update default cutoffs

rpetit3 · Aug 26, 2024 · caacfa5 · caacfa5
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Showing 3 changed files with 9 additions and 5 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,9 @@
 # Releases
 
+## v2.2.1 rpetit3/pasty "HB13" - 2024/08/25
+
+- adjust default parameters for `--min-pident` and `--min-coverage` to 90 each
+
 ## v2.2.0 rpetit3/pasty "JBPA" - 2024/08/25
 
 - add default parameters for `--min-pident` and `--min-coverage` in the YAML

diff --git a/README.md b/README.md
@@ -52,8 +52,8 @@ pasty --help
 │                                 [required]                                                    │
 │    --outdir        -o  PATH     Directory to write output [default: ./]                       │
 │    --prefix        -p  TEXT     Prefix to use for output files [default: camlhmp]             │
-│    --min-pident        INTEGER  Minimum percent identity to count a hit [default: 80]         │
-│    --min-coverage      INTEGER  Minimum percent coverage to count a hit [default: 80]         │
+│    --min-pident        INTEGER  Minimum percent identity to count a hit [default: 90]         │
+│    --min-coverage      INTEGER  Minimum percent coverage to count a hit [default: 90]         │
 │    --force                      Overwrite existing reports                                    │
 │    --verbose                    Increase the verbosity of output                              │
 │    --silent                     Only critical errors will be printed                          │

diff --git a/data/pa-osa.yaml b/data/pa-osa.yaml
@@ -5,7 +5,7 @@ metadata:
   id: "pasty"                                                     # id of the schema
   name: "P. aeruginosa serogrouping"                              # name of the schema
   description: "Serogrouping of Pseudomonas aeruginosa isolates"  # description of the schema
-  version: "2.2.0"                                                # version of the schema
+  version: "2.2.1"                                                # version of the schema
   curators:                                                       # A list of curators of the schema
     - "Robert A. Petit III"
 
@@ -14,8 +14,8 @@ engine:
   type: blast  # The type of tool used to generate the data
   tool: blastn # The tool used to generate the data
   params:
-    min_pident: 80     # The minimum percent identity for a hit to be considered
-    min_coverage: 80   # The minimum query coverage for a hit to be considered
+    min_pident: 90     # The minimum percent identity for a hit to be considered
+    min_coverage: 90   # The minimum query coverage for a hit to be considered
 
 # targets provides a list of sequence targets (primers, genes, proteins, etc...)
 targets: