{"id":13296952,"url":"https://github.com/NCI-GDC/samtools-mpileup-cwl","last_synced_at":"2025-03-10T09:32:46.316Z","repository":{"id":53551583,"uuid":"235491353","full_name":"NCI-GDC/samtools-mpileup-cwl","owner":"NCI-GDC","description":"CWL for GDC samtools mpileup","archived":false,"fork":false,"pushed_at":"2024-08-05T16:10:52.000Z","size":19,"stargazers_count":0,"open_issues_count":0,"forks_count":1,"subscribers_count":9,"default_branch":"master","last_synced_at":"2024-08-05T18:58:49.137Z","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":"2020-01-22T03:29:43.000Z","updated_at":"2024-08-05T16:10:55.000Z","dependencies_parsed_at":"2022-09-13T11:41:27.474Z","dependency_job_id":null,"html_url":"https://github.com/NCI-GDC/samtools-mpileup-cwl","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NCI-GDC%2Fsamtools-mpileup-cwl","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NCI-GDC%2Fsamtools-mpileup-cwl/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NCI-GDC%2Fsamtools-mpileup-cwl/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NCI-GDC%2Fsamtools-mpileup-cwl/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/NCI-GDC","download_url":"https://codeload.github.com/NCI-GDC/samtools-mpileup-cwl/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":221164312,"owners_count":16767305,"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":["bioinformatics","cwl","workflow"],"created_at":"2024-07-29T17:21:20.469Z","updated_at":"2024-10-23T06:30:47.014Z","avatar_url":"https://github.com/NCI-GDC.png","language":"Common Workflow Language","funding_links":[],"categories":[],"sub_categories":[],"readme":"# GDC Samtools mpileup cwl\n![Version badge](https://img.shields.io/badge/samtools-1.1-\u003cCOLOR\u003e.svg)\n\nOriginal samtools: https://www.htslib.org/\n\n## Docker\n\nAll the docker images are built from `Dockerfile`s at https://github.com/NCI-GDC/samtools-mpileup-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 `tools/samtools_mpileup.cwl` or `tools/multi_samtools_mpileup.cwl`.\n\nTo run multithreading samtools mpileup CWL:\n\n```\n\u003e\u003e\u003e\u003e\u003e\u003e\u003e\u003e\u003e\u003eMultithreading samtools mpileup\u003c\u003c\u003c\u003c\u003c\u003c\u003c\u003c\u003c\u003c\ncwltool multi_samtools_mpileup.cwl -h\n/home/ubuntu/.virtualenvs/p2/bin/cwltool 1.0.20180306163216\nResolved 'multi_samtools_mpileup.cwl' to 'file:///mnt/SCRATCH/githubs/samtools-mpileup-cwl/tools/multi_samtools_mpileup.cwl'\nusage: multi_samtools_mpileup.cwl [-h] [--min_MQ MIN_MQ] --normal_bam\n                                  NORMAL_BAM --ref REF --region REGION\n                                  --thread_count THREAD_COUNT --tumor_bam\n                                  TUMOR_BAM\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  --min_MQ MIN_MQ\n  --normal_bam NORMAL_BAM\n  --ref REF\n  --region REGION\n  --thread_count THREAD_COUNT\n  --tumor_bam TUMOR_BAM\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%2Fsamtools-mpileup-cwl","html_url":"https://awesome.ecosyste.ms/projects/github.com%2FNCI-GDC%2Fsamtools-mpileup-cwl","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FNCI-GDC%2Fsamtools-mpileup-cwl/lists"}