{"id":49047095,"url":"https://github.com/alermol/chocallate","last_synced_at":"2026-04-25T16:01:49.111Z","repository":{"id":289464935,"uuid":"971301058","full_name":"alermol/ChoCallate","owner":"alermol","description":"ChoCallate: Nextflow pipeline for SNVs/InDels consensus calling using ensemble of callers","archived":false,"fork":false,"pushed_at":"2026-04-19T16:52:48.000Z","size":242477,"stargazers_count":1,"open_issues_count":3,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2026-04-19T18:09:27.533Z","etag":null,"topics":["calling","consensus","indels","nextflow","snp"],"latest_commit_sha":null,"homepage":"","language":"Nextflow","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/alermol.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":"ROADMAP.md","authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2025-04-23T10:07:53.000Z","updated_at":"2026-04-19T16:48:48.000Z","dependencies_parsed_at":"2025-07-09T13:22:52.674Z","dependency_job_id":"6afb03bd-f448-451a-a850-eb0c07ccc012","html_url":"https://github.com/alermol/ChoCallate","commit_stats":null,"previous_names":["alermol/chocallate"],"tags_count":3,"template":false,"template_full_name":null,"purl":"pkg:github/alermol/ChoCallate","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/alermol%2FChoCallate","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/alermol%2FChoCallate/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/alermol%2FChoCallate/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/alermol%2FChoCallate/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/alermol","download_url":"https://codeload.github.com/alermol/ChoCallate/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/alermol%2FChoCallate/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":32267710,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-04-25T09:15:33.318Z","status":"ssl_error","status_checked_at":"2026-04-25T09:15:31.997Z","response_time":59,"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":["calling","consensus","indels","nextflow","snp"],"created_at":"2026-04-19T18:06:05.775Z","updated_at":"2026-04-25T16:01:49.105Z","avatar_url":"https://github.com/alermol.png","language":"Nextflow","funding_links":[],"categories":[],"sub_categories":[],"readme":"# ChoCallate 🍫\n\n![GitHub Release](https://img.shields.io/github/v/release/alermol/ChoCallate) [![Static Badge](https://img.shields.io/badge/Changelog-orange)](https://github.com/alermol/ChoCallate/blob/main/CHANGELOG.md) ![GitHub License](https://img.shields.io/github/license/alermol/chocallate) [![Static Badge](https://img.shields.io/badge/Wiki-red?link=https%3A%2F%2Fgithub.com%2Falermol%2FChoCallate%2Fwiki)\n](https://github.com/alermol/ChoCallate/wiki)\n\n\n**ChoCallate** (**Cho**rus of **Call**ers) - a **Nextflow** pipeline for **consensus-based variant calling**. \n\nChoCallate runs several variant callers and applies configurable consensus rules to produce high-confidence **SNVs** and **INDELs**. It addresses a critical challenge in variant calling: individual variant callers can produce different results for the same genomic data, leading to uncertainty in variant identification. By implementing a consensus-driven approach, ChoCallate combines results from multiple state-of-the-art variant callers and applies configurable consensus rules to generate reliable, high-quality variant calls.\n\n## Requirements\n\n- **Linux** (tested). macOS/Windows are not currently tested.\n- **Conda** (Miniconda/Anaconda) or **Mamba**\n- **Git**\n- **Nextflow**\n\n## Installation\n\n```bash\ngit clone --depth 1 https://github.com/alermol/ChoCallate.git\ncd ChoCallate\nconda env create -y -f environment.yaml\nconda activate ChoCallate\n```\n\nOptional verification and cleanup:\n\n```bash\ncd test_run\nbash run_test.sh\nbash cleanup.sh\n```\n\n## Docker\n\nChoCallate is available as a Docker image on DockerHub. For a fuller walkthrough, see the Wiki: [Installing ChoCallate](https://github.com/alermol/ChoCallate/wiki/Installing-ChoCallate#use-the-docker-container).\n\n```bash\ndocker pull alermol/chocallate:latest\n```\n\nMount your run directory to `/workspace` and run:\n\n```bash\ndocker run --rm \\\n  -u \"$(id -u):$(id -g)\" \\\n  -v \"${PWD}/input_data:/workspace\" \\\n  -w /workspace \\\n  alermol/chocallate:latest \\\n  -params-file config.yaml\n```\n\nOutputs will be written to the configured `outdir` (default: `ChoCallate_output`) inside `input_data`.\n\n## Usage\n\nChoCallate is configured via a Nextflow params YAML file. Start from the template.\n\n```bash\ncp assets/templates/config.yaml my_run.yaml\n```\n\nMinimum set of parameters in `my_run.yaml`:\n\n- **`samples_tsv`**: input samples TSV (formats below)\n- **`reference_genome`**: reference FASTA (plain or bgzip-compressed)\n- **`reference_index_dir`**: path to directory with index files for reference genome\n\nAfter configuration is complete you can run the ChoCallate\n\n```bash\nnextflow run main.nf -params-file my_run.yaml\n```\n\n## Inputs\n\n- **Reads**: FASTQs (`input_format: \"fastq\"`) or a pre-aligned BAM (`input_format: \"bam\"`). If you provide a BAM, mapping is skipped.\n- **Reference genome**: Plain or bgzipped FASTA file.\n- **Indexes of reference genome**: All indexes required by the selected mapper/callers.\n- **Tip**: Use **absolute paths** for inputs.\n\n`samples_tsv` formats:\n\n- **FASTQ + paired-end** (`reads_type: \"pe\"`): `sample_id\u003cTAB\u003eR1\u003cTAB\u003eR2`\n- **FASTQ + single-end** (`reads_type: \"se\"`): `sample_id\u003cTAB\u003eR1`\n- **FASTQ + mixed** (`reads_type: \"mx\"`): `sample_id\u003cTAB\u003eR1\u003cTAB\u003eR2\u003cTAB\u003eU` (Bowtie2 mapping only)\n- **BAM** (`input_format: \"bam\"`): `sample_id\u003cTAB\u003ebam_path`\n\n## Outputs\n\nPublished outputs are written to `outdir` (default: `ChoCallate_output`), including standard Nextflow reports:\n\n- `pipeline_report.html`\n- `timeline_report.html`\n- `trace.txt`\n\nConsensus outputs depend on `output.type` and `output.format`:\n\n- **Per-sample**: `\u003coutdir\u003e/per_sample/\u003csample_id\u003e/consensus.bcf` (default) or `consensus.vcf.gz`\n- **Single merged**: `\u003coutdir\u003e/consensus.bcf` or `\u003coutdir\u003e/consensus.vcf.gz`\n\n## Additional documentation\n\n- **Wiki home**: [ChoCallate Wiki](https://github.com/alermol/ChoCallate/wiki)\n- **Install**: [Installing ChoCallate](https://github.com/alermol/ChoCallate/wiki/Installing-ChoCallate)\n- **Quick start / config \u0026 CLI**: [CLI Reference](https://github.com/alermol/ChoCallate/wiki/CLI-Reference)\n- **Outputs**: [Output Structure](https://github.com/alermol/ChoCallate/wiki/Output-Structure)\n\n## Contribution\n\nSee [CONTRIBUTING.md](https://github.com/alermol/ChoCallate/blob/main/CONTRIBUTING.md)\n\n## License\n\n[MIT](https://github.com/alermol/ChoCallate/blob/main/LICENSE)\n\n\n## Development roadmap\n\nSee [Development Roadmap](https://github.com/alermol/ChoCallate/blob/main/ROADMAP.md) for planned container support and additional callers/mappers.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Falermol%2Fchocallate","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Falermol%2Fchocallate","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Falermol%2Fchocallate/lists"}