{"id":20425007,"url":"https://github.com/databio/ppqc","last_synced_at":"2026-03-19T15:46:20.174Z","repository":{"id":84558882,"uuid":"197839750","full_name":"databio/ppqc","owner":"databio","description":"QC samples for PEPPRO pipeline","archived":false,"fork":false,"pushed_at":"2022-08-29T14:08:23.000Z","size":85,"stargazers_count":1,"open_issues_count":1,"forks_count":1,"subscribers_count":15,"default_branch":"master","last_synced_at":"2025-01-15T15:08:44.047Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","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":"2019-07-19T20:46:06.000Z","updated_at":"2022-08-29T14:08:27.000Z","dependencies_parsed_at":"2023-03-12T23:37:54.358Z","dependency_job_id":null,"html_url":"https://github.com/databio/ppqc","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/databio%2Fppqc","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2Fppqc/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2Fppqc/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2Fppqc/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/databio","download_url":"https://codeload.github.com/databio/ppqc/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":241966977,"owners_count":20050324,"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":[],"created_at":"2024-11-15T07:11:56.408Z","updated_at":"2026-02-04T11:36:29.555Z","avatar_url":"https://github.com/databio.png","language":null,"funding_links":[],"categories":[],"sub_categories":[],"readme":"# Peppro QC PEP\n\n\n## Get source samples using geofetch\n```\ngeofetch -i sra_accessions.txt -n ppqc\n```\n\n## Grab the source sample metadata here:\n```\nwget -r http://big.databio.org/peppro/sra_meta/ppqc/ .\n```\n\n## Get RNA-seq spike-in samples here:\n```\nwget http://big.databio.org/peppro/fastq/K562_[1-9]0pct_RNArc_r2.fastq.gz .\n```\n\n## Validate the configuration file with [`eido`](https://github.com/pepkit/eido) like so:\n```\neido -p peppro_paper.yaml -s http://schema.databio.org/pipelines/ProseqPEP.yaml\n```\n\n## Create user-specific environment variables\n - `$CODE`: this is a path to the parent directory where scripts and code are stored\n    - For example:`CODE=/scratch/userid/src/`\n - `$DATA`: this is a path to the parent directory where input files are stored\n    - For example:`DATA=/project/shefflab/data/`\n - `$PROCESSED`: this is a path to the parent directory to where output should be written\n    - For example:`PROCESSED=/project/shefflab/processed/`\n\n## Run in looper:\n```\nlooper run ppqc/peppro_paper.yaml\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\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdatabio%2Fppqc","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdatabio%2Fppqc","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdatabio%2Fppqc/lists"}