{"id":27452215,"url":"https://github.com/epigen/microtest","last_synced_at":"2025-07-01T09:07:24.135Z","repository":{"id":112747660,"uuid":"60338357","full_name":"epigen/microtest","owner":"epigen","description":"Small test data from various data types for testing pipelines","archived":false,"fork":false,"pushed_at":"2020-10-07T20:33:52.000Z","size":3045,"stargazers_count":1,"open_issues_count":2,"forks_count":3,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-06-10T07:44:01.958Z","etag":null,"topics":["bioinformatics","test-data"],"latest_commit_sha":null,"homepage":"","language":"Shell","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/epigen.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}},"created_at":"2016-06-03T10:03:23.000Z","updated_at":"2020-11-16T21:24:17.000Z","dependencies_parsed_at":"2023-09-13T22:32:32.901Z","dependency_job_id":null,"html_url":"https://github.com/epigen/microtest","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/epigen/microtest","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/epigen%2Fmicrotest","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/epigen%2Fmicrotest/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/epigen%2Fmicrotest/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/epigen%2Fmicrotest/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/epigen","download_url":"https://codeload.github.com/epigen/microtest/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/epigen%2Fmicrotest/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":262933316,"owners_count":23386784,"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":["bioinformatics","test-data"],"created_at":"2025-04-15T11:42:28.105Z","updated_at":"2025-07-01T09:07:24.125Z","avatar_url":"https://github.com/epigen.png","language":"Shell","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Microtest test data\n\nMicrotest is a repository of small test data from various data types, for testing pipelines.\n\n## Data descriptions\n(please include here a short description of any data files you add)\n\n* `atac-seq_PE.bam`: Random sample of paired-end ATAC-seq\n* `atac-seq_SE.bam`: Random sample of single-end ATAC-seq\n* `bs_aln_k1k3.bam`: Bisulfite data aligned to the methylated/unmethylated spike-in control sequences (k1/k3).\n* `chip-seq_PE.bam`: Random sample of paired-end ChIP-seq\n* `chip-seq_SE.bam`: Random sample of single-end ChIP-seq\n* `chipmentation_PE.bam`: Random sample of paired-end ChIPmentation\n* `chipmentation_SE.bam`: Random sample of single-end ChIPmentation\n* `dropseq_human.bam`: Random sample of Drop-seq from human\n* `dropseq_mouse.bam`: Random sample of Drop-seq from mouse\n* `hichip_PE.bam`: Random sample of paired-end Hi-ChIP\n* `wgbs1.bam`/`wgbs2.bam`: Random samples of unaligned WGBS data.\n\n\n## Usage\n\n### With looper/pypiper in a virtualev\n\n\n```bash\n# create and activate a virtual environment\nvirtualenv microtestenv; cd microtestenv; . ./bin/activate\n\n# install the stack\npip install \"peppy\u003e=0.30.2,\u003c1.0.0\" \"looper\u003e=1.2.0,\u003c2.0.0\" \"piper\u003e=0.12.1,\u003c1.0.0\"\n\n# clone open_pipelines and microtest\ngit clone https://github.com/epigen/open_pipelines\ngit clone https://github.com/epigen/microtest\n\n# run\nexport CODE=`pwd`\n# run only tutorial pipeline (no additional dependecies)\nlooper run microtest/config/microtest_config.yaml --sel-attr protocol --sel-incl Amplicon\n\n# or run all (would require additional software dependecies)\n# for now only ATAC-seq has been adapted\nlooper run microtest/config/microtest_config.yaml --sel-attr protocol --sel-incl ATAC-seq\n```\n\n\n### Single pipeline usage\n\n```bash\nAMPLICON=`sed 's/,/\\t/g' microtest/config/microtest_annotation.tutorial.csv | tail -n 1 | cut -f 14`\nGUIDE=`sed 's/,/\\t/g' microtest/config/microtest_annotation.tutorial.csv | tail -n 1 | cut -f 15`\n\npython \\\n\topen_pipelines/pipelines/amplicon_simple.py \\\n\t-S microtest_amplicon \\\n\t-i microtest/data/amplicon.fastq.gz \\\n\t-g $GUIDE \\\n\t-a $AMPLICON \\\n\t-O microtest_amplicon\n```\n\n## Test data production\n\nHow samples were made:\n\n```bash\nsamtools view -s .0001 sample.bam -b \u003e new_sample.bam\n```\n\n## Automatic testing with a Github hook\n\n1. Open a listening port for webhooks:\n    1. Get ngrok at https://ngrok.com and open a port: `./ngrok 3456`\n    2. add that URL + \"/payload\" to the github webhook with a secret key\n2. Create a listening server:\n    1. `git clone git@github.com:afrendeiro/github-webhook-handler.git`\n    2. modify `github-webhook-handler/repos.json` with your repositories that should trigger the testing and the secret key(s)\n    3. start the server and leave it running: `python github-webhook-handler/index.py 4567`\n\nWhen there is a push to your repositories, `run_microtest.sh` will run.\nThis creates an isolated virtual environment, installs dependencies (not pipeline-specific ones though!)\nand runs the pipelines on the microtest data (similar to the example above).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fepigen%2Fmicrotest","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fepigen%2Fmicrotest","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fepigen%2Fmicrotest/lists"}