{"id":19749485,"url":"https://github.com/mskcc/simba","last_synced_at":"2026-02-25T23:32:47.055Z","repository":{"id":231327496,"uuid":"781480921","full_name":"mskcc/simba","owner":"mskcc","description":"Runs all thenextflow workflow scripts for IMPACT processing","archived":false,"fork":false,"pushed_at":"2024-11-13T15:30:41.000Z","size":192,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-11-09T09:33:34.494Z","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":"2024-04-03T13:16:15.000Z","updated_at":"2025-02-11T20:19:58.000Z","dependencies_parsed_at":"2024-04-03T14:56:01.246Z","dependency_job_id":"d0a2f51d-12f9-48c3-a075-3d0cc92efdcd","html_url":"https://github.com/mskcc/simba","commit_stats":null,"previous_names":["mskcc/simba"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/mskcc/simba","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Fsimba","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Fsimba/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Fsimba/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Fsimba/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/mskcc","download_url":"https://codeload.github.com/mskcc/simba/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Fsimba/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29844872,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-25T22:37:40.667Z","status":"ssl_error","status_checked_at":"2026-02-25T22:37:25.960Z","response_time":61,"last_error":"SSL_read: 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":"2024-11-12T02:26:44.712Z","updated_at":"2026-02-25T23:32:47.022Z","avatar_url":"https://github.com/mskcc.png","language":"Nextflow","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![GitHub Actions CI Status](https://github.com/mskcc/simba/actions/workflows/ci.yml/badge.svg)](https://github.com/mskcc/simba/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/mskcc/simba/actions/workflows/linting.yml/badge.svg)](https://github.com/mskcc/simba/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://tower.nf/launch?pipeline=https://github.com/mskcc/simba)\n\n## Introduction\n\n**mskcc/simba** is a bioinformatics pipeline that runs the variant calling pipeline using other a collection of other nextflow workflows\n\n1. Reallignment ([`Arrakis`](https://github.com/mskcc/arrakis))\n2. Variant Calling ([`Odin`](https://github.com/mskcc/odin))\n3. Structural Variants ([`Sif`](https://github.com/mskcc/sif))\n4. Copy Number Variants ([`Loki`](https://github.com/mskcc/loki))\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### Cloning the repo\n\nThis repository has submodules, make sure to update it with:\n\n```\ngit submodule init\ngit submodule update\n```\n\nAfter you clone the repo.\n\n### Setting up inputs\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\npairId,tumorBam,normalBam,assay,normalType,bedFile\nfoo_sample,foo_tumor.rg.md.bam,foo_normal.rg.md.bam,IMPACT505,MATCHED,foo_tumor.foo_normal.fci.bed\nbar_sample,bar_tumor.rg.md.bam,bar_normal.rg.md.bam,IMPACT505,MATCHED,bar_tumor.bar_normal.fci.bed\n```\n### Running the pipeline\n\nNow, you can run the pipeline using:\n\n\u003c!-- TODO nf-core: update the following command to include all required parameters for a minimal example --\u003e\n\n```bash\nnextflow run main.nf \\\n   -profile singularity,test_juno \\\n   --input samplesheet.csv \\\n   --outdir \u003cOUTDIR\u003e\n```\n\n\u003e [!NOTE]\n\u003e You must include `test_juno` as your profile for the workflow to run properly\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\nmskcc/arrakis was originally written by Nikhil Kumar ([@nikhil](https://github.com/nikhil)).\n\nWe 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\n## Citations\n\n- Lisle E Mose, Charles M Perou, Joel S Parker, Improved indel detection in DNA and RNA via realignment with ABRA2, Bioinformatics, Volume 35, Issue 17, September 2019, Pages 2966–2973, https://doi.org/10.1093/bioinformatics/btz033\n- “Picard Toolkit.” 2019. Broad Institute, GitHub Repository. https://broadinstitute.github.io/picard/; Broad Institute\n- Van der Auwera, G. A., Carneiro, M. O., Hartl, C., Poplin, R., Del Angel, G., Levy-Moonshine, A., Jordan, T., Shakir, K., Roazen, D., Thibault, J., Banks, E., Garimella, K. V., Altshuler, D., Gabriel, S., \u0026 DePristo, M. A. (2013). From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline. Current protocols in bioinformatics, 43(1110), 11.10.1–11.10.33. https://doi.org/10.1002/0471250953.bi1110s43\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%2Fsimba","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmskcc%2Fsimba","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmskcc%2Fsimba/lists"}