Merge pull request #156 from Plant-Food-Research-Open/update/template

Updated template to version 3.0.2
Plant-Food-Research-Open · Oct 13, 2024 · 789ae12 · 789ae12
2 parents 1030136 + 05b9eed
commit 789ae12
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Showing 15 changed files with 40 additions and 39 deletions.
diff --git a/.gitignore b/.gitignore
@@ -14,3 +14,4 @@ testing*
 # nf-test files
 .nf-test/
 .nf-test.log
+null/
diff --git a/.nf-core.yml b/.nf-core.yml
@@ -1,5 +1,8 @@
 bump_version: null
 lint:
+  actions_ci: false
+  multiqc_config: false
+  template_strings: false
   files_exist:
     - conf/igenomes.config
     - conf/igenomes_ignored.config
@@ -13,22 +16,20 @@ lint:
     - .github/workflows/awsfulltest.yml
   files_unchanged:
     - LICENSE
+    - .gitignore
     - .github/CONTRIBUTING.md
     - .github/PULL_REQUEST_TEMPLATE.md
     - .github/workflows/branch.yml
     - .github/workflows/linting.yml
     - docs/README.md
-  multiqc_config: false
-  template_strings: false
-  actions_ci: false
   nextflow_config:
     - manifest.name
     - manifest.homePage
     - validation.help.beforeText
     - validation.help.afterText
     - validation.summary.beforeText
     - validation.summary.afterText
-nf_core_version: 3.0.1
+nf_core_version: 3.0.2
 org_path: null
 repository_type: pipeline
 template:
@@ -44,5 +45,5 @@ template:
     - igenomes
     - multiqc
     - fastqc
-  version: 2.2.0+dev
+  version: 2.2.0dev
 update: null
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,12 +3,12 @@
 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).
 
-## v2.2.0+dev - [10-Oct-2024]
+## v2.2.0dev - [10-Oct-2024]
 
 ### `Added`
 
 1. Added Gfastats [#126](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/126)
-2. Updated nf-core/template to 3.0.1 [#149](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/149)
+2. Updated nf-core/template to 3.0.2 [#149](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/149)
 3. Updated `samtools faidx` to 1.21
 4. Now using nf-test for pipeline level testing [#153](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/153)
 5. Added `text/html` as content mime type for the report file [#146](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/146)

diff --git a/CITATION.cff b/CITATION.cff
@@ -25,7 +25,7 @@ authors:
   - family-names: "Deng"
     given-names: "Cecilia"
 title: "AssemblyQC: A Nextflow pipeline for reproducible reporting of assembly quality"
-version: 2.2.0+dev
+version: 2.2.0dev
 date-released: 2024-07-30
 url: "https://github.com/Plant-Food-Research-Open/assemblyqc"
 doi: 10.1093/bioinformatics/btae477
diff --git a/modules.json b/modules.json
@@ -281,12 +281,12 @@
                     },
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "f533459a222ac53eb4c6bb7a5f574e4069197cdb",
+                        "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "f533459a222ac53eb4c6bb7a5f574e4069197cdb",
+                        "git_sha": "1b6b9a3338d011367137808b49b923515080e3ba",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfschema_plugin": {

diff --git a/nextflow.config b/nextflow.config
@@ -272,7 +272,7 @@ manifest {
     description     = """A Nextflow pipeline which evaluates assembly quality with multiple QC tools and presents the results in a unified html report."""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=24.04.2'
-    version         = '2.2.0+dev'
+    version         = '2.2.0dev'
     doi             = 'https://doi.org/10.1093/bioinformatics/btae477'
 }
 

diff --git a/subworkflows/local/utils_nfcore_assemblyqc_pipeline/main.nf b/subworkflows/local/utils_nfcore_assemblyqc_pipeline/main.nf
@@ -49,7 +49,6 @@ workflow PIPELINE_INITIALISATION {
         workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1
     )
 
-
     //
     // Validate parameters and generate parameter summary to stdout
     //
@@ -59,7 +58,6 @@ workflow PIPELINE_INITIALISATION {
         null // schema path: nextflow_schema
     )
 
-
     //
     // Check config provided to the pipeline
     //
@@ -190,10 +188,9 @@ workflow PIPELINE_COMPLETION {
     take:
     email           //  string: email address
     email_on_fail   //  string: email address sent on pipeline failure
-    plaintext_email // boolean: Send plain-text email instead of HTML
-
-    outdir          //    path: Path to output directory where results will be published
-    monochrome_logs // boolean: Disable ANSI colour codes in log output
+    plaintext_email //  boolean: Send plain-text email instead of HTML
+    outdir          //  path: Path to output directory where results will be published
+    monochrome_logs //  boolean: Disable ANSI colour codes in log output
     hook_url        //  string: hook URL for notifications
 
 

diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
diff --git a/tests/hicparam/main.nf.test.snap b/tests/hicparam/main.nf.test.snap
@@ -68,7 +68,7 @@
                         "pigz": "2.3.4"
                     },
                     "Workflow": {
-                        "plant-food-research-open/assemblyqc": "v2.2.0+dev"
+                        "plant-food-research-open/assemblyqc": "v2.2.0dev"
                     }
                 },
                 "stable paths": [
@@ -99,4 +99,4 @@
         },
         "timestamp": "2024-10-10T16:11:00.660108"
     }
-}
+}
diff --git a/tests/invalid/main.nf.test.snap b/tests/invalid/main.nf.test.snap
@@ -35,7 +35,7 @@
                         "pigz": "2.3.4"
                     },
                     "Workflow": {
-                        "plant-food-research-open/assemblyqc": "v2.2.0+dev"
+                        "plant-food-research-open/assemblyqc": "v2.2.0dev"
                     }
                 },
                 "stable paths": [
@@ -51,4 +51,4 @@
         },
         "timestamp": "2024-10-10T15:59:12.150838"
     }
-}
+}
diff --git a/tests/minimal/main.nf.test.snap b/tests/minimal/main.nf.test.snap
@@ -35,7 +35,7 @@
                         "pigz": "2.3.4"
                     },
                     "Workflow": {
-                        "plant-food-research-open/assemblyqc": "v2.2.0+dev"
+                        "plant-food-research-open/assemblyqc": "v2.2.0dev"
                     }
                 },
                 "stable paths": [

diff --git a/tests/noltr/main.nf.test.snap b/tests/noltr/main.nf.test.snap
@@ -50,7 +50,7 @@
                         "seqkit": "v2.8.0"
                     },
                     "Workflow": {
-                        "plant-food-research-open/assemblyqc": "v2.2.0+dev"
+                        "plant-food-research-open/assemblyqc": "v2.2.0dev"
                     }
                 },
                 "stable paths": [
@@ -84,4 +84,4 @@
         },
         "timestamp": "2024-10-10T20:38:08.028244"
     }
-}
+}
diff --git a/tests/stub/main.nf.test.snap b/tests/stub/main.nf.test.snap
@@ -230,7 +230,7 @@
                         "untar": 1.34
                     },
                     "Workflow": {
-                        "plant-food-research-open/assemblyqc": "v2.2.0+dev"
+                        "plant-food-research-open/assemblyqc": "v2.2.0dev"
                     }
                 },
                 "stable paths": [
@@ -304,4 +304,4 @@
         },
         "timestamp": "2024-10-10T14:56:44.730644"
     }
-}
+}
diff --git a/tests/tiny/main.nf.test.snap b/tests/tiny/main.nf.test.snap
@@ -29,7 +29,7 @@
                         "pigz": "2.3.4"
                     },
                     "Workflow": {
-                        "plant-food-research-open/assemblyqc": "v2.2.0+dev"
+                        "plant-food-research-open/assemblyqc": "v2.2.0dev"
                     }
                 },
                 "stable paths": [
@@ -44,4 +44,4 @@
         },
         "timestamp": "2024-10-10T14:46:59.600343"
     }
-}
+}