Merge pull request #26 from caravagnalab/dev

First release final fixes

.nf-core.yml

@@ -2,8 +2,8 @@ nf_core_version: 3.2.0
 repository_type: pipeline
 template:
   author: Nicola Calonaci, Elena Buscaroli, Katsiaryna Davydzenka, Giorgia Gandolfi,
-    Virginia Gazziero, Brandon Hastings, Davide Rambaldi, Rodolfo Tolloi, Lucrezia Valeriani
-    and Giulio Caravagna
+    Virginia Gazziero, Brandon Hastings, Davide Rambaldi, Rodolfo Tolloi, Lucrezia
+    Valeriani and Giulio Caravagna
   description: Analysis pipleine to model tumour clonal evolution from WGS data (driver
     annotation, quality control of copy number calls, subclonal and mutational signature
     deconvolution)
@@ -12,8 +12,8 @@ template:
   name: tumourevo
   org: nf-core
   outdir: .
-  version: 1.0dev
+  version: 1.0.0
 lint:
-  modules_config: False
+  modules_config: false
   files_exist:
     - conf/modules.config

CHANGELOG.md

@@ -3,14 +3,6 @@
 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).
 
-## v1.0dev - [date]
+## v1.0.0 - [2025-01-30] - Expanding Clone
 
 Initial release of nf-core/tumourevo, created with the [nf-core](https://nf-co.re/) template.
-
-### `Added`
-
-### `Fixed`
-
-### `Dependencies`
-
-### `Deprecated`

assets/multiqc_config.yml

@@ -1,7 +1,8 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/tumourevo/tree/dev" target="_blank">nf-core/tumourevo</a>
-  analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/tumourevo/dev/docs/output" target="_blank">documentation</a>.
+  This report has been generated by the <a href="https://github.com/nf-core/tumourevo/releases/tag/1.0.0"
+  target="_blank">nf-core/tumourevo</a> analysis pipeline. For information about how
+  to interpret these results, please see the <a href="https://nf-co.re/tumourevo/1.0.0/docs/output"
+  target="_blank">documentation</a>.
 report_section_order:
   "nf-core-tumourevo-methods-description":
     order: -1000

nextflow.config

@@ -215,7 +215,7 @@ params {
 
 // Container slug. Stable releases should specify release tag!
 // Developmental code should specify :dev
-process.container = 'nfcore/tumourevo:dev'
+process.container = 'nfcore/tumourevo:1.0.0'
 
 // Load base.config by default for all pipelines
 
@@ -348,7 +348,7 @@ includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${pa
 
 // Load nf-core/tumourevo custom profiles from different institutions.
 // TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
-// includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/tumourevo.config" : "/dev/null"
+includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/tumourevo.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
@@ -487,7 +487,7 @@ manifest {
     mainScript      = 'main.nf'
     defaultBranch   = 'master'
     nextflowVersion = '!>=24.04.2'
-    version         = '1.0dev'
+    version         = '1.0.0'
     doi             = ''
 }