefix=config["reads"] if "reads" in config else "" +reads_prefix_full=config["reads"] if "reads" in config else "" +reads_prefix=os.path.basename(reads_prefix_full) k=config["kmer"] if "kmer" in config else None genomes = config["genomes"] if "genomes" in config else "" @@ -75,7 +76,7 @@ rule ntedit_reads: params = f"-k {k} -t {t} -z {z} -j {j} -Y {Y} --solid ", vcf_input = f"-l {l}" if l else "" shell: - "{params.benchmark} run-ntedit snv --reference {reference} --reads {reads_prefix} {params.params} " + "{params.benchmark} run-ntedit snv --reference {reference} --reads {reads_prefix_full} {params.params} " "{params.vcf_input}" rule ntedit_genome: