From ece618af7a237fb77a4baee241ae6086b7ff68b3 Mon Sep 17 00:00:00 2001 From: LiaOb21 Date: Thu, 11 Apr 2024 15:40:43 +0100 Subject: [PATCH] updated config --- config/config_test.yaml | 19 +++++++++++++++++-- 1 file changed, 17 insertions(+), 2 deletions(-) diff --git a/config/config_test.yaml b/config/config_test.yaml index fa7c988..55dff22 100644 --- a/config/config_test.yaml +++ b/config/config_test.yaml @@ -1,5 +1,20 @@ # config file for test data +# Set memory and threads for high demanding rules +high: + mem_mb: 32000 # memory in MB + t: 4 # number of threads + +# Set memory and threads for medium demanding rules +medium: + mem_mb: 8000 # memory in MB + t: 4 # number of threads + +# Set memory and threads for low demanding rules +low: + mem_mb: 1000 # memory in MB + t: 4 # number of threads + # Path to hifi reads hifi_path: "resources/raw_hifi/" @@ -55,14 +70,14 @@ minimap2: hifiasm: t: 4 # number of threads mem_mb: 1000 # memory in MB + phased_assembly: False # set to true if you want to obtain a phased assembly optional_params: - phased_assembly: False # set to true if you want to obtain a phased assembly "-f": "0" # used for small datasets "-l": "" # purge level. 0: no purging; 1: light; 2/3: aggressive [0 for trio; 3 for unzip] "--ul": "" # use this if you have also ont data you want to integrate in your assembly #Set this to False if you want to skip the fcsgx step: -include_fcsgx: True #inlcude this rule only if you have preiously downloaded the database (recommended to run fcsgx only on a HPC. It requires around 500 GB of space on your disk and a large RAM) +include_fcsgx: False #inlcude this rule only if you have preiously downloaded the database (recommended to run fcsgx only on a HPC. It requires around 500 GB of space on your disk and a large RAM) # Customisable parameters for fcsgx fcsgx: