preprocessing v3.0.2

.nf-core.yml

@@ -39,4 +39,4 @@ template:
   org: nf-cmgg
   outdir: .
   skip_features: ["fastqc"]
-  version: 3.0.1
+  version: 3.0.2

CHANGELOG.md

@@ -3,7 +3,11 @@
 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).
 
-## 3.0.1dev
+## 3.0.2
+
+- remove common plugins in favor of defining them in the nf-cmgg/configs, which will be used across all nf-cmgg pipelines. This allows for better version control and consistency across pipelines, as well as reducing the maintenance burden of keeping plugins up to date in multiple repositories.
+
+## 3.0.1
 
 - Add parameter typing to make strict syntax runs work more properly
 - Bumped minimal Nextflow version to 26.04.0 to allow for strict syntax and other improvements

assets/multiqc_config.yml

@@ -1,5 +1,5 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-cmgg/preprocessing/releases/tag/3.0.1" target="_blank">nf-cmgg/preprocessing</a> analysis pipeline.
+  This report has been generated by the <a href="https://github.com/nf-cmgg/preprocessing/releases/tag/3.0.2" target="_blank">nf-cmgg/preprocessing</a> analysis pipeline.
 report_section_order:
   "nf-cmgg-preprocessing-methods-description":
     order: -1000

nextflow.config

@@ -197,36 +197,20 @@ manifest {
     mainScript      = 'main.nf'
     defaultBranch   = 'main'
     nextflowVersion = '!>=26.04.0'
-    version         = '3.0.1'
+    version         = '3.0.2'
     doi             = ''
 }
 
 // Nextflow plugins
 plugins {
-    id 'nf-cgroup-metrics@1.0.1'
-    id 'nf-cmgg@0.2.1'
     id 'nf-schema@2.7.2'
-    id 'nf-teams@0.1.1'
 }
 
 validation {
     defaultIgnoreParams = ["genomes"].toSet()
     monochromeLogs      = params.monochrome_logs.toBoolean()
 }
 
-// TODO remove this once minimal nf-version is 26.0X with strict syntax.
-cmgg {
-    samplesheets.enabled = true
-    done.enabled         = true
-}
-teams {
-    enabled            = true
-    webHook {
-        url = params.hook_url ? params.hook_url : System.getenv('TEAMS_WEBHOOK_URL')
-    }
-    onComplete.enabled = true
-}
-
 // Load modules.config for DSL2 module specific options
 includeConfig 'conf/modules.config'
 

ro-crate-metadata.json

@@ -22,7 +22,7 @@
             "@id": "./",
             "@type": "Dataset",
             "creativeWorkStatus": "Stable",
-            "datePublished": "2026-05-19T19:42:24+00:00",
+            "datePublished": "2026-05-27T13:33:39+00:00",
             "description": "# nf-cmgg/preprocessing\n\n[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://github.com/codespaces/new/nf-cmgg/preprocessing)\n[![GitHub Actions CI Status](https://github.com/nf-cmgg/preprocessing/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-cmgg/preprocessing/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-cmgg/preprocessing/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-cmgg/preprocessing/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-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)\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/preprocessing)\n\n## Introduction\n\n**nf-cmgg/preprocessing** is a bioinformatics pipeline that demultiplexes and aligns raw sequencing data.\nIt also performs basic QC and coverage analysis.\n\nThe pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.\n\nSteps include:\n\n- Demultiplexing using [`BCLconvert`](https://emea.support.illumina.com/sequencing/sequencing_software/bcl-convert.html)\n- Run QC using [`MultiQC SAV`](https://github.com/MultiQC/MultiQC_SAV)\n- Read QC and trimming using [`fastp`](https://github.com/OpenGene/fastp) or [`falco`](https://github.com/smithlabcode/falco)\n- Alignment using either [`bwa`](https://github.com/lh3/bwa), [`bwa-mem2`](https://github.com/bwa-mem2/bwa-mem2), [`bowtie2`](https://github.com/BenLangmead/bowtie2), [`dragmap`](https://github.com/Illumina/DRAGMAP), [`snap`](https://github.com/amplab/snap) or [`strobe`](https://github.com/ksahlin/strobealign) for DNA-seq and [`STAR`](https://github.com/alexdobin/STAR) for RNA-seq\n- Duplicate marking using [`bamsormadup`](https://gitlab.com/german.tischler/biobambam2) or [`samtools markdup`](http://www.htslib.org/doc/samtools-markdup.html)\n- Coverage analysis using [`mosdepth`](https://github.com/brentp/mosdepth) and [`samtools coverage`](http://www.htslib.org/doc/samtools-coverage.html)\n- Alignment QC using [`samtools flagstat`](http://www.htslib.org/doc/samtools-flagstat.html), [`samtools stats`](http://www.htslib.org/doc/samtools-stats.html), [`samtools idxstats`](http://www.htslib.org/doc/samtools-idxstats.html) and [`picard CollectHsMetrics`](https://broadinstitute.github.io/picard/command-line-overview.html#CollectHsMetrics), [`picard CollectWgsMetrics`](https://broadinstitute.github.io/picard/command-line-overview.html#CollectWgsMetrics), [`picard CollectMultipleMetrics`](https://broadinstitute.github.io/picard/command-line-overview.html#CollectMultipleMetrics)\n- QC aggregation using [`multiqc`](https://multiqc.info/)\n\n<picture>\n\n  <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/metro_map_dark.svg\">\n  <source media=\"(prefers-color-scheme: light)\" srcset=\"docs/images/metro_map_light.svg\">\n  <img alt=\"Fallback image description\" src=\"docs/images/metro_map_light.svg\">\n</picture>\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nThe full documentation can be found [here](docs/README.md)\n\nFirst, prepare a samplesheet with your input data. Check the [usage docs](docs/usage.md) for details on the required format and example files.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-cmgg/preprocessing \\\n   -profile <docker/singularity/...> \\\n   --igenomes_base /path/to/genomes \\\n   --input samplesheet.<csv|yaml|json> \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;\n> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).\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\n## Credits\n\nnf-cmgg/preprocessing was originally written by the CMGG ICT team.\n\n## Support\n\nThis 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).\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
             "hasPart": [
                 {
@@ -102,7 +102,7 @@
             },
             "mentions": [
                 {
-                    "@id": "#5cac7e80-de46-45b1-a79f-4bce656b0d47"
+                    "@id": "#cb12ae76-cc32-4dd8-b67d-d06d643513d2"
                 }
             ],
             "name": "nf-cmgg/preprocessing"
@@ -134,8 +134,11 @@
                     "@id": "https://orcid.org/0000-0003-2555-3114"
                 }
             ],
-            "dateCreated": "",
-            "dateModified": "2026-05-19T21:42:24Z",
+            "dateCreated": [
+                "",
+                "2026-05-20T09:02:37Z"
+            ],
+            "dateModified": "2026-05-27T15:33:39Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
             "keywords": [
                 "nf-core",
@@ -163,10 +166,10 @@
             },
             "url": [
                 "https://github.com/nf-cmgg/preprocessing",
-                "https://nf-co.re/nf-cmgg/preprocessing/3.0.1/"
+                "https://nf-co.re/nf-cmgg/preprocessing/3.0.2/"
             ],
             "version": [
-                "3.0.1"
+                "3.0.2"
             ]
         },
         {
@@ -182,11 +185,11 @@
             "version": "!>=26.04.0"
         },
         {
-            "@id": "#5cac7e80-de46-45b1-a79f-4bce656b0d47",
+            "@id": "#cb12ae76-cc32-4dd8-b67d-d06d643513d2",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#fc81fe8f-371d-4a82-b52b-8b2262a9f3ca"
+                    "@id": "#f36a54e6-3b86-47eb-8f1d-f94369a34a5c"
                 }
             ],
             "mainEntity": {
@@ -195,7 +198,7 @@
             "name": "Test suite for nf-cmgg/preprocessing"
         },
         {
-            "@id": "#fc81fe8f-371d-4a82-b52b-8b2262a9f3ca",
+            "@id": "#f36a54e6-3b86-47eb-8f1d-f94369a34a5c",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing nf-cmgg/preprocessing",
             "resource": "repos/nf-cmgg/preprocessing/actions/workflows/nf-test.yml",