{"id":19749483,"url":"https://github.com/mskcc/rediscoverte","last_synced_at":"2026-03-03T18:03:07.512Z","repository":{"id":246950622,"uuid":"822729678","full_name":"mskcc/REdiscoverTE","owner":"mskcc","description":"Pipeline for quantifying genome-wide TE expression in RNA sequencing data","archived":false,"fork":false,"pushed_at":"2024-07-23T22:16:26.000Z","size":193,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":4,"default_branch":"master","last_synced_at":"2026-01-26T14:22:31.138Z","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":null,"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":"2024-07-01T17:44:15.000Z","updated_at":"2024-07-23T22:15:28.000Z","dependencies_parsed_at":"2025-01-17T05:31:02.236Z","dependency_job_id":null,"html_url":"https://github.com/mskcc/REdiscoverTE","commit_stats":null,"previous_names":["mskcc/rediscoverte"],"tags_count":2,"template":false,"template_full_name":null,"purl":"pkg:github/mskcc/REdiscoverTE","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2FREdiscoverTE","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2FREdiscoverTE/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2FREdiscoverTE/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2FREdiscoverTE/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/mskcc","download_url":"https://codeload.github.com/mskcc/REdiscoverTE/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2FREdiscoverTE/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":30054003,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-03-03T17:46:22.538Z","status":"ssl_error","status_checked_at":"2026-03-03T17:46:22.036Z","response_time":61,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"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":"2024-11-12T02:26:44.477Z","updated_at":"2026-03-03T18:03:07.484Z","avatar_url":"https://github.com/mskcc.png","language":"Nextflow","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![GitHub Actions CI Status](https://github.com/mskcc/rediscoverte/actions/workflows/ci.yml/badge.svg)](https://github.com/msk/rediscoverte/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/mskcc/rediscoverte/actions/workflows/linting.yml/badge.svg)](https://github.com/msk/rediscoverte/actions/workflows/linting.yml)[![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/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000\u0026logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000\u0026logo=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/mskcc/rediscoverte)\n\n## Introduction\n\n**msk/rediscoverte** is a bioinformatics pipeline that quantifies genome-wide TE expression in RNA sequencing data. This is the nextflow pipeline for REdiscoverTE found here: https://github.com/ucsffrancislab/REdiscoverTE\n\n1. Index transcriptome ([`Salmon Index`](https://combine-lab.github.io/salmon/getting_started/#indexing-txome))\n2. Quantify reads ([`Salmon Quant`](https://combine-lab.github.io/salmon/getting_started/#quantifying-samples))\n3. Run REdiscoverTE ([`REdiscoverTE`](https://github.com/ucsffrancislab/REdiscoverTE))\n\n## Usage\n\n\u003e [!NOTE]\n\u003e 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#### Running nextflow @ MSKCC\n\nIf you are runnning this pipeline on a MSKCC cluster you need to make sure nextflow is properly configured for the HPC envirornment:\n\n```bash\nmodule load java/jdk-17.0.8\nmodule load singularity/3.7.1\nexport PATH=$PATH:/path/to/nextflow/binary\nexport SINGULARITY_TMPDIR=/path/to/network/storage/for/singularity/tmp/files\nexport NXF_SINGULARITY_CACHEDIR=/path/to/network/storage/for/singularity/cache\n```\n\n### Running the pipeline\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq\nSAMPLE_SINGLE_END,input_R1.fq.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 main.nf \\\n   -profile singularity,juno \\\n   --input samplesheet.csv \\\n   --outdir \u003cOUTDIR\u003e\n```\n\n\u003e [!WARNING]\n\u003e 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**_;\n\u003e see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).\n\n## Credits\n\nmsk/rediscoverte was originally written by [nikhil](https://github.com/nikhil).\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\u003c!-- TODO nf-core: If applicable, make list of people who have also contributed --\u003e\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\u003e Kong, Y., Rose, C.M., Cass, A.A. et al. Transposable element expression in tumors is associated with immune infiltration and increased antigenicity. Nat Commun 10, 5228 (2019). https://doi.org/10.1038/s41467-019-13035-2\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nThis pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/master/LICENSE).\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%2Frediscoverte","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmskcc%2Frediscoverte","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmskcc%2Frediscoverte/lists"}