ro-crate-metadata.json

{
    "@context": [
        "https://w3id.org/ro/crate/1.1/context",
        {
            "GithubService": "https://w3id.org/ro/terms/test#GithubService",
            "JenkinsService": "https://w3id.org/ro/terms/test#JenkinsService",
            "PlanemoEngine": "https://w3id.org/ro/terms/test#PlanemoEngine",
            "TestDefinition": "https://w3id.org/ro/terms/test#TestDefinition",
            "TestInstance": "https://w3id.org/ro/terms/test#TestInstance",
            "TestService": "https://w3id.org/ro/terms/test#TestService",
            "TestSuite": "https://w3id.org/ro/terms/test#TestSuite",
            "TravisService": "https://w3id.org/ro/terms/test#TravisService",
            "definition": "https://w3id.org/ro/terms/test#definition",
            "engineVersion": "https://w3id.org/ro/terms/test#engineVersion",
            "instance": "https://w3id.org/ro/terms/test#instance",
            "resource": "https://w3id.org/ro/terms/test#resource",
            "runsOn": "https://w3id.org/ro/terms/test#runsOn"
        }
    ],
    "@graph": [
        {
            "@id": "./",
            "@type": "Dataset",
            "creativeWorkStatus": "InProgress",
            "datePublished": "2025-07-08T11:39:27+00:00",
            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-tfactivity_logo_dark.png\">\n    <img alt=\"nf-core/tfactivity\" src=\"docs/images/nf-core-tfactivity_logo_light.png\">\n  </picture>\n</h1>\n\n[![GitHub Actions CI Status](https://github.com/nf-core/tfactivity/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/tfactivity/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/tfactivity/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/tfactivity/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/tfactivity/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%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/tfactivity)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23tfactivity-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/tfactivity)[![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/tfactivity** is a bioinformatics pipeline that can identify the most differentially active transcription factors (TFs) between multiple conditions. It takes a count matrix and open chromatin data (ATAC-seq, DNase-seq, HM-ChIP-seq) as input. It produces a ranking of transcription factors.\n\n![Metro map](docs/images/metromap.png)\n\n1. Identify accessible regions (can perform footprinting between close ChIP-seq peaks or take ATAC-seq peaks)\n2. Calculate affinity scores for combinations of transcription factors and target genes (TGs) using [STARE](https://doi.org/10.1093/bioinformatics/btad062)\n3. Identify differentially expressed genes between conditions\n4. Utilize linear regression to identify the transcription factors that are most likely to be responsible for the differential gene expression\n5. Calculate the TF-TG score based on:\n   1. Differential expression of the target genes\n   2. Affinity of the transcription factors to the target genes\n   3. The regression coefficient of the transcription factors\n6. Perform a Mann-Whitney U test and create a ranking of the transcription factors\n\nA more biological visualization of the workflow can be found here:\n\n> [!NOTE]\n> The following image was created for the TF-Prioritizer publication. Parts of the workflow have been adapted for the nf-core pipeline, but the general idea is still valid.\n\n![TF-Prioritizer workflow](docs/images/tfprio.jpeg)\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nThe pipeline supports processing of previously called peaks from ATAC-seq, DNase-seq, or histone modification ChIP-seq data. The peaks can then either be used as-is or be subjected to footprinting analysis. Additionally, BAM files can be provided in a separate samplesheet, which will be used to predict enhancer regions.\n\n```csv title=\"samplesheet.csv\"\nsample,condition,assay,peak_file\ncondition1_H3K27ac_1,condition1,H3K27ac,condition1_H3K27ac_1.broadPeak\ncondition1_H3K27ac_2,condition1,H3K27ac,condition1_H3K27ac_2.broadPeak\ncondition1_H3K4me3,condition1,H3K4me3,condition1_H3K4me3.broadPeak\ncondition2_H3K27ac,condition2,H3K27ac,condition2_H3K27ac.broadPeak\ncondition3_H3K27ac,condition3,H3K27ac,condition3_H3K27ac.broadPeak\ncondition3_H3K4me3,condition3,H3K4me3,condition3_H3K4me3.broadPeak\n```\n\nEach row represents a peak file. The `sample` column should contain a unique identifier for each peak file. The `peak_file` column should contain the path to the peak file. Peak files need to be in a format that is compatible with the `bed` format. Only the first three columns of the `bed` format are used.\n\n```csv title=\"samplesheet_bam.csv\"\nsample,condition,assay,signal,control\ncondition1_H3K27ac_1,condition1,H3K27ac,condition1_H3K27ac_1.bam,condition1_control.bam\ncondition1_H3K27ac_2,condition1,H3K27ac,condition1_H3K27ac_2.bam,condition1_control.bam\ncondition1_H3K4me3,condition1,H3K4me3,condition1_H3K4me3.bam,condition1_control.bam\ncondition2_H3K27ac,condition2,H3K27ac,condition2_H3K27ac.bam,condition2_control.bam\ncondition3_H3K27ac,condition3,H3K27ac,condition3_H3K27ac.bam,condition3_control.bam\ncondition3_H3K4me3,condition3,H3K4me3,condition3_H3K4me3.bam,condition3_control.bam\n```\n\nThe first three columns are the same as in the peak file samplesheet. The `signal` column should contain the path to the signal BAM file. The `control` column should contain the path to the control BAM file.\n\nSecond, you need a raw count matrix (e.g. from [nf-core/rnaseq](https://nf-co.re/rnaseq)) with gene IDs as rows and samples as columns. You also need a design matrix that specifies the conditions of the samples in the count matrix. The design matrix should look as follows:\n\n```csv title=\"design_matrix.csv\"\nsample,condition\nsample1,condition1\nsample2,condition1\nsample3,condition2\nsample4,condition3\n```\n\nThe `sample` column should match the columns in the expression matrix. The `condition` column is needs to match the `condition` column in the samplesheet. Additionally,batches can be added to the design matrix and will be considered in the differential expression analysis.\n\n:::tip\nThere is an alternative way of providing expression values. Instead of providing a single count matrix for all samples, you can provide a gene list and one count file per sample. Details can be found in the [usage documentation](https://nf-co.re/tfactivity/usage).\n:::\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/tfactivity \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --genome GRCh38 \\\n   --counts <EXPRESSION_MATRIX> \\\n   --counts_design design_matrix.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/tfactivity/usage) and the [parameter documentation](https://nf-co.re/tfactivity/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/tfactivity/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/tfactivity/output).\n\n## Credits\n\nnf-core/tfactivity was originally written by [Nico Trummer](https://github.com/nictru).\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [Markus Hoffmann](https://scholar.google.com/citations?user=_qXUS28AAAAJ) (project and scientific management)\n- [Leon Hafner](https://www.linkedin.com/in/leon-hafner/) (implementations)\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 `#tfactivity` channel](https://nfcore.slack.com/channels/tfactivity) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nnf-core/tfactivity is based on the previously published \"TF-Prioritizer\" pipeline. As long as there is no dedicated nf-core/tfactivity publication, please cite the following paper:\n\n> **TF-Prioritizer: a Java pipeline to prioritize condition-specific transcription factors**\n>\n> Markus Hoffmann, Nico Trummer, Leon Schwartz, Jakub Jankowski, Hye Kyung Lee, Lina-Liv Willruth, Olga Lazareva, Kevin Yuan, Nina Baumgarten, Florian Schmidt, Jan Baumbach, Marcel H Schulz, David B Blumenthal, Lothar Hennighausen & Markus List\n>\n> GigaScience, Volume 12, 2023, giad026, https://doi.org/10.1093/gigascience/giad026\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/tfactivity for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\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"
                },
                {
                    "@id": "assets/"
                },
                {
                    "@id": "conf/"
                },
                {
                    "@id": "docs/"
                },
                {
                    "@id": "docs/images/"
                },
                {
                    "@id": "workflows/"
                },
                {
                    "@id": "subworkflows/"
                },
                {
                    "@id": "nextflow.config"
                },
                {
                    "@id": "README.md"
                },
                {
                    "@id": "nextflow_schema.json"
                },
                {
                    "@id": "CHANGELOG.md"
                },
                {
                    "@id": "LICENSE"
                },
                {
                    "@id": "CODE_OF_CONDUCT.md"
                },
                {
                    "@id": "CITATIONS.md"
                },
                {
                    "@id": "modules.json"
                },
                {
                    "@id": "docs/usage.md"
                },
                {
                    "@id": "docs/output.md"
                },
                {
                    "@id": ".nf-core.yml"
                },
                {
                    "@id": ".pre-commit-config.yaml"
                },
                {
                    "@id": ".prettierignore"
                }
            ],
            "isBasedOn": "https://github.com/nf-core/tfactivity",
            "license": "MIT",
            "mainEntity": {
                "@id": "main.nf"
            },
            "mentions": [
                {
                    "@id": "#b55260aa-41b6-4759-90f5-46e2bf50c735"
                }
            ],
            "name": "nf-core/tfactivity"
        },
        {
            "@id": "ro-crate-metadata.json",
            "@type": "CreativeWork",
            "about": {
                "@id": "./"
            },
            "conformsTo": [
                {
                    "@id": "https://w3id.org/ro/crate/1.1"
                },
                {
                    "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"
                }
            ]
        },
        {
            "@id": "main.nf",
            "@type": [
                "File",
                "SoftwareSourceCode",
                "ComputationalWorkflow"
            ],
            "creator": [
                {
                    "@id": "https://orcid.org/0000-0002-4639-0935"
                }
            ],
            "dateCreated": "",
            "dateModified": "2025-11-20T09:32:30Z",
            "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
            "keywords": [
                "nf-core",
                "nextflow",
                "open-chromatin-regions",
                "transcription-factors",
                "transcriptomics"
            ],
            "license": [
                "MIT"
            ],
            "maintainer": [
                {
                    "@id": "https://orcid.org/0000-0002-4639-0935"
                }
            ],
            "name": [
                "nf-core/tfactivity"
            ],
            "programmingLanguage": {
                "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow"
            },
            "sdPublisher": {
                "@id": "https://nf-co.re/"
            },
            "url": [
                "https://github.com/nf-core/tfactivity",
                "https://nf-co.re/tfactivity/dev/"
            ],
            "version": [
                "0.0.1dev"
            ]
        },
        {
            "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow",
            "@type": "ComputerLanguage",
            "identifier": {
                "@id": "https://www.nextflow.io/"
            },
            "name": "Nextflow",
            "url": {
                "@id": "https://www.nextflow.io/"
            },
            "version": "!>=25.04.0"
        },
        {
            "@id": "#b55260aa-41b6-4759-90f5-46e2bf50c735",
            "@type": "TestSuite",
            "instance": [
                {
                    "@id": "#412782bd-d602-4e3a-befc-c7604fbade27"
                }
            ],
            "mainEntity": {
                "@id": "main.nf"
            },
            "name": "Test suite for nf-core/tfactivity"
        },
        {
            "@id": "#412782bd-d602-4e3a-befc-c7604fbade27",
            "@type": "TestInstance",
            "name": "GitHub Actions workflow for testing nf-core/tfactivity",
            "resource": "repos/nf-core/tfactivity/actions/workflows/nf-test.yml",
            "runsOn": {
                "@id": "https://w3id.org/ro/terms/test#GithubService"
            },
            "url": "https://api.github.com"
        },
        {
            "@id": "https://w3id.org/ro/terms/test#GithubService",
            "@type": "TestService",
            "name": "Github Actions",
            "url": {
                "@id": "https://github.com"
            }
        },
        {
            "@id": "assets/",
            "@type": "Dataset",
            "description": "Additional files"
        },
        {
            "@id": "conf/",
            "@type": "Dataset",
            "description": "Configuration files"
        },
        {
            "@id": "docs/",
            "@type": "Dataset",
            "description": "Markdown files for documenting the pipeline"
        },
        {
            "@id": "docs/images/",
            "@type": "Dataset",
            "description": "Images for the documentation files"
        },
        {
            "@id": "workflows/",
            "@type": "Dataset",
            "description": "Main pipeline workflows to be executed in main.nf"
        },
        {
            "@id": "subworkflows/",
            "@type": "Dataset",
            "description": "Smaller subworkflows"
        },
        {
            "@id": "nextflow.config",
            "@type": "File",
            "description": "Main Nextflow configuration file"
        },
        {
            "@id": "README.md",
            "@type": "File",
            "description": "Basic pipeline usage information"
        },
        {
            "@id": "nextflow_schema.json",
            "@type": "File",
            "description": "JSON schema for pipeline parameter specification"
        },
        {
            "@id": "CHANGELOG.md",
            "@type": "File",
            "description": "Information on changes made to the pipeline"
        },
        {
            "@id": "LICENSE",
            "@type": "File",
            "description": "The license - should be MIT"
        },
        {
            "@id": "CODE_OF_CONDUCT.md",
            "@type": "File",
            "description": "The nf-core code of conduct"
        },
        {
            "@id": "CITATIONS.md",
            "@type": "File",
            "description": "Citations needed when using the pipeline"
        },
        {
            "@id": "modules.json",
            "@type": "File",
            "description": "Version information for modules from nf-core/modules"
        },
        {
            "@id": "docs/usage.md",
            "@type": "File",
            "description": "Usage documentation"
        },
        {
            "@id": "docs/output.md",
            "@type": "File",
            "description": "Output documentation"
        },
        {
            "@id": ".nf-core.yml",
            "@type": "File",
            "description": "nf-core configuration file, configuring template features and linting rules"
        },
        {
            "@id": ".pre-commit-config.yaml",
            "@type": "File",
            "description": "Configuration file for pre-commit hooks"
        },
        {
            "@id": ".prettierignore",
            "@type": "File",
            "description": "Ignore file for prettier"
        },
        {
            "@id": "https://nf-co.re/",
            "@type": "Organization",
            "name": "nf-core",
            "url": "https://nf-co.re/"
        },
        {
            "@id": "https://orcid.org/0000-0002-4639-0935",
            "@type": "Person",
            "email": "nictru32@gmail.com",
            "name": "Nico Trummer"
        }
    ]
}