updating test config

config/config_test.yaml

@@ -16,10 +16,10 @@ low:
   t: 4 # number of threads
 
 # Path to hifi reads
-hifi_path: "resources/raw_hifi/"
+hifi_path: "test_data/raw_hifi/"
 
 # Path to hic reads
-hic_path: "resources/raw_hic/"
+hic_path: "test_data/raw_hic/"
 
 # Customisable parameters for kmc
 kmc:
@@ -41,34 +41,34 @@ genomescope2:
 oatk:
   k: 1001 # kmer size [1001]
   c: 150 #  minimum kmer coverage [3]
-  m: "resources/oatkDB/dikarya_mito.fam" # mitochondria gene annotation HMM profile database [NULL]
+  m: "test_data/oatkDB/dikarya_mito.fam" # mitochondria gene annotation HMM profile database [NULL]
   optional_params: 
     "-p": "" # to use for species that have a plastid db
 
 # Customisable parameters for fastp
 fastp:
   optional_params:
-#    "--cut_front": True # to use only with Arima Hi-C library prep kit generated data
-#    "--cut_front_window_size": 5 # to use only with Arima Hi-C library prep kit generated data
+    "--cut_front": True # to use only with Arima Hi-C library prep kit generated data
+    "--cut_front_window_size": 5 # to use only with Arima Hi-C library prep kit generated data
 
 # Customisable parameters for hifiasm
 hifiasm:
-  phased_assembly: False # set to true if you want to obtain a phased assembly
+  phased_assembly: True # set to true if you want to obtain a phased assembly
   optional_params: 
     "-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: False #inlcude this rule only if you have previously 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: True #inlcude this rule only if you have previously 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:
   ncbi_tax_id: 4932
   path_to_gx_db: "resources/gx_test_db/test-only"
 
 # Set this to False if you want to skip purge_dups steps:
-include_purge_dups: True
+include_purge_dups: False
 
 
 # Customisable parameters for arima mapping pipeline:
@@ -90,4 +90,4 @@ quast:
 
 # Customisable parameters for busco
 busco:
-  lineage: "resources/saccharomycetes_odb10" # lineage to be used for busco analysis
+  lineage: "test_data/busco_db/saccharomycetes_odb10" # lineage to be used for busco analysis