From 888aeed1d9fdfeebdfdb7450486b56d40d3c7e74 Mon Sep 17 00:00:00 2001 From: Florian Wuennemann Date: Thu, 26 Jun 2025 19:54:41 +0000 Subject: [PATCH 1/6] Bump fastqc, seqtk/trim and multiqc module versions. --- modules.json | 6 +++--- modules/nf-core/fastqc/environment.yml | 2 ++ modules/nf-core/fastqc/main.nf | 2 +- modules/nf-core/multiqc/environment.yml | 4 +++- modules/nf-core/multiqc/main.nf | 4 ++-- .../nf-core/multiqc/tests/main.nf.test.snap | 18 +++++++++--------- modules/nf-core/multiqc/tests/tags.yml | 2 -- modules/nf-core/seqtk/trim/environment.yml | 2 ++ modules/nf-core/seqtk/trim/tests/tags.yml | 2 -- 9 files changed, 22 insertions(+), 20 deletions(-) delete mode 100644 modules/nf-core/multiqc/tests/tags.yml delete mode 100644 modules/nf-core/seqtk/trim/tests/tags.yml diff --git a/modules.json b/modules.json index 20ebb91..d92b55a 100644 --- a/modules.json +++ b/modules.json @@ -7,17 +7,17 @@ "nf-core": { "fastqc": { "branch": "master", - "git_sha": "08108058ea36a63f141c25c4e75f9f872a5b2296", + "git_sha": "b1966f36ec9de31927b2603d8f499960b2a4c294", "installed_by": ["modules"] }, "multiqc": { "branch": "master", - "git_sha": "f0719ae309075ae4a291533883847c3f7c441dad", + "git_sha": "e594e9dfaffa7572afc11bafc634984fd4cbd87b", "installed_by": ["modules"] }, "seqtk/trim": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", "installed_by": ["modules"] } } diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml index 691d4c7..f9f54ee 100644 --- a/modules/nf-core/fastqc/environment.yml +++ b/modules/nf-core/fastqc/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index 033f415..23e1663 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -29,7 +29,7 @@ process FASTQC { // The total amount of allocated RAM by FastQC is equal to the number of threads defined (--threads) time the amount of RAM defined (--memory) // https://github.com/s-andrews/FastQC/blob/1faeea0412093224d7f6a07f777fad60a5650795/fastqc#L211-L222 // Dividing the task.memory by task.cpu allows to stick to requested amount of RAM in the label - def memory_in_mb = task.memory ? task.memory.toUnit('MB').toFloat() / task.cpus : null + def memory_in_mb = task.memory ? task.memory.toUnit('MB') / task.cpus : null // FastQC memory value allowed range (100 - 10000) def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb) diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index a27122c..812fc4c 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::multiqc=1.27 + - bioconda::multiqc=1.29 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 58d9313..0ac3c36 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,8 +3,8 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.27--pyhdfd78af_0' : - 'biocontainers/multiqc:1.27--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.29--pyhdfd78af_0' : + 'biocontainers/multiqc:1.29--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index 7b7c132..88e9057 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "multiqc_versions_single": { "content": [ [ - "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f" + "versions.yml:md5,c1fe644a37468f6dae548d98bc72c2c1" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nextflow": "25.04.2" }, - "timestamp": "2025-01-27T09:29:57.631982377" + "timestamp": "2025-05-22T11:50:41.182332996" }, "multiqc_stub": { "content": [ @@ -17,25 +17,25 @@ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f" + "versions.yml:md5,c1fe644a37468f6dae548d98bc72c2c1" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nextflow": "25.04.2" }, - "timestamp": "2025-01-27T09:30:34.743726958" + "timestamp": "2025-05-22T11:51:22.448739369" }, "multiqc_versions_config": { "content": [ [ - "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f" + "versions.yml:md5,c1fe644a37468f6dae548d98bc72c2c1" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nextflow": "25.04.2" }, - "timestamp": "2025-01-27T09:30:21.44383553" + "timestamp": "2025-05-22T11:51:06.198928424" } } \ No newline at end of file diff --git a/modules/nf-core/multiqc/tests/tags.yml b/modules/nf-core/multiqc/tests/tags.yml deleted file mode 100644 index bea6c0d..0000000 --- a/modules/nf-core/multiqc/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -multiqc: - - modules/nf-core/multiqc/** diff --git a/modules/nf-core/seqtk/trim/environment.yml b/modules/nf-core/seqtk/trim/environment.yml index 693aa5c..b1d11cb 100644 --- a/modules/nf-core/seqtk/trim/environment.yml +++ b/modules/nf-core/seqtk/trim/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/seqtk/trim/tests/tags.yml b/modules/nf-core/seqtk/trim/tests/tags.yml deleted file mode 100644 index 250a138..0000000 --- a/modules/nf-core/seqtk/trim/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -seqtk/trim: - - "modules/nf-core/seqtk/trim/**" From a423ed361e9b709b74b2ffd555228862296afd2b Mon Sep 17 00:00:00 2001 From: Florian Wuennemann Date: Thu, 26 Jun 2025 20:05:12 +0000 Subject: [PATCH 2/6] Bump version for release 1.0.2 --- .nf-core.yml | 2 +- assets/multiqc_config.yml | 4 +- nextflow.config | 2 +- ro-crate-metadata.json | 18 ++--- tests/.nftignore | 1 + tests/default.nf.test.snap | 132 ------------------------------------- 6 files changed, 14 insertions(+), 145 deletions(-) delete mode 100644 tests/default.nf.test.snap diff --git a/.nf-core.yml b/.nf-core.yml index 1477c6b..faab988 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -8,4 +8,4 @@ template: name: demo org: nf-core outdir: . - version: 1.0.2dev + version: 1.0.2 diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 58dd0d3..0eaa69f 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/demo analysis pipeline. For information about how to - interpret these results, please see the documentation. report_section_order: "nf-core-demo-methods-description": diff --git a/nextflow.config b/nextflow.config index f5a29f7..ae80308 100644 --- a/nextflow.config +++ b/nextflow.config @@ -250,7 +250,7 @@ manifest { mainScript = 'main.nf' defaultBranch = 'master' nextflowVersion = '!>=24.04.2' - version = '1.0.2dev' + version = '1.0.2' doi = '10.5281/zenodo.12192442' } diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index ac45d9b..2d5cbcf 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -21,8 +21,8 @@ { "@id": "./", "@type": "Dataset", - "creativeWorkStatus": "InProgress", - "datePublished": "2025-06-25T14:34:33+00:00", + "creativeWorkStatus": "Stable", + "datePublished": "2025-06-26T20:03:01+00:00", "description": "

\n \n \n \"nf-core/demo\"\n \n

\n\n[![GitHub Actions CI Status](https://github.com/nf-core/demo/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/demo/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/demo/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/demo/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/demo/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.12192442-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.12192442)\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/demo)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23demo-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/demo)[![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/demo** is a simple nf-core style bioinformatics pipeline for workshops and demonstrations. It was created using the nf-core template and is designed to run quickly using small test data files.\n\n![nf-core/demo metro map](docs/images/nf-core-demo-subway.png)\n\n1. Read QC ([`FASTQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))\n2. Adapter and quality trimming ([`SEQTK_TRIM`](https://github.com/lh3/seqtk))\n3. Present QC for raw reads ([`MULTIQC`](http://multiqc.info/))\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,fastq_1,fastq_2\nSAMPLE1_PE,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample1_R1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample1_R2.fastq.gz\nSAMPLE2_PE,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample2_R1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample2_R2.fastq.gz\nSAMPLE3_SE,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample1_R1.fastq.gz,\nSAMPLE3_SE,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample2_R1.fastq.gz,\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/demo \\\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/demo/usage) and the [parameter documentation](https://nf-co.re/demo/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/demo/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/demo/output).\n\n## Credits\n\nnf-core/demo was originally written by Chris Hakkaart ([@christopher-hakkaart](https://github.com/christopher-hakkaart)).\n\n\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 `#demo` channel](https://nfcore.slack.com/channels/demo) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/demo for your analysis, please cite it using the following doi: [10.5281/zenodo.12192442](https://doi.org/10.5281/zenodo.12192442)\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": [ { @@ -99,7 +99,7 @@ }, "mentions": [ { - "@id": "#dc664a18-147f-4bf5-9d5d-5298edf06ed4" + "@id": "#0df73e30-5e9c-44f6-b881-81824440495b" } ], "name": "nf-core/demo" @@ -132,7 +132,7 @@ } ], "dateCreated": "", - "dateModified": "2025-06-25T14:34:33Z", + "dateModified": "2025-06-26T20:03:01Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": [ "nf-core", @@ -156,10 +156,10 @@ }, "url": [ "https://github.com/nf-core/demo", - "https://nf-co.re/demo/dev/" + "https://nf-co.re/demo/1.0.2/" ], "version": [ - "1.0.2dev" + "1.0.2" ] }, { @@ -175,11 +175,11 @@ "version": "!>=24.04.2" }, { - "@id": "#dc664a18-147f-4bf5-9d5d-5298edf06ed4", + "@id": "#0df73e30-5e9c-44f6-b881-81824440495b", "@type": "TestSuite", "instance": [ { - "@id": "#11d98977-d4ef-4731-b43d-8bf6862f2f7c" + "@id": "#783b785f-805a-40a5-a0a1-0ad9c9dcc7a2" } ], "mainEntity": { @@ -188,7 +188,7 @@ "name": "Test suite for nf-core/demo" }, { - "@id": "#11d98977-d4ef-4731-b43d-8bf6862f2f7c", + "@id": "#783b785f-805a-40a5-a0a1-0ad9c9dcc7a2", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/demo", "resource": "repos/nf-core/demo/actions/workflows/nf-test.yml", diff --git a/tests/.nftignore b/tests/.nftignore index 1624b27..fa91753 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -6,6 +6,7 @@ multiqc/multiqc_data/multiqc_sources.txt multiqc/multiqc_data/multiqc_software_versions.txt multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png} multiqc/multiqc_report.html +multiqc/multiqc_data/BETA-multiqc.parquet fastqc/**/*_fastqc.{html,zip} pipeline_info/*.{html,json,txt,yml} diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap deleted file mode 100644 index 96abe2c..0000000 --- a/tests/default.nf.test.snap +++ /dev/null @@ -1,132 +0,0 @@ -{ - "-profile test": { - "content": [ - 7, - { - "FASTQC": { - "fastqc": "0.12.1" - }, - "SEQTK_TRIM": { - "seqtk": "1.4-r122" - }, - "Workflow": { - "nf-core/demo": "v1.0.2dev" - } - }, - [ - "fastqc", - "fastqc/SAMPLE1_PE", - "fastqc/SAMPLE1_PE/SAMPLE1_PE_1_fastqc.html", - "fastqc/SAMPLE1_PE/SAMPLE1_PE_2_fastqc.html", - "fastqc/SAMPLE2_PE", - "fastqc/SAMPLE2_PE/SAMPLE2_PE_1_fastqc.html", - "fastqc/SAMPLE2_PE/SAMPLE2_PE_2_fastqc.html", - "fastqc/SAMPLE3_SE", - "fastqc/SAMPLE3_SE/SAMPLE3_SE_1_fastqc.html", - "fastqc/SAMPLE3_SE/SAMPLE3_SE_2_fastqc.html", - "fq", - "fq/SAMPLE1_PE", - "fq/SAMPLE1_PE/SAMPLE1_PE_sample1_R1.fastq.gz", - "fq/SAMPLE1_PE/SAMPLE1_PE_sample1_R2.fastq.gz", - "fq/SAMPLE2_PE", - "fq/SAMPLE2_PE/SAMPLE2_PE_sample2_R1.fastq.gz", - "fq/SAMPLE2_PE/SAMPLE2_PE_sample2_R2.fastq.gz", - "fq/SAMPLE3_SE", - "fq/SAMPLE3_SE/SAMPLE3_SE_sample1_R1.fastq.gz", - "fq/SAMPLE3_SE/SAMPLE3_SE_sample2_R1.fastq.gz", - "multiqc", - "multiqc/multiqc_data", - "multiqc/multiqc_data/fastqc-status-check-heatmap.txt", - "multiqc/multiqc_data/fastqc_overrepresented_sequences_plot.txt", - "multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt", - "multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot.txt", - "multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt", - "multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt", - "multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt", - "multiqc/multiqc_data/fastqc_sequence_counts_plot.txt", - "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt", - "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt", - "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt", - "multiqc/multiqc_data/multiqc.log", - "multiqc/multiqc_data/multiqc_citations.txt", - "multiqc/multiqc_data/multiqc_data.json", - "multiqc/multiqc_data/multiqc_fastqc.txt", - "multiqc/multiqc_data/multiqc_general_stats.txt", - "multiqc/multiqc_data/multiqc_software_versions.txt", - "multiqc/multiqc_data/multiqc_sources.txt", - "multiqc/multiqc_plots", - "multiqc/multiqc_plots/pdf", - "multiqc/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf", - "multiqc/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf", - "multiqc/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf", - "multiqc/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf", - "multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf", - "multiqc/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", - "multiqc/multiqc_plots/pdf/general_stats_table.pdf", - "multiqc/multiqc_plots/png", - "multiqc/multiqc_plots/png/fastqc-status-check-heatmap.png", - "multiqc/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png", - "multiqc/multiqc_plots/png/fastqc_per_base_n_content_plot.png", - "multiqc/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png", - "multiqc/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png", - "multiqc/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png", - "multiqc/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png", - "multiqc/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png", - "multiqc/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png", - "multiqc/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", - "multiqc/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png", - "multiqc/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", - "multiqc/multiqc_plots/png/general_stats_table.png", - "multiqc/multiqc_plots/svg", - "multiqc/multiqc_plots/svg/fastqc-status-check-heatmap.svg", - "multiqc/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg", - "multiqc/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg", - "multiqc/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg", - "multiqc/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg", - "multiqc/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg", - "multiqc/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg", - "multiqc/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg", - "multiqc/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg", - "multiqc/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", - "multiqc/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg", - "multiqc/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", - "multiqc/multiqc_plots/svg/general_stats_table.svg", - "multiqc/multiqc_report.html", - "pipeline_info", - "pipeline_info/nf_core_demo_software_mqc_versions.yml" - ], - [ - "SAMPLE1_PE_sample1_R1.fastq.gz:md5,7dd2fd0d542d9259d9aed53550907fae", - "SAMPLE1_PE_sample1_R2.fastq.gz:md5,1995fe8488384d801807805f26ceca8a", - "SAMPLE2_PE_sample2_R1.fastq.gz:md5,05dba9c26396cbdbe0e6da26f037106e", - "SAMPLE2_PE_sample2_R2.fastq.gz:md5,63d5e4ac37927c2ecec4b74d2ff99a10", - "SAMPLE3_SE_sample1_R1.fastq.gz:md5,7dd2fd0d542d9259d9aed53550907fae", - "SAMPLE3_SE_sample2_R1.fastq.gz:md5,05dba9c26396cbdbe0e6da26f037106e", - "fastqc-status-check-heatmap.txt:md5,0f1975c565a16bf09be08a05c204ded7", - "fastqc_overrepresented_sequences_plot.txt:md5,4b23cea39c4e23deef6b97810bc1ee46", - "fastqc_per_base_n_content_plot.txt:md5,037692101c0130c72493d3bbfa3afac1", - "fastqc_per_base_sequence_quality_plot.txt:md5,bfe735f3e31befe13bdf6761bb297d6e", - "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,7108d19c46ef7883e864ba274c457d2e", - "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,23f527c80a148e4f34e5a43f6e520a90", - "fastqc_per_sequence_quality_scores_plot.txt:md5,a0cc0e6df7bfb05257da1cfc88b13c50", - "fastqc_sequence_counts_plot.txt:md5,c6e4e1588e6765fe8df27812a1322fbd", - "fastqc_sequence_duplication_levels_plot.txt:md5,3cde2db4033f6c64648976d1174db925", - "fastqc_sequence_length_distribution_plot.txt:md5,e82b9b14a7e24c0c5f27af97cebb6870", - "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", - "multiqc_fastqc.txt:md5,1a41c2158adc9947bff9232962f70110", - "multiqc_general_stats.txt:md5,0b54e4e764665bd57fe0f95216744a78" - ] - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.2" - }, - "timestamp": "2025-06-25T15:13:33.021500703" - } -} \ No newline at end of file From a3887fef4ecfb239c2a13b5d40f9f7bc172f6471 Mon Sep 17 00:00:00 2001 From: Florian Wuennemann Date: Thu, 26 Jun 2025 20:11:14 +0000 Subject: [PATCH 3/6] Update CHANGELOG and nf-test snapshots. --- CHANGELOG.md | 14 ++-- tests/default.nf.test.snap | 130 +++++++++++++++++++++++++++++++++++++ 2 files changed, 138 insertions(+), 6 deletions(-) create mode 100644 tests/default.nf.test.snap diff --git a/CHANGELOG.md b/CHANGELOG.md index 4f9832b..3aa3bd7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,12 +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). -## dev - -### `Changed` - -[#34](https://github.com/nf-core/demo/pull/34) Updated the JSON schema to make input validation stricter, thus preventing more errors during the pipeline run. - ## 1.0.2 ### Credits @@ -17,9 +11,17 @@ Special thanks to the following for their reviews and assistance: - [Chris Hakkaart](https://github.com/christopher-hakkaart) - [Marcel Ribeiro-Dantas](https://github.com/mribeirodantas) +- [Maxime Garcia](https://github.com/maxulysse) +- [Geraldine Van der Auwera](https://github.com/vdauwera) +- [Florian Wuennemann](https://github.com/FloWuenne) ### Changed +[#39][https://github.com/nf-core/demo/pull/39] - Remove -C from bach in nextflow.config +[#38][https://github.com/nf-core/demo/pull/38] - Template update for nf-core/tools v3.3.1 +[#36][https://github.com/nf-core/demo/pull/36] - Template update for nf-core/tools v3.2.1 +[#34][https://github.com/nf-core/demo/pull/34] - updated nextflow_schema.json +[#32][https://github.com/nf-core/demo/pull/32] - Minor fixes and template update [#29](https://github.com/nf-core/demo/pull/29) - Template update for nf-core/tools v3.2.0 [#23](https://github.com/nf-core/demo/pull/23) - Update to latest `seqtk` and `fastqc` modules [#21](https://github.com/nf-core/demo/pull/21) - Template update for nf-core/tools v3.1.0 diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap new file mode 100644 index 0000000..fb90df8 --- /dev/null +++ b/tests/default.nf.test.snap @@ -0,0 +1,130 @@ +{ + "-profile test": { + "content": [ + 7, + { + "FASTQC": { 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"multiqc/multiqc_plots/svg", + "multiqc/multiqc_plots/svg/fastqc-status-check-heatmap.svg", + "multiqc/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg", + "multiqc/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg", + "multiqc/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg", + "multiqc/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg", + "multiqc/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", + "multiqc/multiqc_report.html", + "pipeline_info", + "pipeline_info/nf_core_demo_software_mqc_versions.yml" + ], + [ + "SAMPLE1_PE_sample1_R1.fastq.gz:md5,7dd2fd0d542d9259d9aed53550907fae", + "SAMPLE1_PE_sample1_R2.fastq.gz:md5,1995fe8488384d801807805f26ceca8a", + "SAMPLE2_PE_sample2_R1.fastq.gz:md5,05dba9c26396cbdbe0e6da26f037106e", + "SAMPLE2_PE_sample2_R2.fastq.gz:md5,63d5e4ac37927c2ecec4b74d2ff99a10", + "SAMPLE3_SE_sample1_R1.fastq.gz:md5,7dd2fd0d542d9259d9aed53550907fae", + "SAMPLE3_SE_sample2_R1.fastq.gz:md5,05dba9c26396cbdbe0e6da26f037106e", + "fastqc-status-check-heatmap.txt:md5,0f1975c565a16bf09be08a05c204ded7", + "fastqc_overrepresented_sequences_plot.txt:md5,4b23cea39c4e23deef6b97810bc1ee46", + "fastqc_per_base_n_content_plot.txt:md5,037692101c0130c72493d3bbfa3afac1", + "fastqc_per_base_sequence_quality_plot.txt:md5,bfe735f3e31befe13bdf6761bb297d6e", + "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,7108d19c46ef7883e864ba274c457d2e", + 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nextflow.config | 16 ++++++++++++++++ 2 files changed, 18 insertions(+) diff --git a/README.md b/README.md index 1eff54a..4f3b6e0 100644 --- a/README.md +++ b/README.md @@ -71,6 +71,8 @@ For more details about the output files and reports, please refer to the nf-core/demo was originally written by Chris Hakkaart ([@christopher-hakkaart](https://github.com/christopher-hakkaart)). +The pipeline is currently being maintained by the Nextflow community team as well as [Geraldine Van der Auwera](https://github.com/vdauwera) and [Florian Wuennemann](https://github.com/FloWuenne). + ## Contributions and Support diff --git a/nextflow.config b/nextflow.config index ae80308..b1f28e4 100644 --- a/nextflow.config +++ b/nextflow.config @@ -244,6 +244,22 @@ manifest { contribution: ['author', 'maintainer'], // List of contribution types ('author', 'maintainer' or 'contributor') orcid: '0000-0001-5007-2684' ], + [ + name: 'Florian Wuennemann', + affiliation: 'Seqera', + email: 'flowuenne@gmail.com', + github: '@flowuenne', + contribution: ['contributor', 'maintainer'], // List of contribution types ('author', 'maintainer' or 'contributor') + orcid: '0000-0002-0978-6076' + ], + [ + name: 'Geraldine Van der Auwera', + affiliation: 'Seqera', + email: 'geraldine.vdauwera@seqera.io', + github: '@vdauwera', + contribution: ['contributor', 'maintainer'], // List of contribution types ('author', 'maintainer' or 'contributor') + orcid: '0000-0002-0978-6076' + ], ] homePage = 'https://github.com/nf-core/demo' description = """An nf-core demo pipeline""" From 94ec9994257adc46db30ffcb29953fe512599958 Mon Sep 17 00:00:00 2001 From: Florian Wuennemann Date: Fri, 27 Jun 2025 13:33:16 +0000 Subject: [PATCH 5/6] Fix lint error. --- ro-crate-metadata.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 2d5cbcf..238d22b 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -23,7 +23,7 @@ "@type": "Dataset", "creativeWorkStatus": "Stable", "datePublished": "2025-06-26T20:03:01+00:00", - "description": "

\n \n \n \"nf-core/demo\"\n \n

\n\n[![GitHub Actions CI Status](https://github.com/nf-core/demo/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/demo/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/demo/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/demo/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/demo/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.12192442-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.12192442)\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/demo)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23demo-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/demo)[![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/demo** is a simple nf-core style bioinformatics pipeline for workshops and demonstrations. It was created using the nf-core template and is designed to run quickly using small test data files.\n\n![nf-core/demo metro map](docs/images/nf-core-demo-subway.png)\n\n1. Read QC ([`FASTQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))\n2. Adapter and quality trimming ([`SEQTK_TRIM`](https://github.com/lh3/seqtk))\n3. Present QC for raw reads ([`MULTIQC`](http://multiqc.info/))\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,fastq_1,fastq_2\nSAMPLE1_PE,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample1_R1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample1_R2.fastq.gz\nSAMPLE2_PE,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample2_R1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample2_R2.fastq.gz\nSAMPLE3_SE,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample1_R1.fastq.gz,\nSAMPLE3_SE,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample2_R1.fastq.gz,\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/demo \\\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/demo/usage) and the [parameter documentation](https://nf-co.re/demo/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/demo/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/demo/output).\n\n## Credits\n\nnf-core/demo was originally written by Chris Hakkaart ([@christopher-hakkaart](https://github.com/christopher-hakkaart)).\n\n\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 `#demo` channel](https://nfcore.slack.com/channels/demo) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/demo for your analysis, please cite it using the following doi: [10.5281/zenodo.12192442](https://doi.org/10.5281/zenodo.12192442)\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", + "description": "

\n \n \n \"nf-core/demo\"\n \n

\n\n[![GitHub Actions CI Status](https://github.com/nf-core/demo/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/demo/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/demo/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/demo/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/demo/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.12192442-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.12192442)\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/demo)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23demo-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/demo)[![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/demo** is a simple nf-core style bioinformatics pipeline for workshops and demonstrations. It was created using the nf-core template and is designed to run quickly using small test data files.\n\n![nf-core/demo metro map](docs/images/nf-core-demo-subway.png)\n\n1. Read QC ([`FASTQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))\n2. Adapter and quality trimming ([`SEQTK_TRIM`](https://github.com/lh3/seqtk))\n3. Present QC for raw reads ([`MULTIQC`](http://multiqc.info/))\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,fastq_1,fastq_2\nSAMPLE1_PE,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample1_R1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample1_R2.fastq.gz\nSAMPLE2_PE,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample2_R1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample2_R2.fastq.gz\nSAMPLE3_SE,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample1_R1.fastq.gz,\nSAMPLE3_SE,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample2_R1.fastq.gz,\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/demo \\\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/demo/usage) and the [parameter documentation](https://nf-co.re/demo/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/demo/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/demo/output).\n\n## Credits\n\nnf-core/demo was originally written by Chris Hakkaart ([@christopher-hakkaart](https://github.com/christopher-hakkaart)).\n\nThe pipeline is currently being maintained by the Nextflow community team as well as [Geraldine Van der Auwera](https://github.com/vdauwera) and [Florian Wuennemann](https://github.com/FloWuenne).\n\n\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 `#demo` channel](https://nfcore.slack.com/channels/demo) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/demo for your analysis, please cite it using the following doi: [10.5281/zenodo.12192442](https://doi.org/10.5281/zenodo.12192442)\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" From ddf7ea1c874282d0904a79f8e84012cf4a07cc3e Mon Sep 17 00:00:00 2001 From: Florian Wuennemann Date: Fri, 27 Jun 2025 13:45:30 +0000 Subject: [PATCH 6/6] Fix Geraldine's ORCID ID. --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index b1f28e4..7cca8e8 100644 --- a/nextflow.config +++ b/nextflow.config @@ -258,7 +258,7 @@ manifest { email: 'geraldine.vdauwera@seqera.io', github: '@vdauwera', contribution: ['contributor', 'maintainer'], // List of contribution types ('author', 'maintainer' or 'contributor') - orcid: '0000-0002-0978-6076' + orcid: '0000-0001-9751-7820' ], ] homePage = 'https://github.com/nf-core/demo'