Merge pull request #151 from Plant-Food-Research-Open/update/template301

Updated nf-core/template to 3.0.1

.editorconfig

@@ -11,7 +11,6 @@ indent_style = space
 [*.{md,yml,yaml,html,css,scss,js,cff}]
 indent_size = 2
 
-
 # These files are edited and tested upstream in nf-core/modules
 [/modules/nf-core/**]
 charset = unset
@@ -43,7 +42,6 @@ indent_style = unset
 [/assets/email*]
 indent_size = unset
 
-
 # ignore python and markdown
 [*.{py,md}]
 indent_style = unset

.github/CONTRIBUTING.md

@@ -82,7 +82,7 @@ Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json
 
 ### Default processes resource requirements
 
-Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.
+Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.
 
 The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${task.memory}` variables in the `script:` block.
 

.github/version_checks.sh

@@ -12,3 +12,8 @@ fi
 
 head -10 CHANGELOG.md | grep "## v$config_version - " >/dev/null \
     || (echo 'Failed to match CHANGELOG version'; exit 1)
+
+# Check .nf-core.yml version
+
+tail -5 .nf-core.yml | grep "version: $config_version" >/dev/null \
+    || (echo 'Failed to match .nf-core.yml version'; exit 1)

.github/workflows/clean-up.yml

@@ -12,9 +12,9 @@ jobs:
     steps:
       - uses: actions/stale@28ca1036281a5e5922ead5184a1bbf96e5fc984e # v9
         with:
-          stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days."
-          stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful."
-          close-issue-message: "This issue was closed because it has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor and then staled for 20 days with no activity."
+          stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback. Remove stale label or add a comment otherwise this issue will be closed in 20 days."
+          stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback. Remove stale label or add a comment if it is still useful."
+          close-issue-message: "This issue was closed because it has been tagged as awaiting-changes or awaiting-feedback and then staled for 20 days with no activity."
           days-before-stale: 30
           days-before-close: 20
           days-before-pr-close: -1

.nf-core.yml

@@ -27,14 +27,14 @@ lint:
     - validation.help.afterText
     - validation.summary.beforeText
     - validation.summary.afterText
-nf_core_version: 3.0.0
+nf_core_version: 3.0.1
 org_path: null
 repository_type: pipeline
 template:
   author: Usman Rashid, Ken Smith, Ross Crowhurst, Chen Wu, Marcus Davy
   description: A NextFlow pipeline which evaluates assembly quality with multiple
     QC tools and presents the results in a unified html report.
-  force: true
+  force: false
   is_nfcore: false
   name: assemblyqc
   org: plant-food-research-open
@@ -43,5 +43,5 @@ template:
     - igenomes
     - multiqc
     - fastqc
-  version: 3.0.0
+  version: 2.2.0+dev
 update: null

.prettierignore

@@ -1,4 +1,3 @@
-
 email_template.html
 adaptivecard.json
 slackreport.json

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 - [09-Oct-2024]
+## v2.2.0+dev - [10-Oct-2024]
 
 ### `Added`
 
 1. Added Gfastats [#126](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/126)
-2. Updated nf-core/template to 3.0.0 [#149](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/149)
+2. Updated nf-core/template to 3.0.1 [#149](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/149)
 
 ### `Fixed`
 

README.md

@@ -183,7 +183,7 @@ If you use plant-food-research-open/assemblyqc for your analysis, please cite it
 
 An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
 
-This pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/master/LICENSE).
+This pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/main/LICENSE).
 
 > **The nf-core framework for community-curated bioinformatics pipelines.**
 >

modules.json

@@ -271,12 +271,12 @@
                     },
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "d20fb2a9cc3e2835e9d067d1046a63252eb17352",
+                        "git_sha": "9d05360da397692321d377b6102d2fb22507c6ef",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "2fdce49d30c0254f76bc0f13c55c17455c1251ab",
+                        "git_sha": "772684d9d66f37b650c8ba5146ac1ee3ecba2acb",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfschema_plugin": {

nextflow.config

@@ -213,6 +213,7 @@ includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${pa
 
 // Load plant-food-research-open/assemblyqc custom profiles from different institutions.
 // includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/assemblyqc.config" : "/dev/null"
+
 // Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
 // Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled
 // Set to your registry if you have a mirror of containers
@@ -293,4 +294,3 @@ validation {
 
 // Load modules.config for DSL2 module specific options
 includeConfig 'conf/modules.config'
-

subworkflows/local/utils_nfcore_assemblyqc_pipeline/main.nf

@@ -20,9 +20,9 @@ include { UTILS_NFCORE_PIPELINE     } from '../../nf-core/utils_nfcore_pipeline'
 include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline'
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     SUBWORKFLOW TO INITIALISE PIPELINE
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 workflow PIPELINE_INITIALISATION {
@@ -180,9 +180,9 @@ workflow PIPELINE_INITIALISATION {
 }
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     SUBWORKFLOW FOR PIPELINE COMPLETION
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 workflow PIPELINE_COMPLETION {
@@ -228,9 +228,9 @@ workflow PIPELINE_COMPLETION {
 }
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     FUNCTIONS
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 //
 // Check and validate pipeline parameters