{"id":30019669,"url":"https://github.com/veupathdb/bowtie-mapping-nextflow","last_synced_at":"2026-02-12T23:33:03.046Z","repository":{"id":37544841,"uuid":"500457536","full_name":"VEuPathDB/bowtie-mapping-nextflow","owner":"VEuPathDB","description":"Nextflow conversion of BowtieMappingTask","archived":false,"fork":false,"pushed_at":"2025-06-26T16:34:38.000Z","size":37905,"stargazers_count":0,"open_issues_count":0,"forks_count":1,"subscribers_count":16,"default_branch":"main","last_synced_at":"2025-09-10T10:17:06.912Z","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/VEuPathDB.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,"zenodo":null}},"created_at":"2022-06-06T14:04:59.000Z","updated_at":"2025-06-25T19:50:21.000Z","dependencies_parsed_at":"2024-08-13T19:31:56.696Z","dependency_job_id":"7d860551-8329-4286-8899-4f37118ec79d","html_url":"https://github.com/VEuPathDB/bowtie-mapping-nextflow","commit_stats":null,"previous_names":["veupathdb/bowtie-mapping-nextflow"],"tags_count":2,"template":false,"template_full_name":null,"purl":"pkg:github/VEuPathDB/bowtie-mapping-nextflow","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/VEuPathDB%2Fbowtie-mapping-nextflow","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/VEuPathDB%2Fbowtie-mapping-nextflow/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/VEuPathDB%2Fbowtie-mapping-nextflow/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/VEuPathDB%2Fbowtie-mapping-nextflow/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/VEuPathDB","download_url":"https://codeload.github.com/VEuPathDB/bowtie-mapping-nextflow/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/VEuPathDB%2Fbowtie-mapping-nextflow/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29386220,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-12T22:07:52.078Z","status":"ssl_error","status_checked_at":"2026-02-12T22:07:49.026Z","response_time":55,"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":[],"created_at":"2025-08-06T01:20:32.176Z","updated_at":"2026-02-12T23:33:03.041Z","avatar_url":"https://github.com/VEuPathDB.png","language":"Nextflow","funding_links":[],"categories":[],"sub_categories":[],"readme":"THIS REPO IS 🚧 UNDER CONSTRUCTION 🚧 and NOT Used in ANY production CODE\n# bowtieMapping\n\n***\u003cp align=center\u003ebowtieMapping (From sra download)\u003c/p\u003e***  \n```mermaid\nflowchart TD\n    p0((Channel.fromList))\n    p1[bowtieMapping:sra:downloadFiles]\n    p2(( ))\n    p3(( ))\n    p4[bowtieMapping:sra:bowtie]\n    p5[bowtieMapping:sra:PCRDuplicates]\n    p6(( ))\n    p0 --\u003e|ids| p1\n    p1 --\u003e p4\n    p2 --\u003e|indexfiles| p4\n    p3 --\u003e|indexFileBasename| p4\n    p4 --\u003e p5\n    p5 --\u003e p6\n```\n\n***\u003cp align=center\u003ebowtieMapping (from local files)\u003c/p\u003e***  \n```mermaid\nflowchart TD\n    p0((Channel.fromFilePairs))\n    p1(( ))\n    p2(( ))\n    p3[bowtieMapping:local:bowtie]\n    p4[bowtieMapping:local:PCRDuplicates]\n    p5(( ))\n    p0 --\u003e|files| p3\n    p1 --\u003e|indexfiles| p3\n    p2 --\u003e|indexFileBasename| p3\n    p3 --\u003e p4\n    p4 --\u003e p5\n```\n\nDescription of nextflow configuration parameters:\n\n| param         | value type        | description  |\n| ------------- | ------------- | ------------ |\n| inputFilePath  | string | Path to input file |\n| outputDir | string | Path to where you would like output files stored |\n| databaseFasta | string | Path to the fasta file that you would like to use a the database for Psipred |\n| preconfiguredDatabase | boolean | Are you using a preconfigured database? |\n| writeBedFile | boolean | If you would like to output an additional bedfile. |\n| isSingleEnd | boolean | Is the data single-end or paired-end? |\n| isColorspace | boolean | Is the data colorspace data? |\n| removePCRDuplicates | boolean | Would you like PCR duplicates removed? |\n| input | path | Path to input tsv file if downloading from sra or path to directory holding input files |\n| downloadMethod | string | Either 'sra' or 'local' |\n| databaseFileDir | path | Path to database file dir|\n| indexFileBasename | string | Basename for bt2 files. Ex \"index\" if files start index.1.bt2, index.2.bt2, etc |\n| mateAQual | path | Path to qual file for mateA |\n| mateBQual | path | Path to qual fiel for mateB |\n\n### Get Started\n  * Install Nextflow\n    \n    `curl https://get.nextflow.io | bash`\n  \n  * Run the script\n    \n    `nextflow run VEuPathDB/blastSimilarity -with-trace -c  \u003cconfig_file\u003e -r main`\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fveupathdb%2Fbowtie-mapping-nextflow","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fveupathdb%2Fbowtie-mapping-nextflow","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fveupathdb%2Fbowtie-mapping-nextflow/lists"}