Merge pull request #122 from phac-nml/dev

updated nextflow schema for ectyper.
phac-nml · Sep 25, 2024 · cccd460 · cccd460
2 parents 37daa4d + 456e539
commit cccd460
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,12 +3,14 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## `Unreleased`
+## [0.4.2] - 2024-09-25
 
 ### `Fixed`
 
 - Fixed broken link in readme. [PR 117](https://github.com/phac-nml/mikrokondo/pull/117)
 
+- Fixed ectyper parameter types in the `nextflow_schema.json` from `number` to `integer`. [PR 121](https://github.com/phac-nml/mikrokondo/pull/121)
+
 ## [0.4.1] - 2024-09-16
 
 ### `Fixed`
@@ -162,6 +164,8 @@ Initial release of phac-nml/mikrokondo. Mikrokondo currently supports: read trim
 
 - Added integration testing using [nf-test](https://www.nf-test.com/).
 
+[0.4.2]: https://github.com/phac-nml/mikrokondo/releases/tag/0.4.2
+[0.4.1]: https://github.com/phac-nml/mikrokondo/releases/tag/0.4.1
 [0.4.0]: https://github.com/phac-nml/mikrokondo/releases/tag/0.4.0
 [0.3.0]: https://github.com/phac-nml/mikrokondo/releases/tag/0.3.0
 [0.2.1]: https://github.com/phac-nml/mikrokondo/releases/tag/0.2.1

diff --git a/nextflow.config b/nextflow.config
@@ -1195,7 +1195,7 @@ manifest {
     description     = """Mikrokondo"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '0.4.1'
+    version         = '0.4.2'
     defaultBranch   = 'main'
     doi             = ''
 }

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -444,28 +444,28 @@
             "default": "",
             "properties": {
                 "ec_opid": {
-                    "type": "number",
+                    "type": "integer",
                     "default": 90,
                     "description": "Minimum percent identity to determine O antigens presence",
                     "minimum": 0,
                     "maximum": 100
                 },
                 "ec_opcov": {
-                    "type": "number",
+                    "type": "integer",
                     "default": 90,
                     "description": "Minimum percent coverage of O antigen",
                     "minimum": 0,
                     "maximum": 100
                 },
                 "ec_hpid": {
-                    "type": "number",
+                    "type": "integer",
                     "default": 95,
                     "description": "Miniumum percent identity to determine H antigens presence",
                     "minimum": 0,
                     "maximum": 100
                 },
                 "ec_hpcov": {
-                    "type": "number",
+                    "type": "integer",
                     "default": 50,
                     "description": "Minimum percent coverage of H antigen",
                     "minimum": 0,