{"id":20371784,"url":"https://github.com/biosustain/dsp_nf-msdap","last_synced_at":"2026-05-21T16:44:49.520Z","repository":{"id":242062702,"uuid":"682455336","full_name":"biosustain/dsp_nf-msdap","owner":"biosustain","description":"Nextflow pipeline for MS-DAP, a downstream pipeline to generate statistical reports for MS data","archived":false,"fork":false,"pushed_at":"2024-05-31T11:36:18.000Z","size":169,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":5,"default_branch":"main","last_synced_at":"2025-01-15T06:20:14.369Z","etag":null,"topics":["downstream-analysis","nextflow-pipeline","proteomics"],"latest_commit_sha":null,"homepage":"","language":"R","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/biosustain.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":"2023-08-24T07:53:07.000Z","updated_at":"2024-05-31T11:36:21.000Z","dependencies_parsed_at":"2024-05-31T12:54:15.929Z","dependency_job_id":"0889a109-9847-4dc8-aa6c-21b354ac3052","html_url":"https://github.com/biosustain/dsp_nf-msdap","commit_stats":null,"previous_names":["biosustain/dsp_nf-msdap"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biosustain%2Fdsp_nf-msdap","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biosustain%2Fdsp_nf-msdap/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biosustain%2Fdsp_nf-msdap/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biosustain%2Fdsp_nf-msdap/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/biosustain","download_url":"https://codeload.github.com/biosustain/dsp_nf-msdap/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":241916805,"owners_count":20041980,"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":["downstream-analysis","nextflow-pipeline","proteomics"],"created_at":"2024-11-15T01:09:46.214Z","updated_at":"2026-05-21T16:44:49.461Z","avatar_url":"https://github.com/biosustain.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# dsp_nf-msdap\nNextflow pipeline for MS-DAP, a downstream pipeline to generate statistical PDF reports for MS data\n\nThis repository aims to serve as a headless launcher for msdap - https://github.com/biosustain/msdap \n\nThis very early development verion is only compatible with Spectronaut output, but all formats supported by msdap will be compatible with the final version.\n\nto generate a pdf report with MS-DAP, the following are needed:\n\n* Mass Spec report as would be needed for MS DAP.\n* Fasta file with proteome / TAXID for species to autodownload from Uniprot.\n* ordered list of replicate group names.\n\nThe enviromnent running this script will need following dependencies:\n\n* Nextflow\n* Docker with min 16 gb of ram for the R installation with MS-DAP\n* python3 with pandas\n\n\nExample to initiate this pipeline (9606 indicates that proteome for human will be downloaded):\n\n```\n./nextflow run flow_main.nf ## nexflow workflow file\n--library reference ## Directory where the reference proteomes and fasta files should be found/downloaded\n--force.download False ## Whether to force download of fasta file\n--taxid 9606 ## NCBI Taxonomic identifier of studied organism\n--file [full_path]/data/DIA_Report.csv ## Processed proteomics file (e.g., output spectronaut)\n--groups [full_path]/data/groups.xlsx ## File specifying conditions to be contrasted\n--format spectronaut ## Format of the proteomics file\n```\n\ncontent of groups.xlsx:\n```\nsample_id / group\n```\n![metromap](metromap.png)\n\nAttributions: \nMetromap adapted in part with remixed components from nf-co.re/sarek \n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiosustain%2Fdsp_nf-msdap","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbiosustain%2Fdsp_nf-msdap","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiosustain%2Fdsp_nf-msdap/lists"}