{"id":18598208,"url":"https://github.com/cmdoret/vapormap","last_synced_at":"2026-01-23T08:02:51.167Z","repository":{"id":100715543,"uuid":"225945726","full_name":"cmdoret/vapormap","owner":"cmdoret","description":"Cloud based pipeline for parallelized iterative alignment of Hi-C data","archived":false,"fork":false,"pushed_at":"2020-09-25T16:08:05.000Z","size":78036,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-05-16T14:11:42.971Z","etag":null,"topics":["aws-batch","genomics","hi-c","nextflow"],"latest_commit_sha":null,"homepage":"","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/cmdoret.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":"2019-12-04T19:54:02.000Z","updated_at":"2020-09-25T16:08:07.000Z","dependencies_parsed_at":null,"dependency_job_id":"a13fd8a6-f877-4420-9bad-a542bea6a121","html_url":"https://github.com/cmdoret/vapormap","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/cmdoret/vapormap","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmdoret%2Fvapormap","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmdoret%2Fvapormap/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmdoret%2Fvapormap/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmdoret%2Fvapormap/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/cmdoret","download_url":"https://codeload.github.com/cmdoret/vapormap/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmdoret%2Fvapormap/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28684003,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-23T05:48:07.525Z","status":"ssl_error","status_checked_at":"2026-01-23T05:48:07.129Z","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":["aws-batch","genomics","hi-c","nextflow"],"created_at":"2024-11-07T01:31:37.581Z","updated_at":"2026-01-23T08:02:51.140Z","avatar_url":"https://github.com/cmdoret.png","language":"Nextflow","readme":"# ![Vapormap logo](docs/vapormap_logo.svg) Vapormap\n\nVapormap is a cloud-based alignment pipeline for Hi-C. Each fastq file is split into a number of chunks which are all aligned in parallel on aws batch. Jobs are managed using nextflow. The pipeline has 4 profiles:\n* standard: Run the pipeline on the local machine directly.\n* docker: Run the pipeline on the local machine inside a docker container (requires docker).\n* singularity: Run the pipeline on the local machine inside a singularity container (requires singularity).\n* aws: Runs the pipeline on aws batch.\n* pasteur: Profile specific to institut Pasteur's HPC, to run the pipeline via singularity in a SLURM.\n\n![Vapormap flowchart](docs/vapormap_flowchart.svg)\n\nHi-C reads can be aligned using iterative mapping. All configuration is done through `nextflow.config`. When using the aws profile, you need to set the input path on a s3 bucket (e.g. \"s3://dir/input/\").\n\n### Prerequisites\n\nsdk should be installed and configured for your account. A bucket with input files should also be online.\n\n\n### Installation\n\nYou can get nextflow with the following command:\n\n```bash\nwget -qO- https://get.nextflow.io | bash\n```\n\n### Usage\n\nFirst, edit the parameters and paths in `nextflow.config`. Then run the pipeline using:\n\n```bash\n./nextflow run main.nf -profile docker\n```\nWhere the profile can be any of {docker,singularity,aws,pasteur}.\n\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcmdoret%2Fvapormap","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcmdoret%2Fvapormap","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcmdoret%2Fvapormap/lists"}