nf-core · nschan · May 22, 2025 · May 22, 2025 · Jun 2, 2025 · Jun 26, 2025
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
@@ -79,6 +79,7 @@ If you wish to contribute a new step, please use the following coding standards:
 6. Add sanity checks and validation for all relevant parameters.
 7. Perform local tests to validate that the new code works as expected.
 8. If applicable, add a new test in the `tests` directory.
+9. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`.
 
 ### Default values
 

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
@@ -78,7 +78,7 @@ jobs:
           - isMain: false
             profile: "singularity"
         NXF_VER:
-          - "25.04.0"
+          - "25.10.0"
           - "latest-everything"
     env:
       NXF_ANSI_LOG: false

diff --git a/.gitignore b/.gitignore
@@ -9,3 +9,4 @@ testing*
 null/
 .nf-test/
 .nf-test.log
+schema.md
diff --git a/.nf-core.yml b/.nf-core.yml
@@ -7,6 +7,9 @@ lint:
   files_unchanged:
     - assets/sendmail_template.txt
     - .github/CONTRIBUTING.md
+    - assets/nf-core-genomeassembler_logo_light.png
+    - docs/images/nf-core-genomeassembler_logo_light.png
+    - docs/images/nf-core-genomeassembler_logo_dark.png
 nf_core_version: 3.5.1
 repository_type: pipeline
 template:
@@ -20,4 +23,4 @@ template:
   skip_features:
     - multiqc
     - igenomes
-  version: 1.1.0
+  version: 2.0.0dev
diff --git a/.prettierignore b/.prettierignore
@@ -14,5 +14,3 @@ bin/
 ro-crate-metadata.json
 modules/nf-core/
 subworkflows/nf-core/
-*.svg
-tests/
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,53 @@
 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).
 
+## v2.0.0 'Saffron Vulture' - [2026-xx-xx]
+
+This is a major release, with breaking changes.
+v2.0.0 of genomeassembler is a large refactor of the pipeline to facilitate sample-level parameteristation. This allows to either parameterise the _pipeline_ using `params`, or parameterise _samples_ via the `input` samplesheet. In case both types of parameterisations are used, sample parameters will take priority.
+
+Since this workflow follows a sample-centric implementation, nextflow will always render the full pipeline dag, but depending on configuration samples may not travel through the whole pipeline. This may also cause terminal output to show task instances that will never become an active process.
+
+In addition, v2.0.0 contains these changes:
+
+### `Added`
+
+- fastplong for long-read trimming and qc
+- fastp for short-read trimming and qc
+- migration to nf-test
+- increased flexibility of the scaffolding strategy
+- added option to group samples
+- `dorado polish` added as an alternative to `medaka` for ONT polishing. This is an **experimental feature**, due to `dorado` being under active development.
+- HiC scaffolding subworkflow:
+  - mapping with `bwamem2` or `minimap2`
+  - duplicate removal with `picard`
+  - scaffolding with `yahs`
+- Switched to the versions topic, requires nextflow >=25.10.0
+
+### `Fixed`
+
+### `Dependencies`
+
+- `fastplong`
+- `fastp`
+- `dorado`
+- `bwamem2`
+- `picard`
+- `yahs`
+
+### `Deprecated`
+
+The following tools are no longer used:
+
+- `nanoq`
+- `porechop`
+- `lima`
+- `trimgalor`
+
+The following param is no longer implemented:
+
+- `dump`, used to dump jellyfish output.
+
 ## v1.1.0 'Brass Pigeon' - [2025-07-21]
 
 ### `Added`
@@ -72,3 +119,5 @@ Initial release of nf-core/genomeassembler, created with the [nf-core](https://n
 ### `Dependencies`
 
 ### `Deprecated`
+
+Codenames for v1.x are various types of metallic pigeons, v2.x are vultures of different colors.
diff --git a/CITATIONS.md b/CITATIONS.md
@@ -12,19 +12,11 @@
 
 ### Preprocessing
 
-- [lima](https://github.com/pacificbiosciences/barcoding/)
+- [fastp](https://github.com/OpenGene/fastp/) and [fastplong](https://github.com/OpenGene/fastplong/)
 
-- [nanoq](https://github.com/esteinig/nanoq)
+  > Shifu Chen. 2023. Ultrafast one-pass FASTQ data preprocessing, quality control, and deduplication using fastp. iMeta 2: e107. https://doi.org/10.1002/imt2.107
 
-  > Steinig and Coin (2022). Nanoq: ultra-fast quality control for nanopore reads. Journal of Open Source Software, 7(69), 2991, https://doi.org/10.21105/joss.02991
-
-- [porechop](https://github.com/rrwick/Porechop)
-
-  > Wick RR, Judd LM, Gorrie CL, Holt KE. Completing bacterial genome assemblies with multiplex MinION sequencing. Microb Genom. 2017;3(10):e000132. Published 2017 Sep 14. doi:10.1099/mgen.0.000132
-
-- [TrimGalore](https://github.com/FelixKrueger/TrimGalore)
-
-  > Felix Krueger, Frankie James, Phil Ewels, Ebrahim Afyounian, Michael Weinstein, Benjamin Schuster-Boeckler, Gert Hulselmans, & sclamons. (2023). FelixKrueger/TrimGalore. Zenodo. https://doi.org/10.5281/zenodo.7598955
+  > Shifu Chen, Yanqing Zhou, Yaru Chen, Jia Gu; fastp: an ultra-fast all-in-one FASTQ preprocessor, Bioinformatics, Volume 34, Issue 17, 1 September 2018, Pages i884–i890, https://doi.org/10.1093/bioinformatics/bty560
 
 ### Assembly
 
@@ -52,6 +44,8 @@
 
 - [medaka](https://github.com/nanoporetech/medaka)
 
+- [dorado](https://github.com/nanoporetech/dorado)
+
 ### Scaffolding
 
 - [LINKS](https://github.com/bcgsc/LINKS)
@@ -62,6 +56,10 @@
 
   > Coombe L, Li JX, Lo T, Wong J, Nikolic V, Warren RL and Birol I. LongStitch: high-quality genome assembly correction and scaffolding using long reads. BMC Bioinformatics 22, 534 (2021). https://doi.org/10.1186/s12859-021-04451-7
 
+- [yahs](https://github.com/c-zhou/yahs)
+
+  > Chenxi Zhou, Shane A. McCarthy, Richard Durbin. YaHS: yet another Hi-C scaffolding tool. Bioinformatics, 39(1), btac808.
+
 - [RagTag](https://github.com/malonge/RagTag)
 
   > Alonge, Michael, et al. "Automated assembly scaffolding elevates a new tomato system for high-throughput genome editing." Genome Biology (2022). https://doi.org/10.1186/s13059-022-02823-7
@@ -108,6 +106,16 @@
 
 > Petr Danecek, James K Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Martin O Pollard, Andrew Whitwham, Thomas Keane, Shane A McCarthy, Robert M Davies, Heng Li (2021) Twelve years of SAMtools and BCFtools. GigaScience, Volume 10, Issue 2, February 2021, giab008, https://doi.org/10.1093/gigascience/giab008
 
+- [bwa-mem2](https://github.com/bwa-mem2/bwa-mem2)
+
+  > Vasimuddin Md, Sanchit Misra, Heng Li, Srinivas Aluru. Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. IEEE Parallel and Distributed Processing Symposium (IPDPS), 2019.
+
+  > Li H. (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997v2 [q-bio.GN]. (if you use the BWA-MEM algorithm or the fastmap command, or want to cite the whole BWA package)
+
+- [picard](https://broadinstitute.github.io/picard/)
+
+  > “Picard Toolkit.” 2019. Broad Institute, GitHub Repository. https://broadinstitute.github.io/picard/; Broad Institute
+
 ## Software packaging/containerisation tools
 
 - [Anaconda](https://anaconda.com)

diff --git a/README.md b/README.md
@@ -10,7 +10,7 @@
 [![GitHub Actions Linting Status](https://github.com/nf-core/genomeassembler/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/genomeassembler/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/genomeassembler/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.14986998)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
-[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
 [![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)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
@@ -21,44 +21,31 @@
 
 ## Introduction
 
-**nf-core/genomeassembler** is a bioinformatics pipeline that carries out genome assembly, polishing and scaffolding from long reads (ONT or pacbio). Assembly can be done via `flye` or `hifiasm`, polishing can be carried out with `medaka` (ONT), or `pilon` (requires short-reads), and scaffolding can be done using `LINKS`, `Longstitch`, or `RagTag` (if a reference is available). Quality control includes `BUSCO`, `QUAST` and `merqury` (requires short-reads).
-Currently, this pipeline does not implement phasing of polyploid genomes or HiC scaffolding.
+**nf-core/genomeassembler** is a bioinformatics pipeline that carries out genome assembly, polishing and scaffolding from long reads (ONT or pacbio). Assembly can be done via `flye` or `hifiasm`, or combinations of both, polishing can be carried out with `medaka` (ONT), `dorado` (ONT only, experimental) or `pilon` (requires short-reads), and scaffolding can be done using `LINKS`, `Longstitch`, both using long-reads, `yahs` if HiC reads are availble, or `RagTag` if a reference is available. Quality control includes `BUSCO`, `QUAST` and `merqury` (requires short-reads).
+Currently, this pipeline does not implement phasing of polyploid genomes.
 
 <picture>
   <source media="(prefers-color-scheme: dark)" srcset="docs/images/genomeassembler.dark.png">
-  <img alt="nf-core/genomeassembler" src="docs/images/genomeassembler.light.png">
+  <img alt="nf-core/genomeassembler" src="docs/images/genomeassembler_v2.light.png">
 </picture>
 
 ## Usage
 
 > [!NOTE]
 > 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.
 
-First, prepare a samplesheet with your input data that looks as follows:
+nf-core/genomeassembler can be set up via pipeline parameters, or via a samplesheet, or a combination of both. For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/genomeassembler/usage) and the [parameter documentation](https://nf-co.re/genomeassembler/parameters).
 
-`samplesheet.csv`:
-
-```csv
-sample,ontreads,hifireads,ref_fasta,ref_gff,shortread_F,shortread_R,paired
-sampleName,ontreads.fa.gz,hifireads.fa.gz,assembly.fasta.gz,reference.fasta,reference.gff,short_F1.fastq,short_F2.fastq,true
-```
-
-Each row represents one genome to be assembled. `sample` should contain the name of the sample, `ontreads` should contain a path to ONT reads (fastq.gz), `hifireads` a path to HiFi reads (fastq.gz), `ref_fasta` and `ref_gff` contain reference genome fasta and annotations. `shortread_F` and `shortread_R` contain paths to short-read data, `paired` indicates if short-reads are paired. Columns can be omitted if they contain no data, with the exception of `shortread_R`, which needs to be present if `shortread_F` is there, even if it is empty.
-
-Now, you can run the pipeline using:
+The pipeline can be run with a test-profile via:
 
 ```bash
 nextflow run nf-core/genomeassembler \
-   -profile <docker/singularity/.../institute> \
-   --input samplesheet.csv \
-   --outdir <OUTDIR>
+   -profile test,<docker/singularity/.../institute> \
 ```
 
 > [!WARNING]
 > 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**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).
 
-For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/genomeassembler/usage) and the [parameter documentation](https://nf-co.re/genomeassembler/parameters).
-
 ## Pipeline output
 
 To see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/genomeassembler/results) tab on the nf-core website pipeline page.
@@ -67,12 +54,14 @@ For more details about the output files and reports, please refer to the
 
 ## Credits
 
-nf-core/genomeassembler was originally written by [Niklas Schandry](https://github.com/nschan), of the Faculty of Biology of the Ludwig-Maximilians University (LMU) in Munich, Germany.
+nf-core/genomeassembler was written, and is currently maintained by [Niklas Schandry](https://github.com/nschan), of the Faculty of Biology of the Ludwig-Maximilians University (LMU) in Munich, Germany, with funding support from the German Research Foundation (Deutsche Forschungsgemeinschaft [DFG], via Transregional Research Center TRR356 grant 491090170-A05 to Niklas Schandry).
 
-I thank the following people for their extensive assistance and constructive reviews during the development of this pipeline:
+I thank the following people for constructive reviews and discussion during the development of this pipeline:
 
+- [Jim Downie](https://github.com/prototaxites)
 - [Mahesh Binzer-Panchal](https://github.com/mahesh-panchal)
 - [Matthias Hörtenhuber](https://github.com/mashehu)
+- [Evangelos Karatzas](https://github.com/vagkaratzas)
 - [Louis Le Nézet](https://github.com/LouisLeNezet)
 - [Júlia Mir Pedrol](https://github.com/mirpedrol)
 - [Daniel Straub](https://github.com/d4straub)

diff --git a/assets/nf-core-genomeassembler_logo_light.png b/assets/nf-core-genomeassembler_logo_light.png
diff --git a/assets/report/_brand.yml b/assets/report/_brand.yml
@@ -0,0 +1,38 @@
+color:
+  palette:
+    green: "#24B064"
+    brown: "#3F2B29"
+    yellow: "#ECDC86"
+    white: "#f9f9f9"
+    gray-dark: "#343a40"
+    gray-100: "#f8f9fa"
+    gray-200: "#e9ecef"
+    gray-300: "#dee2e6"
+    gray-400: "#ced4da"
+    gray-500: "#adb5bd"
+    gray-600: "#6c757d"
+    gray-700: "#495057"
+    gray-800: "#343a40"
+    gray-900: "#212529"
+  background: white
+  foreground: gray-dark
+  primary: green
+  secondary: yellow
+  tertiary: brown
+  light: "#f8f9fa"
+  dark: "#212529"
+
+logo:
+  images:
+    banner: "nf-core-logo.png"
+    apple: "nf-core-logo-square.png"
+  small: apple
+  medium: banner
+  large: banner
+
+typography:
+  fonts:
+    - family: Maven Pro
+      source: google
+  base: Maven Pro
+  headings: Maven Pro