{"id":19749455,"url":"https://github.com/mskcc/forte","last_synced_at":"2025-02-28T00:40:45.707Z","repository":{"id":251386600,"uuid":"577830358","full_name":"mskcc/forte","owner":"mskcc","description":"Functional Observation of RNA Transcriptome Elements/Expression","archived":false,"fork":false,"pushed_at":"2025-02-25T15:28:30.000Z","size":22284,"stargazers_count":7,"open_issues_count":28,"forks_count":0,"subscribers_count":15,"default_branch":"main","last_synced_at":"2025-02-25T16:30:06.668Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Nextflow","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/mskcc.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":".github/CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":"CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":"CITATIONS.md","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2022-12-13T16:13:15.000Z","updated_at":"2024-08-02T14:08:39.000Z","dependencies_parsed_at":"2024-08-02T16:59:40.928Z","dependency_job_id":"c0a9e390-0d89-4460-b4b3-9c7b3c9369ca","html_url":"https://github.com/mskcc/forte","commit_stats":null,"previous_names":["mskcc/forte"],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Fforte","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Fforte/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Fforte/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Fforte/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/mskcc","download_url":"https://codeload.github.com/mskcc/forte/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":241079698,"owners_count":19906109,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-11-12T02:26:34.278Z","updated_at":"2025-02-28T00:40:45.683Z","avatar_url":"https://github.com/mskcc.png","language":"Nextflow","funding_links":[],"categories":[],"sub_categories":[],"readme":"# FORTE\n\n## Introduction\n\n**mskcc/forte** is a best-practice analysis pipeline for bulk RNAseq.\n\n- **F**unctional\n- **O**bservation of\n- **R**NA\n- **T**ranscriptome\n- **E**lements/**E**xpression\n\n### Features\n\n1. Read pre-processing\n   1. Trimming\n   2. UMI extraction and deduplication\n2. Alignment\n3. Transcript quantification\n4. Fusion calling and annotation\n5. FASTQ and BAM QC\n6. Fillouts\n\n## Quick Start\n\n1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`\u003e=21.10.3`)\n\n2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) (you can follow [this tutorial](https://singularity-tutorial.github.io/01-installation/)), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(you can use [`Conda`](https://conda.io/miniconda.html) both to install Nextflow itself and also to manage software within pipelines. Please only use it within pipelines as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_.\n\n3. Clone the pipeline repository and test it on a minimal dataset with the following steps:\n\n   ```bash\n   nextflow run /path/to/clonedrepo/main.nf -profile test,singularity --outdir \u003cOUTDIR\u003e\n   ```\n\n   Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (`YOURPROFILE` in the example command above). You can chain multiple config profiles in a comma-separated string.\n\n## Usage\n\n:::note\nIf you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how\nto set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline)\nwith `-profile test` before running the workflow on actual data.\n:::\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run /path/to/clonedrepo/main.nf \\\n  --input samplesheet.csv \\\n  --outdir \u003cOUTDIR\u003e \\\n  --genome GRCh37 \\\n  -profile singularity\n```\n\n:::warning\nPlease provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those\nprovided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;\nsee [docs](https://nf-co.re/usage/configuration#custom-configuration-files).\n:::\n\nFor more details and further functionality, please refer to the [usage documentation](docs/usage.md).\n\n## Pipeline output\n\nFor more details about the output files and reports, please refer to the\n[output documentation](docs/output.md).\n\n## Credits\n\nmskcc/forte was originally written by Anne Marie Noronha \u003cnoronhaa@mskcc.org\u003e.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- Allison Richards \u003crichara4@mskcc.org\u003e\n- Alexandria Pinto \u003cpintoa1@mskcc.org\u003e\n- Yixiao Gong \u003cgongy@mskcc.org\u003e\n\nWe also thank the following contributors:\n\n- Sam Tischfield \u003ctischfis@mskcc.org\u003e\n- Martina Bradic \u003cbradicm@mskcc.org\u003e\n- Jun Woo \u003cwooh@mskcc.org\u003e\n- Mark Donoghue \u003cdonoghum@mskcc.org\u003e\n- Helen Won\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\n## Citations\n\n\u003c!-- 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. --\u003e\n\u003c!-- If you use  mskcc/forte for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) --\u003e\n\n\u003c!-- TODO nf-core: Add bibliography of tools and data used in your pipeline --\u003e\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\u003e **The nf-core framework for community-curated bioinformatics pipelines.**\n\u003e\n\u003e Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso \u0026 Sven Nahnsen.\n\u003e\n\u003e _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmskcc%2Fforte","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmskcc%2Fforte","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmskcc%2Fforte/lists"}