diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 1f9ed4d6..e01c8db1 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -79,7 +79,6 @@ 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/actions/nf-test/action.yml b/.github/actions/nf-test/action.yml index ddfac57b..bf44d961 100644 --- a/.github/actions/nf-test/action.yml +++ b/.github/actions/nf-test/action.yml @@ -54,8 +54,6 @@ runs: conda-solver: libmamba conda-remove-defaults: true - # TODO Skip failing conda tests and document their failures - # https://github.com/nf-core/modules/issues/7017 - name: Run nf-test shell: bash env: diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 5584fa4c..9a5a5254 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -27,7 +27,7 @@ jobs: strategy: matrix: NXF_VER: - - "24.04.2" + - "24.10.5" - "latest-everything" ASSEMBLER: - "hifi_flye" diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index f2d7d1dd..8b0f88c3 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -13,7 +13,7 @@ jobs: steps: - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 - - name: Set up Python 3.12 + - name: Set up Python 3.13 uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5 with: python-version: "3.13" diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index 7e8050fb..d43797d9 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Download lint results - uses: dawidd6/action-download-artifact@4c1e823582f43b179e2cbb49c3eade4e41f992e2 # v10 + uses: dawidd6/action-download-artifact@ac66b43f0e6a346234dd65d4d0c8fbb31cb316e5 # v11 with: workflow: linting.yml workflow_conclusion: completed diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index c5d931da..e7b58449 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -1,12 +1,5 @@ name: Run nf-test on: - push: - paths-ignore: - - "docs/**" - - "**/meta.yml" - - "**/*.md" - - "**/*.png" - - "**/*.svg" pull_request: paths-ignore: - "docs/**" @@ -35,8 +28,8 @@ jobs: nf-test-changes: name: nf-test-changes runs-on: # use self-hosted runners - - runs-on=$-nf-test-changes - - runner4cpu-linux-x64 + - runs-on=${{ github.run_id }}-nf-test-changes + - runner=4cpu-linux-x64 outputs: shard: ${{ steps.set-shards.outputs.shard }} total_shards: ${{ steps.set-shards.outputs.total_shards }} @@ -69,7 +62,7 @@ jobs: needs: [nf-test-changes] if: ${{ needs.nf-test-changes.outputs.total_shards != '0' }} runs-on: # use self-hosted runners - - runs-on=$-nf-test + - runs-on=${{ github.run_id }}-nf-test - runner=4cpu-linux-x64 strategy: fail-fast: false @@ -85,7 +78,7 @@ jobs: - isMain: false profile: "singularity" NXF_VER: - - "24.04.2" + - "24.10.5" - "latest-everything" env: NXF_ANSI_LOG: false @@ -97,21 +90,39 @@ jobs: fetch-depth: 0 - name: Run nf-test + id: run_nf_test uses: ./.github/actions/nf-test + continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }} env: NFT_WORKDIR: ${{ env.NFT_WORKDIR }} with: profile: ${{ matrix.profile }} shard: ${{ matrix.shard }} total_shards: ${{ env.TOTAL_SHARDS }} + + - name: Report test status + if: ${{ always() }} + run: | + if [[ "${{ steps.run_nf_test.outcome }}" == "failure" ]]; then + echo "::error::Test with ${{ matrix.NXF_VER }} failed" + # Add to workflow summary + echo "## ❌ Test failed: ${{ matrix.profile }} | ${{ matrix.NXF_VER }} | Shard ${{ matrix.shard }}/${{ env.TOTAL_SHARDS }}" >> $GITHUB_STEP_SUMMARY + if [[ "${{ matrix.NXF_VER }}" == "latest-everything" ]]; then + echo "::warning::Test with latest-everything failed but will not cause workflow failure. Please check if the error is expected or if it needs fixing." + fi + if [[ "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then + exit 1 + fi + fi + confirm-pass: needs: [nf-test] if: always() runs-on: # use self-hosted runners - - runs-on=$-confirm-pass + - runs-on=${{ github.run_id }}-confirm-pass - runner=2cpu-linux-x64 steps: - - name: One or more tests failed + - name: One or more tests failed (excluding latest-everything) if: ${{ contains(needs.*.result, 'failure') }} run: exit 1 @@ -130,11 +141,3 @@ jobs: echo "DEBUG: toJSON(needs) = ${{ toJSON(needs) }}" echo "DEBUG: toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}" echo "::endgroup::" - - - name: Clean Workspace # Purge the workspace in case it's running on a self-hosted runner - if: always() - run: | - ls -la ./ - rm -rf ./* || true - rm -rf ./.??* || true - ls -la ./ diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml index 4abaf484..0f732495 100644 --- a/.github/workflows/release-announcements.yml +++ b/.github/workflows/release-announcements.yml @@ -30,7 +30,7 @@ jobs: bsky-post: runs-on: ubuntu-latest steps: - - uses: zentered/bluesky-post-action@4aa83560bb3eac05dbad1e5f221ee339118abdd2 # v0.2.0 + - uses: zentered/bluesky-post-action@6461056ea355ea43b977e149f7bf76aaa572e5e8 # v0.3.0 with: post: | Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! diff --git a/.nf-core.yml b/.nf-core.yml index 14b85bf0..377951a7 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -7,7 +7,7 @@ lint: - assets/multiqc_config.yml files_unchanged: - .github/CONTRIBUTING.md -nf_core_version: 3.3.1 +nf_core_version: 3.3.2 repository_type: pipeline template: author: Niklas Schandry diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 4c219f64..402f0a1c 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -4,7 +4,7 @@ repos: hooks: - id: prettier additional_dependencies: - - prettier@3.5.0 + - prettier@3.6.2 - repo: https://github.com/pre-commit/pre-commit-hooks rev: v5.0.0 hooks: diff --git a/CHANGELOG.md b/CHANGELOG.md index aadac002..02c6831d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,6 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Added` +[#170](https://github.com/nf-core/genomeassembler/issues/170) - Switched to nf-core template 3.3.2 + [#164](https://github.com/nf-core/genomeassembler/issues/164) - Switched to nf-core template 3.3.1 [#153](https://github.com/nf-core/genomeassembler/issues/153) - Switched to nf-core template 3.2.1 diff --git a/README.md b/README.md index b01a4e21..5719717b 100644 --- a/README.md +++ b/README.md @@ -9,13 +9,14 @@ [![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.14986998-1073c8?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%A524.04.2-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-3.3.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.1) +[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.10.5-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-3.3.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.2) [![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/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) [![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-core/genomeassembler) +[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23genomeassembler-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/genomeassembler)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core) [![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23genomeassembler-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/genomeassembler)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core) ## Introduction diff --git a/conf/base.config b/conf/base.config index 10a24838..da8ec780 100644 --- a/conf/base.config +++ b/conf/base.config @@ -56,5 +56,6 @@ process { } withLabel: process_gpu { ext.use_gpu = { workflow.profile.contains('gpu') } + accelerator = { workflow.profile.contains('gpu') ? 1 : null } } } diff --git a/modules.json b/modules.json index 21003454..daa2af82 100644 --- a/modules.json +++ b/modules.json @@ -12,7 +12,7 @@ }, "fastqc": { "branch": "master", - "git_sha": "b1966f36ec9de31927b2603d8f499960b2a4c294", + "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", "installed_by": ["modules"] }, "flye": { diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml index 2b2e62b8..c8d9d025 100644 --- a/modules/nf-core/fastqc/meta.yml +++ b/modules/nf-core/fastqc/meta.yml @@ -29,9 +29,10 @@ input: description: | List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. + ontologies: [] output: - - html: - - meta: + html: + - - meta: type: map description: | Groovy Map containing sample information @@ -40,8 +41,9 @@ output: type: file description: FastQC report pattern: "*_{fastqc.html}" - - zip: - - meta: + ontologies: [] + zip: + - - meta: type: map description: | Groovy Map containing sample information @@ -50,11 +52,14 @@ output: type: file description: FastQC report archive pattern: "*_{fastqc.zip}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@drpatelh" - "@grst" diff --git a/nextflow.config b/nextflow.config index 068f2858..17bb4d91 100644 --- a/nextflow.config +++ b/nextflow.config @@ -310,14 +310,15 @@ manifest { homePage = 'https://github.com/nf-core/genomeassembler' description = """Assemble genomes from long ONT or pacbio HiFi reads""" mainScript = 'main.nf' - nextflowVersion = '!>=24.04.2' + defaultBranch = 'master' + nextflowVersion = '!>=24.10.5' version = '1.1.0' doi = '10.5281/zenodo.14986998' } // Nextflow plugins plugins { - id 'nf-schema@2.2.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet + id 'nf-schema@2.4.2' // Validation of pipeline parameters and creation of an input channel from a sample sheet } validation { diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 741020af..8545a1f2 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -22,8 +22,8 @@ "@id": "./", "@type": "Dataset", "creativeWorkStatus": "Stable", - "datePublished": "2025-06-03T11:01:26+00:00", - "description": "

\n \n \n \"nf-core/genomeassembler\"\n \n

\n\n[![GitHub Actions CI Status](https://github.com/nf-core/genomeassembler/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/genomeassembler/actions/workflows/ci.yml)\n[![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.14986998-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.14986998)\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%A524.04.2-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-3.3.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.1)\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-core/genomeassembler)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23genomeassembler-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/genomeassembler)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**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).\nCurrently, this pipeline does not implement phasing of polyploid genomes or HiC scaffolding.\n\n\n \n \"nf-core/genomeassembler\"\n\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\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,ontreads,hifireads,ref_fasta,ref_gff,shortread_F,shortread_R,paired\nsampleName,ontreads.fa.gz,hifireads.fa.gz,assembly.fasta.gz,reference.fasta,reference.gff,short_F1.fastq,short_F2.fastq,true\n```\n\nEach 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.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/genomeassembler \\\n -profile \\\n --input samplesheet.csv \\\n --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**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor 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).\n\n## Pipeline output\n\nTo 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.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/genomeassembler/output).\n\n## Credits\n\nnf-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.\n\nI thank the following people for their extensive assistance and constructive reviews during the development of this pipeline:\n\n- [Mahesh Binzer-Panchal](https://github.com/mahesh-panchal)\n- [Matthias H\u00f6rtenhuber](https://github.com/mashehu)\n- [Louis Le N\u00e9zet](https://github.com/LouisLeNezet)\n- [J\u00falia Mir Pedrol](https://github.com/mirpedrol)\n- [Daniel Straub](https://github.com/d4straub)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#genomeassembler` channel](https://nfcore.slack.com/channels/genomeassembler) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/genomeassembler for your analysis, please cite it using the following doi: [10.5281/zenodo.14986998](https://doi.org/10.5281/zenodo.14986998)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\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", + "datePublished": "2025-07-08T11:38:27+00:00", + "description": "

\n \n \n \"nf-core/genomeassembler\"\n \n

\n\n[![GitHub Actions CI Status](https://github.com/nf-core/genomeassembler/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/genomeassembler/actions/workflows/ci.yml)\n[![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.14986998-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.14986998)\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%A524.10.5-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-3.3.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.2)\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-core/genomeassembler)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23genomeassembler-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/genomeassembler)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23genomeassembler-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/genomeassembler)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**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).\nCurrently, this pipeline does not implement phasing of polyploid genomes or HiC scaffolding.\n\n\n \n \"nf-core/genomeassembler\"\n\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\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,ontreads,hifireads,ref_fasta,ref_gff,shortread_F,shortread_R,paired\nsampleName,ontreads.fa.gz,hifireads.fa.gz,assembly.fasta.gz,reference.fasta,reference.gff,short_F1.fastq,short_F2.fastq,true\n```\n\nEach 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.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/genomeassembler \\\n -profile \\\n --input samplesheet.csv \\\n --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**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor 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).\n\n## Pipeline output\n\nTo 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.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/genomeassembler/output).\n\n## Credits\n\nnf-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.\n\nI thank the following people for their extensive assistance and constructive reviews during the development of this pipeline:\n\n- [Mahesh Binzer-Panchal](https://github.com/mahesh-panchal)\n- [Matthias H\u00f6rtenhuber](https://github.com/mashehu)\n- [Louis Le N\u00e9zet](https://github.com/LouisLeNezet)\n- [J\u00falia Mir Pedrol](https://github.com/mirpedrol)\n- [Daniel Straub](https://github.com/d4straub)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#genomeassembler` channel](https://nfcore.slack.com/channels/genomeassembler) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/genomeassembler for your analysis, please cite it using the following doi: [10.5281/zenodo.14986998](https://doi.org/10.5281/zenodo.14986998)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\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": [ { "@id": "main.nf" @@ -105,7 +105,7 @@ }, "mentions": [ { - "@id": "#cb94731f-386a-4fae-91e7-9fbf9fde0a63" + "@id": "#8601bd11-94fa-4298-805d-fb2c3f6a7eab" } ], "name": "nf-core/genomeassembler" @@ -144,7 +144,7 @@ } ], "dateCreated": "", - "dateModified": "2025-06-03T11:01:26Z", + "dateModified": "2025-07-08T11:38:27Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": [ "nf-core", @@ -181,14 +181,14 @@ "url": { "@id": "https://www.nextflow.io/" }, - "version": "!>=24.04.2" + "version": "!>=24.10.5" }, { - "@id": "#cb94731f-386a-4fae-91e7-9fbf9fde0a63", + "@id": "#8601bd11-94fa-4298-805d-fb2c3f6a7eab", "@type": "TestSuite", "instance": [ { - "@id": "#590a10e6-d2a9-410c-914b-653c68ca442d" + "@id": "#a9fa96cd-308f-4e32-b912-de8b760cb8e2" } ], "mainEntity": { @@ -197,7 +197,7 @@ "name": "Test suite for nf-core/genomeassembler" }, { - "@id": "#590a10e6-d2a9-410c-914b-653c68ca442d", + "@id": "#a9fa96cd-308f-4e32-b912-de8b760cb8e2", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/genomeassembler", "resource": "repos/nf-core/genomeassembler/actions/workflows/nf-test.yml", diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config index 0907ac58..09ef842a 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config @@ -1,5 +1,5 @@ plugins { - id "nf-schema@2.1.0" + id "nf-schema@2.4.2" } validation { diff --git a/tests/nextflow.config b/tests/nextflow.config index 0c642001..f5eb58fd 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -4,8 +4,6 @@ ======================================================================================== */ -// TODO nf-core: Specify any additional parameters here -// Or any resources requirements params.modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' params.pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genomeassembler'