Merge pull request #346 from nf-core/patch

Hotfix: pin nf-validation
nf-core · Mar 20, 2024 · ec1f1b6 · ec1f1b6
2 parents 274042b + e80f5f2
commit ec1f1b6
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Showing 11 changed files with 52 additions and 19 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,23 @@
 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).
 
+## v1.1.5 - [2024-03-20]
+
+### `Added`
+
+### `Fixed`
+
+- [#346](https://github.com/nf-core/funcscan/pull/346) Pinned version of nf-validation to 1.1.3
+
+### `Dependencies`
+
+| Plugin        | Previous | New version |
+| ------------- | -------- | ----------- |
+| Bakta         | 1.8.2    | 1.9.3       |
+| nf-validation | Latest   | 1.1.3       |
+
+### `Deprecated`
+
 ## v1.1.4 - [2023-11-07]
 
 ### `Added`
@@ -20,7 +37,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 | ------------- | ---------------- | ----------- |
 | AMRFinderPlus | 3.10.42          | 3.11.18     |
 | Bakta         | 1.7.0            | 1.8.2       |
-| MultiQC       | 1.14            | 1.15       |
+| MultiQC       | 1.14             | 1.15        |
 
 ### `Deprecated`
 

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/funcscan/releases/tag/1.1.4" target="_blank">nf-core/funcscan</a>
+  This report has been generated by the <a href="https://github.com/nf-core/funcscan/releases/tag/1.1.5" target="_blank">nf-core/funcscan</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/funcscan/1.1.4/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/funcscan/1.1.5/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-funcscan-methods-description":
     order: -1000

diff --git a/modules.json b/modules.json
@@ -47,12 +47,12 @@
                     },
                     "bakta/bakta": {
                         "branch": "master",
-                        "git_sha": "f05fa7c6753f92be861d606378860dcd5c828880",
+                        "git_sha": "9d0f89b445e1f5b2fb30476f4be9a8b519c07846",
                         "installed_by": ["modules"]
                     },
                     "bakta/baktadbdownload": {
                         "branch": "master",
-                        "git_sha": "f05fa7c6753f92be861d606378860dcd5c828880",
+                        "git_sha": "7c06e6820fa3918bc28a040e794f8a2b39fabadb",
                         "installed_by": ["modules"]
                     },
                     "bioawk": {

diff --git a/modules/nf-core/bakta/bakta/environment.yml b/modules/nf-core/bakta/bakta/environment.yml
diff --git a/modules/nf-core/bakta/bakta/main.nf b/modules/nf-core/bakta/bakta/main.nf
diff --git a/modules/nf-core/bakta/bakta/meta.yml b/modules/nf-core/bakta/bakta/meta.yml
diff --git a/modules/nf-core/bakta/baktadbdownload/environment.yml b/modules/nf-core/bakta/baktadbdownload/environment.yml
diff --git a/modules/nf-core/bakta/baktadbdownload/main.nf b/modules/nf-core/bakta/baktadbdownload/main.nf
diff --git a/modules/nf-core/bakta/baktadbdownload/meta.yml b/modules/nf-core/bakta/baktadbdownload/meta.yml
diff --git a/nextflow.config b/nextflow.config
@@ -342,7 +342,7 @@ singularity.registry = 'quay.io'
 
 // Nextflow plugins
 plugins {
-    id 'nf-validation' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+    id 'nf-validation@1.1.3' // Validation of pipeline parameters and creation of an input channel from a sample sheet
 }
 
 // Load igenomes.config if required
@@ -391,7 +391,7 @@ manifest {
     description     = """Pipeline for screening for functional components of assembled contigs"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '1.1.4'
+    version         = '1.1.5'
     doi             = '10.5281/zenodo.7643099'
 }
 

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -311,7 +311,7 @@
                 },
                 "annotation_prokka_retaincontigheaders": {
                     "type": "boolean",
-                    "fa_icon":"fas fa-remove-format",          
+                    "fa_icon": "fas fa-remove-format",
                     "help_text": "This parameter allows prokka to retain the original contig names by activating `PROKKA`'s  `--force` flag. If this parameter is set to `false` it activates `PROKKA`'s flags `--locus-tag PROKKA --centre CENTER` so the locus tags (contig names) will be PROKKA_# and the center tag will be CENTER. By default `PROKKA` changes contig headers to avoid errors that might rise due to long contig headers, so this must be turned on if the user has short contig names that should be retained by `PROKKA`. \n\n> Modifies tool parameter(s):\n> - Prokka: `--locus-tag PROKKA --centre CENTER`\n> - Prokka: `--force`",
                     "description": "Retains contig names."
                 }