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|---|---|---|
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@@ -229,23 +229,22 @@ manifest { | |
| name = 'nf-core/demo' | ||
| author = """Christopher Hakkaart""" // The author field is deprecated from Nextflow version 24.10.0, use contributors instead | ||
| contributors = [ | ||
| // TODO nf-core: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0 | ||
| [ | ||
| name: 'Christopher Hakkaart', | ||
| affiliation: '', | ||
| email: '', | ||
| github: '', | ||
| contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor') | ||
| orcid: '' | ||
| affiliation: 'Seqera', | ||
| email: '[email protected]', | ||
| github: 'christopher-hakkaart', | ||
| contribution: ['author', 'maintainer'], // List of contribution types ('author', 'maintainer' or 'contributor') | ||
| orcid: '0000-0001-5007-2684' | ||
| ], | ||
| ] | ||
| homePage = 'https://github.com/nf-core/demo' | ||
| description = """An nf-core demo pipeline""" | ||
| mainScript = 'main.nf' | ||
| defaultBranch = 'master' | ||
| nextflowVersion = '!>=24.04.2' | ||
| version = '1.0.1' | ||
| doi = '' | ||
| version = '1.1.0dev' | ||
| doi = '10.5281/zenodo.12192442' | ||
| } | ||
|
|
||
| // Nextflow plugins | ||
|
|
||
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@@ -21,9 +21,9 @@ | |
| { | ||
| "@id": "./", | ||
| "@type": "Dataset", | ||
| "creativeWorkStatus": "Stable", | ||
| "datePublished": "2024-12-12T11:23:20+00:00", | ||
| "description": "<h1>\n <picture>\n <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-demo_logo_dark.png\">\n <img alt=\"nf-core/demo\" src=\"docs/images/nf-core-demo_logo_light.png\">\n </picture>\n</h1>\n\n[](https://github.com/nf-core/demo/actions/workflows/ci.yml)\n[](https://github.com/nf-core/demo/actions/workflows/linting.yml)[](https://nf-co.re/demo/results)[](https://doi.org/10.5281/zenodo.XXXXXXX)\n[](https://www.nf-test.com)\n\n[](https://www.nextflow.io/)\n[](https://docs.conda.io/en/latest/)\n[](https://www.docker.com/)\n[](https://sylabs.io/docs/)\n[](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/demo)\n\n[](https://nfcore.slack.com/channels/demo)[](https://twitter.com/nf_core)[](https://mstdn.science/@nf_core)[](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/demo** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n major pipeline sections and the types of output it produces. You're giving an overview to someone new\n to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n workflows use the \"tube map\" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples. -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->\n\n1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))\n2. 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\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n Explain what rows and columns represent. For instance (please edit as appropriate):\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\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/demo \\\n -profile <docker/singularity/.../institute> \\\n --input samplesheet.csv \\\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**_; 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 Christopher Hakkaart.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\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\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/demo for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\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", | ||
| "creativeWorkStatus": "InProgress", | ||
| "datePublished": "2024-12-17T13:10:09+00:00", | ||
| "description": "<h1>\n <picture>\n <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-demo_logo_dark.png\">\n <img alt=\"nf-core/demo\" src=\"docs/images/nf-core-demo_logo_light.png\">\n </picture>\n</h1>\n\n[](https://github.com/nf-core/demo/actions/workflows/ci.yml)\n[](https://github.com/nf-core/demo/actions/workflows/linting.yml)[](https://nf-co.re/demo/results)[](https://doi.org/10.5281/zenodo.12192442)\n[](https://www.nf-test.com)\n\n[](https://www.nextflow.io/)\n[](https://docs.conda.io/en/latest/)\n[](https://www.docker.com/)\n[](https://sylabs.io/docs/)\n[](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/demo)\n\n[](https://nfcore.slack.com/channels/demo)[](https://twitter.com/nf_core)[](https://mstdn.science/@nf_core)[](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\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 <docker/singularity/.../institute> \\\n --input samplesheet.csv \\\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**_; 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<!-- We thank the following people for their extensive assistance in the development of this pipeline: -->\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" | ||
|
|
@@ -99,7 +99,7 @@ | |
| }, | ||
| "mentions": [ | ||
| { | ||
| "@id": "#982a4bc4-c9bb-4f2c-8828-d5321dbd4f47" | ||
| "@id": "#f16b62c8-d661-4d09-a65f-753bb2b5c931" | ||
| } | ||
| ], | ||
| "name": "nf-core/demo" | ||
|
|
@@ -122,8 +122,13 @@ | |
| { | ||
| "@id": "main.nf", | ||
| "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"], | ||
| "creator": [ | ||
| { | ||
| "@id": "https://orcid.org/0000-0002-5599-5565" | ||
| } | ||
| ], | ||
| "dateCreated": "", | ||
| "dateModified": "2024-12-12T11:23:20Z", | ||
| "dateModified": "2024-12-17T14:10:09Z", | ||
| "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", | ||
| "keywords": ["nf-core", "nextflow", "demo", "minimal-example", "training", "tutorial"], | ||
| "license": ["MIT"], | ||
|
|
@@ -134,8 +139,8 @@ | |
| "sdPublisher": { | ||
| "@id": "https://nf-co.re/" | ||
| }, | ||
| "url": ["https://github.com/nf-core/demo", "https://nf-co.re/demo/1.0.0/"], | ||
| "version": ["1.0.0"] | ||
| "url": ["https://github.com/nf-core/demo", "https://nf-co.re/demo/dev/"], | ||
| "version": ["1.1.0dev"] | ||
| }, | ||
| { | ||
| "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow", | ||
|
|
@@ -150,11 +155,11 @@ | |
| "version": "!>=24.04.2" | ||
| }, | ||
| { | ||
| "@id": "#982a4bc4-c9bb-4f2c-8828-d5321dbd4f47", | ||
| "@id": "#f16b62c8-d661-4d09-a65f-753bb2b5c931", | ||
| "@type": "TestSuite", | ||
| "instance": [ | ||
| { | ||
| "@id": "#73fd314c-6213-41e6-9b8d-af1c26cd5ca8" | ||
| "@id": "#9d6f54bc-199d-41c5-93e3-cb09dcf7d1b3" | ||
| } | ||
| ], | ||
| "mainEntity": { | ||
|
|
@@ -163,7 +168,7 @@ | |
| "name": "Test suite for nf-core/demo" | ||
| }, | ||
| { | ||
| "@id": "#73fd314c-6213-41e6-9b8d-af1c26cd5ca8", | ||
| "@id": "#9d6f54bc-199d-41c5-93e3-cb09dcf7d1b3", | ||
| "@type": "TestInstance", | ||
| "name": "GitHub Actions workflow for testing nf-core/demo", | ||
| "resource": "repos/nf-core/demo/actions/workflows/ci.yml", | ||
|
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@@ -290,6 +295,12 @@ | |
| "@type": "Organization", | ||
| "name": "nf-core", | ||
| "url": "https://nf-co.re/" | ||
| }, | ||
| { | ||
| "@id": "https://orcid.org/0000-0002-5599-5565", | ||
| "@type": "Person", | ||
| "email": "[email protected]", | ||
| "name": "Matthias H\u00f6rtenhuber" | ||
| } | ||
| ] | ||
| } | ||