From 2d947538d72061cbfd6c67277964f38792233634 Mon Sep 17 00:00:00 2001 From: rhysnewell Date: Tue, 5 Mar 2024 23:14:40 +0000 Subject: [PATCH] fix: parallel genomes passed to lorikeet correctly --- aviary/modules/strain_analysis/scripts/run_lorikeet.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/aviary/modules/strain_analysis/scripts/run_lorikeet.py b/aviary/modules/strain_analysis/scripts/run_lorikeet.py index d9aeb612..422d7fac 100755 --- a/aviary/modules/strain_analysis/scripts/run_lorikeet.py +++ b/aviary/modules/strain_analysis/scripts/run_lorikeet.py @@ -30,7 +30,7 @@ def run_lorikeet( else: short_reads = "" - lorikeet_cmd = f"lorikeet call -t {threads} -d {mag_directory} -x {mag_extension} -p {parallel_genomes} {short_reads} {long_reads} -o {output_directory} --do-not-call-svs --calculate-dnds --calculate-fst".split() + lorikeet_cmd = f"lorikeet call -t {threads} -d {mag_directory} -x {mag_extension} -P {parallel_genomes} {short_reads} {long_reads} -o {output_directory} --do-not-call-svs --calculate-dnds --calculate-fst".split() run(lorikeet_cmd)