From ebe6afeb0d5ec2409d6b31aaf5aa838976672bdc Mon Sep 17 00:00:00 2001 From: William Rowell Date: Fri, 29 Sep 2023 13:35:14 -0700 Subject: [PATCH] Explicitly pass default `yak count` and `hifiasm` params. --- workflows/de_novo_assembly_trio/de_novo_assembly_trio.wdl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/workflows/de_novo_assembly_trio/de_novo_assembly_trio.wdl b/workflows/de_novo_assembly_trio/de_novo_assembly_trio.wdl index 5db4c29..aa07ffc 100644 --- a/workflows/de_novo_assembly_trio/de_novo_assembly_trio.wdl +++ b/workflows/de_novo_assembly_trio/de_novo_assembly_trio.wdl @@ -56,9 +56,9 @@ workflow de_novo_assembly_trio { # memory for 24 threads is 48GB with bloom filter (<=50x coverage) and 65GB without bloom filter (<=30x coverage) Boolean low_depth = if ((size(samtools_fasta_father.reads_fasta, "GB") < 90) && (size(samtools_fasta_mother.reads_fasta, "GB") < 90)) then true else false - String yak_params = if (low_depth) then "" else "-b37" + String yak_params = if (low_depth) then "-b0" else "-b37" Int yak_mem_gb = if (low_depth) then 70 else 50 - String hifiasm_extra_params = if (low_depth) then "-c1 -d1" else "" + String hifiasm_extra_params = if (low_depth) then "-c1 -d1" else "-c2 -d5" call yak_count as yak_count_father { input: