{"id":20425055,"url":"https://github.com/databio/paqc","last_synced_at":"2026-03-07T07:31:28.415Z","repository":{"id":86287791,"uuid":"245006380","full_name":"databio/paqc","owner":"databio","description":"PEPATAC qc project","archived":false,"fork":false,"pushed_at":"2021-07-09T02:23:26.000Z","size":19,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":6,"default_branch":"master","last_synced_at":"2025-09-11T10:15:51.438Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":null,"has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/databio.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"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":"2020-03-04T21:20:41.000Z","updated_at":"2021-07-09T02:23:28.000Z","dependencies_parsed_at":"2023-03-13T09:28:31.337Z","dependency_job_id":null,"html_url":"https://github.com/databio/paqc","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/databio/paqc","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2Fpaqc","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2Fpaqc/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2Fpaqc/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2Fpaqc/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/databio","download_url":"https://codeload.github.com/databio/paqc/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2Fpaqc/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":30209722,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-03-07T05:23:27.321Z","status":"ssl_error","status_checked_at":"2026-03-07T05:00:17.256Z","response_time":53,"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":[],"created_at":"2024-11-15T07:12:08.501Z","updated_at":"2026-03-07T07:31:28.400Z","avatar_url":"https://github.com/databio.png","language":null,"funding_links":[],"categories":[],"sub_categories":[],"readme":"# PEPATAC QC PEP\n\n\nThe `paqc.yaml` file is the working PEP for these samples.\nThe `paqc_annotation.csv` file is the working annotation file for these samples.\n\n## Download data\n\nGet source data using geofetch\n```\ngeofetch -i accessions.txt -n paqc -m paqc_geo_metadata\n```\n\nYou can set up a default sratoolkit config like this:\n\n```\nexport DATA=\"...\"\necho \"/repository/user/main/public/root = \\\"$DATA\\\"\" \u003e ${HOME}/.ncbi/user-settings.mkfg\n```\n\n## Format your PEP\n\nYou'll need to manually tweak the output of geofetch to adopt the new PEP 2.0.0 specification. Validate the configuration file with [`eido`](https://github.com/pepkit/eido) like so:\n```\neido validate paqc.yaml -s http://schema.databio.org/pipelines/pepatac.yaml\n```\n\n## Convert the SRA files to FASTQ\n\nUse the `sra_convert` amendment to point at the conversion pipeline. Run in looper:\n```\nlooper run paqc.yaml -a sra_convert --lump 25\n```\n\n## Run PEPATAC\n\n```\nPROCESSED=/project/shefflab/processed DATA=/project/shefflab/data/ looper run paqc.yaml -d\n```\n\nThe `peppro_paper.yaml` file is the working PEP for these samples.\nThe `peppro_paper.csv` file is the working annotation file for these samples.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdatabio%2Fpaqc","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdatabio%2Fpaqc","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdatabio%2Fpaqc/lists"}