{"id":23768563,"url":"https://github.com/nci-gdc/somaticsniper-cwl","last_synced_at":"2026-01-27T16:33:44.441Z","repository":{"id":53539263,"uuid":"50619579","full_name":"NCI-GDC/somaticsniper-cwl","owner":"NCI-GDC","description":"CWL for GDC SomaticSniper","archived":false,"fork":false,"pushed_at":"2021-03-25T15:58:23.000Z","size":122,"stargazers_count":0,"open_issues_count":0,"forks_count":1,"subscribers_count":9,"default_branch":"master","last_synced_at":"2025-05-25T14:46:48.513Z","etag":null,"topics":["bioinformatics","cwl","workflow"],"latest_commit_sha":null,"homepage":"","language":"Common Workflow Language","has_issues":false,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/NCI-GDC.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2016-01-28T22:49:06.000Z","updated_at":"2021-03-25T15:58:24.000Z","dependencies_parsed_at":"2022-08-19T01:30:23.751Z","dependency_job_id":null,"html_url":"https://github.com/NCI-GDC/somaticsniper-cwl","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/NCI-GDC/somaticsniper-cwl","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NCI-GDC%2Fsomaticsniper-cwl","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NCI-GDC%2Fsomaticsniper-cwl/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NCI-GDC%2Fsomaticsniper-cwl/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NCI-GDC%2Fsomaticsniper-cwl/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/NCI-GDC","download_url":"https://codeload.github.com/NCI-GDC/somaticsniper-cwl/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NCI-GDC%2Fsomaticsniper-cwl/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28816563,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-27T12:25:15.069Z","status":"ssl_error","status_checked_at":"2026-01-27T12:25:05.297Z","response_time":168,"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":["bioinformatics","cwl","workflow"],"created_at":"2025-01-01T01:37:35.201Z","updated_at":"2026-01-27T16:33:44.426Z","avatar_url":"https://github.com/NCI-GDC.png","language":"Common Workflow Language","funding_links":[],"categories":[],"sub_categories":[],"readme":"# GDC SomaticSniper CWL\n![Version badge](https://img.shields.io/badge/SomaticSniper-1.0.5.0-\u003cCOLOR\u003e.svg)\n\nThe purpose of SomaticSniper is to identify single nucleotide positions that are different between tumor and normal. It takes a tumor bam and a normal bam and compares the two to determine the differences.\n\nOriginal SomaticSniper: http://gmt.genome.wustl.edu/packages/somatic-sniper/index.html\n\n## Docker\n\nAll the docker images are built from `Dockerfile`s at https://github.com/NCI-GDC/somaticsniper-tool.\n\n## CWL\n\nhttps://www.commonwl.org/\n\nThe CWL are tested under multiple `cwltools` environments. The most tested one is:\n* cwltool 1.0.20180306163216\n\n\n## For external users\nThe repository has only been tested on GDC data and in the particular environment GDC is running in. Some of the reference data required for the workflow production are hosted in [GDC reference files](https://gdc.cancer.gov/about-data/data-harmonization-and-generation/gdc-reference-files \"GDC reference files\"). For any questions related to GDC data, please contact the GDC Help Desk at support@nci-gdc.datacommons.io.\n\nThere is a production-ready GDC CWL workflow at https://github.com/NCI-GDC/gdc-somatic-variant-calling-workflow, which uses this repo as a git submodule.\n\nPlease notice that you may want to change the docker image host of `dockerPull:` for each CWL.\n\nTo use CWL directly from this repo, we recommend to run\n* `tools/multi_somaticsniper.cwl` on an array of tumor/normal mpileup files.\n\nTo run CWL:\n\n```\n\u003e\u003e\u003e\u003e\u003e\u003e\u003e\u003e\u003e\u003eMulti SomaticSniper\u003c\u003c\u003c\u003c\u003c\u003c\u003c\u003c\u003c\u003c\ncwltool tools/multi_somaticsniper.cwl  -h\n/home/ubuntu/.virtualenvs/p2/bin/cwltool 1.0.20180306163216\nResolved 'tools/multi_somaticsniper.cwl' to 'file:///mnt/SCRATCH/githubs/submodules/s/somaticsniper-cwl/tools/multi_somaticsniper.cwl'\nusage: tools/multi_somaticsniper.cwl [-h] [--base_q BASE_Q] [--fout FOUT]\n                                     [--gor] [--loh] [--map_q MAP_Q] --mpileup\n                                     MPILEUP [--nhap NHAP] --normal_input\n                                     NORMAL_INPUT [--pd PD] --ppa [--pps PPS]\n                                     --psc --reference REFERENCE\n                                     [--theta THETA] --thread_count\n                                     THREAD_COUNT --tumor_input TUMOR_INPUT\n                                     [job_order]\n\npositional arguments:\n  job_order             Job input json file\n\noptional arguments:\n  -h, --help            show this help message and exit\n  --base_q BASE_Q       filtering somatic snv output with somatic quality less\n                        than this value\n  --fout FOUT           output format (classic/vcf/bed)\n  --gor                 do not report Gain of Reference variants as determined\n                        by genotypes (T/F)\n  --loh                 do not report LOH variants as determined by genotypes\n                        (T/F)\n  --map_q MAP_Q         filtering reads with mapping quality less than this\n                        value\n  --mpileup MPILEUP     mpileup file on t/n pair\n  --nhap NHAP           number of haplotypes in the sample\n  --normal_input NORMAL_INPUT\n  --pd PD               prior of a difference between two haplotypes\n  --ppa                 Use prior probabilities accounting for the somatic\n                        mutation rate (T/F)\n  --pps PPS             prior probability of a somatic mutation (implies -J)\n  --psc                 disable priors in the somatic calculation. Increases\n                        sensitivity for solid tumors (T/F)\n  --reference REFERENCE\n                        human reference genome\n  --theta THETA         theta in maq consensus calling model (for -c/-g)\n  --thread_count THREAD_COUNT\n  --tumor_input TUMOR_INPUT\n```\n\n## For GDC users\n\nSee https://github.com/NCI-GDC/gdc-somatic-variant-calling-workflow.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnci-gdc%2Fsomaticsniper-cwl","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fnci-gdc%2Fsomaticsniper-cwl","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnci-gdc%2Fsomaticsniper-cwl/lists"}