{"id":31805827,"url":"https://github.com/theislab/spapros-pipeline","last_synced_at":"2026-02-18T15:01:04.820Z","repository":{"id":48778443,"uuid":"380249414","full_name":"theislab/spapros-pipeline","owner":"theislab","description":null,"archived":false,"fork":false,"pushed_at":"2024-11-23T15:34:06.000Z","size":3476,"stargazers_count":7,"open_issues_count":0,"forks_count":0,"subscribers_count":0,"default_branch":"master","last_synced_at":"2026-01-15T00:52:42.922Z","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":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/theislab.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,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2021-06-25T13:38:28.000Z","updated_at":"2024-11-23T15:34:10.000Z","dependencies_parsed_at":"2025-10-11T03:09:25.887Z","dependency_job_id":null,"html_url":"https://github.com/theislab/spapros-pipeline","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/theislab/spapros-pipeline","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2Fspapros-pipeline","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2Fspapros-pipeline/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2Fspapros-pipeline/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2Fspapros-pipeline/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/theislab","download_url":"https://codeload.github.com/theislab/spapros-pipeline/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2Fspapros-pipeline/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29582790,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-18T13:56:48.962Z","status":"ssl_error","status_checked_at":"2026-02-18T13:54:34.145Z","response_time":162,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 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":"2025-10-11T02:59:04.615Z","updated_at":"2026-02-18T15:01:04.802Z","avatar_url":"https://github.com/theislab.png","language":"Nextflow","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![Run Example](https://github.com/theislab/spapros-pipeline/actions/workflows/run_example.yml/badge.svg)](https://github.com/theislab/spapros-pipeline/actions/workflows/run_example.yml)\n\nNote that this is an older version of Spapros' probeset evaluation benchmarking pipeline. The new version can be found [here](https://github.com/theislab/spapros-smk)\n\n\n# Spapros-pipeline\n\nThis pipeline aims at providing a heavily parallelized equivalent to the [Spapros](https://github.com/theislab/spapros) package for probeset selection.    \nA runnable example is provided in the run.sh script. We will provide more details and documentation as the project progresses.\nUsage:\n\nThe typical command for running the pipeline is as follows:\n\n```\n    nextflow run . -profile conda --adata data/small_data_raw_counts.h5ad --parameters data/parameters.yml --probeset data/selections_genesets_1.csv --markers data/small_data_marker_list.csv --probeset_ids genesets_1_0,genesets_1_1\n\n    Mandatory arguments:\n      --adata [file]                            Path to h5ad file containing the single-cell data\n      --parameters [file]                       Path to a parameters file. See Spapros documentation\n      --probeset [file]                         Path to the selected probesets as determined by Spapros. See Spapros documentation.\n      --markers [file]                          Path to a file containing the marker genes\n      --probeset_ids [str]                      Comma separated list of probesets to evaluate\n      -profile [str]                            Configuration profile to use. Can use multiple (comma separated)\n                                                Available: docker, singularity, test, awsbatch and more\n\n    Evaluation:\n      --run_cs [bool]                           Whether to run cluster similarity evaluation (true)\n      --run_knn [bool]                          Whether to run KNN graph evaluation (true)\n      --run_rf [bool]                           Whether to run random forest evaluation (true)\n      --run_corr [bool]                         Whether to run correlation evaluation (true)\n\n    Other options:\n      --outdir [file]                           The output directory where the results will be saved\n      --email [email]                           Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits\n      --email_on_fail [email]                   Same as --email, except only send mail if the workflow is not successful\n      -name [str]                               Name for the pipeline run. If not specified, Nextflow will automatically generate a random mnemonic\n\n    AWSBatch options:\n      --awsqueue [str]                          The AWSBatch JobQueue that needs to be set when running on AWSBatch\n      --awsregion [str]                         The AWS Region for your AWS Batch job to run on\n      --awscli [str]                            Path to the AWS CLI tool\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftheislab%2Fspapros-pipeline","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftheislab%2Fspapros-pipeline","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftheislab%2Fspapros-pipeline/lists"}