add params to yaml bump to v2.2.0

.gitignore

@@ -1 +1,2 @@
 /*.tsv
+camlhmp-blast-thresholds/

.gitpod.yml

@@ -1,12 +1,12 @@
-image: nfcore/gitpod:latest
+image: condaforge/miniforge3:24.3.0-0
 
 tasks:
   - name: Initialize
     init: |
       pip install graphviz
       . /opt/conda/etc/profile.d/conda.sh
       conda activate base
-      mamba create -n pasty-dev -y -q -c conda-forge -c bioconda camlhmp
+      conda create -n pasty-dev -y -q -c conda-forge -c bioconda camlhmp
       conda activate pasty-dev
       git checkout main
 vscode:

CHANGELOG.md

@@ -1,5 +1,9 @@
 # Releases
 
+## v2.2.0 rpetit3/pasty "JBPA" - 2024/08/25
+
+- add default parameters for `--min-pident` and `--min-coverage` in the YAML
+
 ## v2.1.0 rpetit3/pasty "LESB58" - 2024/08/19
 
 - add serogroups O15 and O17 https://github.com/rpetit3/pasty/pull/5 @StefaanVerwimp

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: 95]         │
-│    --min-coverage      INTEGER  Minimum percent coverage to count a hit [default: 95]         │
+│    --min-pident        INTEGER  Minimum percent identity to count a hit [default: 80]         │
+│    --min-coverage      INTEGER  Minimum percent coverage to count a hit [default: 80]         │
 │    --force                      Overwrite existing reports                                    │
 │    --verbose                    Increase the verbosity of output                              │
 │    --silent                     Only critical errors will be printed                          │
@@ -84,11 +84,15 @@ The directory to save result files. If the directory does not exist is will be c
 
 ### --min-pident
 
+__*Note: This should be automatically set for you!*__
+
 The minimum percent identity for a blast hit to be considered for serogrouping. The is compared
 against the `pident` column of the blast output.
 
 ### --min-coverage
 
+__*Note: This should be automatically set for you!*__
+
 The minimum coverage of a O-antigen to be considered for serogrouping. This looks at the percent
 of the O-antigen that was aligned to. This calculation does include mismatches and gaps,
 but those should be expected to be minimal if `--min_pident` is set to the default (95%) or

data/pa-osa.yaml

@@ -5,14 +5,17 @@ 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: "2.1.0"                                                # version of the schema
+  version: "2.2.0"                                                # version of the schema
   curators:                                                       # A list of curators of the schema
     - "Robert A. Petit III"
 
 # engine provides information about the tool and parameters used
 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
 
 # targets provides a list of sequence targets (primers, genes, proteins, etc...)
 targets: