Revert nf-cmgg/configs to nf-core/configs

.nf-core.yml

@@ -41,4 +41,4 @@ template:
   skip_features:
     - fastqc
     - is_nfcore
-  version: 1.13.5
+  version: 1.14.0dev

CHANGELOG.md

@@ -3,6 +3,10 @@
 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).
 
+## v1.14.0
+
+- Revert the default configs base to the nf-core configs in preparation of converting nf-cmgg/configs to a private repo
+
 ## v1.13.5
 
 - Set `outdir` type to `String` to avoid file existence checking

assets/multiqc_config.yml

@@ -1,5 +1,5 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-cmgg/smallvariants/releases/tag/1.13.5" target="_blank">nf-cmgg/smallvariants</a> analysis pipeline.
+  This report has been generated by the <a href="https://github.com/nf-cmgg/smallvariants/tree/dev" target="_blank">nf-cmgg/smallvariants</a> analysis pipeline.
 report_section_order:
   "nf-cmgg-smallvariants-methods-description":
     order: -1000

conf/test.config

@@ -27,7 +27,6 @@ params {
 
     // Genome references
     igenomes_ignore = true
-    custom_config_base = null
 
     // References
     fasta           = "https://github.com/nf-cmgg/test-datasets/raw/smallvariants/data/genomics/homo_sapiens/genome/hg38_chr21_22000000_23000000.fasta"

main.nf

@@ -178,24 +178,6 @@ params {
     // Don't output the merged CRAM files.
     skip_merged_cram_output: Boolean = false
 
-    // Git commit id for Institutional configs.
-    custom_config_version: String = 'main'
-
-    // Base directory for Institutional configs.
-    custom_config_base: String = 'https://raw.githubusercontent.com/nf-cmgg/configs/main'
-
-    // Institutional config name.
-    config_profile_name: String?
-
-    // Institutional config description.
-    config_profile_description: String?
-
-    // Institutional config contact information.
-    config_profile_contact: String?
-
-    // Institutional config URL link.
-    config_profile_url: String?
-
     // Display version and exit.
     version: Boolean = false
 

nextflow.config

@@ -22,8 +22,8 @@ params {
     trace_report_suffix          = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
 
     // Config options
-    custom_config_version        = 'main'
-    custom_config_base           = "https://raw.githubusercontent.com/nf-cmgg/configs/${params.custom_config_version}"
+    custom_config_version        = 'master'
+    custom_config_base           = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
 }
 
 // Load base.config by default for all pipelines
@@ -153,9 +153,6 @@ includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !pa
 // Load nf-cmgg/smallvariants custom profiles from different institutions.
 includeConfig params.custom_config_base && params.custom_config_base.contains('nf-cmgg') && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/pipeline/smallvariants.config" : "/dev/null"
 
-// Load igenomes.config if required
-includeConfig !params.igenomes_ignore as Boolean ? 'https://github.com/nf-cmgg/configs/raw/refs/heads/main/conf/genome/igenomes.config' : 'conf/igenomes_ignored.config'
-
 // Export these variables to prevent local Python/R libraries from conflicting with those in the container
 // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
 // See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.
@@ -226,7 +223,7 @@ manifest {
     mainScript      = 'main.nf'
     defaultBranch   = 'main'
     nextflowVersion = '!>=26.04.0'
-    version         = '1.13.5'
+    version         = '1.14.0dev'
     doi             = ''
 }
 

nextflow_schema.json

@@ -337,14 +337,14 @@
                 "custom_config_version": {
                     "type": "string",
                     "description": "Git commit id for Institutional configs.",
-                    "default": "main",
+                    "default": "master",
                     "hidden": true,
                     "fa_icon": "fas fa-users-cog"
                 },
                 "custom_config_base": {
                     "type": "string",
                     "description": "Base directory for Institutional configs.",
-                    "default": "https://raw.githubusercontent.com/nf-cmgg/configs/main",
+                    "default": "https://raw.githubusercontent.com/nf-core/configs/master",
                     "hidden": true,
                     "help_text": "If you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.",
                     "fa_icon": "fas fa-users-cog"

ro-crate-metadata.json

@@ -21,8 +21,8 @@
         {
             "@id": "./",
             "@type": "Dataset",
-            "creativeWorkStatus": "Stable",
-            "datePublished": "2026-07-22T12:51:01+00:00",
+            "creativeWorkStatus": "InProgress",
+            "datePublished": "2026-08-04T12:19:19+00:00",
             "description": "# nf-cmgg/smallvariants\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-cmgg/smallvariants)\n[![GitHub Actions CI Status](https://github.com/nf-cmgg/smallvariants/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-cmgg/smallvariants/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-cmgg/smallvariants/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-cmgg/smallvariants/actions/workflows/linting.yml)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A526.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.2)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-cmgg/smallvariants)\n\n## Introduction\n\n**nf-cmgg/smallvariants** is a nextflow pipeline for calling and annotating small variants from short DNA reads for WES and WGS data.\n\nThe pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!\n\nPlease have a look at the [documentation](https://nf-cmgg.github.io/smallvariants/latest/) on how to run the pipeline.\n\n## Development environment\n\nA [pixi](https://pixi.prefix.dev/latest/) development environment is available for this pipeline. Run the following command to install the environment:\n\n```\npixi install\n```\n\nThen run `pixi shell` to enter the environment and start developing.\n",
             "hasPart": [
                 {
@@ -99,7 +99,7 @@
             },
             "mentions": [
                 {
-                    "@id": "#e6d7203f-a78f-4daa-a554-428a830bb448"
+                    "@id": "#40185ead-91bc-4727-8e4e-3a7a25298b82"
                 }
             ],
             "name": "nf-cmgg/smallvariants"
@@ -132,7 +132,7 @@
                 }
             ],
             "dateCreated": "",
-            "dateModified": "2026-07-22T14:51:01Z",
+            "dateModified": "2026-08-04T14:19:19Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
             "keywords": [
                 "nf-core",
@@ -160,10 +160,10 @@
             },
             "url": [
                 "https://github.com/nf-cmgg/smallvariants",
-                "https://nf-co.re/nf-cmgg/smallvariants/1.13.5/"
+                "https://nf-co.re/nf-cmgg/smallvariants/dev/"
             ],
             "version": [
-                "1.13.5"
+                "1.14.0dev"
             ]
         },
         {
@@ -179,11 +179,11 @@
             "version": "!>=26.04.0"
         },
         {
-            "@id": "#e6d7203f-a78f-4daa-a554-428a830bb448",
+            "@id": "#40185ead-91bc-4727-8e4e-3a7a25298b82",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#66262067-5e7f-452d-93e4-ca9008107954"
+                    "@id": "#bbc79464-a2e2-41e1-a581-e5fcb3c9da2d"
                 }
             ],
             "mainEntity": {
@@ -192,7 +192,7 @@
             "name": "Test suite for nf-cmgg/smallvariants"
         },
         {
-            "@id": "#66262067-5e7f-452d-93e4-ca9008107954",
+            "@id": "#bbc79464-a2e2-41e1-a581-e5fcb3c9da2d",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing nf-cmgg/smallvariants",
             "resource": "repos/nf-cmgg/smallvariants/actions/workflows/nf-test.yml",