{"id":19434404,"url":"https://github.com/likelet/exomepipe","last_synced_at":"2026-02-28T22:03:02.258Z","repository":{"id":86650738,"uuid":"112591345","full_name":"likelet/ExomePipe","owner":"likelet","description":null,"archived":false,"fork":false,"pushed_at":"2020-09-24T01:53:17.000Z","size":200,"stargazers_count":7,"open_issues_count":0,"forks_count":3,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-04-22T00:18:50.060Z","etag":null,"topics":["nextflow","ngs","pipeline"],"latest_commit_sha":null,"homepage":"","language":"Nextflow","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/likelet.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2017-11-30T09:21:04.000Z","updated_at":"2023-04-12T01:22:21.000Z","dependencies_parsed_at":null,"dependency_job_id":"a1c2229c-a15e-4a3b-a678-5c4485888a0c","html_url":"https://github.com/likelet/ExomePipe","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/likelet/ExomePipe","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/likelet%2FExomePipe","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/likelet%2FExomePipe/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/likelet%2FExomePipe/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/likelet%2FExomePipe/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/likelet","download_url":"https://codeload.github.com/likelet/ExomePipe/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/likelet%2FExomePipe/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29953212,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-28T18:42:55.706Z","status":"ssl_error","status_checked_at":"2026-02-28T18:42:48.811Z","response_time":90,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 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":["nextflow","ngs","pipeline"],"created_at":"2024-11-10T14:46:20.969Z","updated_at":"2026-02-28T22:02:57.232Z","avatar_url":"https://github.com/likelet.png","language":"Nextflow","funding_links":[],"categories":[],"sub_categories":[],"readme":"# ExomePipe\n## dependencies\n   * fastp\n   * bwa \n   * picard/samtools \n   * gatk4 (CNV analysis)\n   * mutect2\n   * annovar and annovar DB(deprecated)\n   * vep and vep DB(very huge ~15G)\n   * vcf2maftools\n   * MAFtools(only avaliable when multiple sample paired envolved) \n   * some in-house script \n   * msisensor \n\n   * Dependencies for FREEC\n        * Control-freeC\n        * bedtools \n        * samtools \n   * FACET\n        * snp-pileup\n\n   * NGScheckmate\n        * bcftools\n        * python\n        * samtools\n   \n# Input file \n\n*  `sample input file ` TSV file for sample\n\u003e adjusted from https://github.com/SciLifeLab/Sarek/blob/master/docs/INPUT.md\n# TSV file for sample\n\nInput files for ExomeSeqPipe can be specified using a tsv file given to the `--sample` parameter. The tsv file is a Tab Separated Value file with columns: `subject gender status sample lane fastq1 fastq2` or `subject gender status sample bam bai`.\nThe content of these columns should be quite straight-forward:\n\n- `subject` designate the subject, it should be the ID of the Patient, or if you don't have one, it could be the Normal ID Sample.\n- `gender` is the gender of the Patient, (XX or XY)\n- `status` is the status of the Patient, (0 for Normal or 1 for Tumor)\n- `sample` designate the Sample, it should be the ID of the Sample (it is possible to have more than one tumor sample for each patient)\n- `fastq1` is the path to the first pair of the fastq file\n- `fastq2` is the path to the second pair of the fastq file\n- `bam` is the bam file\n- `bai` is the index\n\nAll examples are given for a normal/tumor pair. If no tumors are listed in the TSV file, then the workflow will proceed as if it was a single normal sample instead of a normal/tumor pair.\n\n* Example TSV file for a normal/tumor pair with FASTQ files\n\nIn this sample for the normal case there are 3 read groups, and 2 for the tumor. It is recommended to add the absolute path of the paired FASTQ files, but relative path should work also. Note, the delimiter is the tab (\\t) character:\nNOTE: assume each sample has only one libraray\n```\nG15511    XX    0    C09DFN    pathToFiles/C09DFACXX111207.1_1.fastq.gz    pathToFiles/C09DFACXX111207.1_2.fastq.gz\nG15511    XX    1    D0ENMT    pathToFiles/D0ENMACXX111207.1_1.fastq.gz    pathToFiles/D0ENMACXX111207.1_2.fastq.gz\n```\n\n# Contribution\n\nQi Zhao(zhaoqi@sysucc.org.cn)","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flikelet%2Fexomepipe","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flikelet%2Fexomepipe","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flikelet%2Fexomepipe/lists"}