{"id":18448823,"url":"https://github.com/sequana/bioconvert","last_synced_at":"2026-04-02T20:18:31.467Z","repository":{"id":115174646,"uuid":"246562338","full_name":"sequana/bioconvert","owner":"sequana","description":"convert files from one format to another using bioconvert","archived":false,"fork":false,"pushed_at":"2026-03-31T21:24:11.000Z","size":781,"stargazers_count":1,"open_issues_count":0,"forks_count":1,"subscribers_count":2,"default_branch":"main","last_synced_at":"2026-04-01T00:29:04.637Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/sequana.png","metadata":{"files":{"readme":"README.rst","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","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":"2020-03-11T12:16:25.000Z","updated_at":"2026-03-31T21:18:30.000Z","dependencies_parsed_at":"2024-01-13T16:25:39.114Z","dependency_job_id":"0ffc0c63-46dd-4568-ad25-a3beb7b68cfe","html_url":"https://github.com/sequana/bioconvert","commit_stats":{"total_commits":22,"total_committers":1,"mean_commits":22.0,"dds":0.0,"last_synced_commit":"74564e538fc547673e29057f39b63f8732f3edd7"},"previous_names":[],"tags_count":3,"template":false,"template_full_name":null,"purl":"pkg:github/sequana/bioconvert","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sequana%2Fbioconvert","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sequana%2Fbioconvert/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sequana%2Fbioconvert/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sequana%2Fbioconvert/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/sequana","download_url":"https://codeload.github.com/sequana/bioconvert/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sequana%2Fbioconvert/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":31315430,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-04-02T12:59:32.332Z","status":"ssl_error","status_checked_at":"2026-04-02T12:54:48.875Z","response_time":89,"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":"2024-11-06T07:17:23.520Z","updated_at":"2026-04-02T20:18:31.462Z","avatar_url":"https://github.com/sequana.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"\n.. image:: https://badge.fury.io/py/sequana-bioconvert.svg\n     :target: https://pypi.python.org/pypi/sequana_bioconvert\n\n.. image:: https://github.com/sequana/bioconvert/actions/workflows/main.yml/badge.svg\n   :target: https://github.com/sequana/bioconvert/actions/workflows/main.yml\n\n.. image:: https://img.shields.io/badge/python-3.10%20%7C%203.11%20%7C%203.12-blue.svg\n    :target: https://pypi.python.org/pypi/sequana_bioconvert\n    :alt: Python 3.10 | 3.11 | 3.12\n\n.. image:: http://joss.theoj.org/papers/10.21105/joss.00352/status.svg\n    :target: http://joss.theoj.org/papers/10.21105/joss.00352\n    :alt: JOSS (journal of open source software) DOI\n\n\nbioconvert — format conversion pipeline\n========================================\n\n:Overview: Parallelise `bioconvert \u003chttps://bioconvert.readthedocs.io\u003e`_ conversions across a set of files\n:Input: Any file format supported by bioconvert (FastQ, BAM, FASTA, VCF, …)\n:Output: Converted files in the target format, MD5 checksums, and an HTML summary report\n:Status: Production\n:Citation: Cokelaer et al, (2017), 'Sequana': a Set of Snakemake NGS pipelines,\n           Journal of Open Source Software, 2(16), 352,\n           `doi:10.21105/joss.00352 \u003chttps://doi.org/10.21105/joss.00352\u003e`_\n\n.. image:: https://raw.githubusercontent.com/sequana/bioconvert/main/sequana_pipelines/bioconvert/dag.png\n   :alt: Pipeline DAG\n\n\nInstallation\n------------\n\n::\n\n    pip install sequana-bioconvert\n\nTo upgrade an existing installation::\n\n    pip install sequana-bioconvert --upgrade\n\nInstall all dependencies via conda/mamba::\n\n    mamba env create -f environment.yml\n\n\nQuick Start\n-----------\n\n**Step 1 — prepare the working directory**\n\nConvert all ``fastq.gz`` files in a directory to ``fasta.gz``::\n\n    sequana_bioconvert \\\n        --input-directory /path/to/data \\\n        --input-ext fastq.gz \\\n        --output-ext fasta.gz \\\n        --command fastq2fasta\n\nThis creates a ``bioconvert/`` working directory with ``config.yaml`` and a\n``bioconvert.sh`` launch script.\n\n**Step 2 — run the pipeline**::\n\n    cd bioconvert\n    sh bioconvert.sh\n\nResults are written to the ``output/`` subdirectory. An HTML summary report is\ngenerated on completion.\n\nUsage\n-----\n\n::\n\n    sequana_bioconvert --help\n\nKey options:\n\n- ``--input-directory``  — directory containing the input files (required)\n- ``--input-ext``        — extension of input files, e.g. ``fastq.gz`` (required)\n- ``--output-ext``       — extension of output files, e.g. ``fasta.gz`` (required)\n- ``--command``          — bioconvert conversion command, e.g. ``fastq2fasta`` (required);\n                          run ``bioconvert --help`` for the full list\n- ``--input-pattern``    — prefix glob to restrict which files are picked up (default: ``*``);\n                          e.g. ``sample_*`` to process only files starting with ``sample_``\n- ``--method``           — override the default conversion method;\n                          run ``bioconvert COMMAND --show-methods`` to list valid methods\n\nUsage with apptainer\n--------------------\n\nAll external tools are available through a pre-built apptainer image. To use\nit, add ``--use-apptainer`` when initialising the pipeline::\n\n    sequana_bioconvert \\\n        --input-directory /path/to/data \\\n        --input-ext fastq.gz \\\n        --output-ext fasta.gz \\\n        --command fastq2fasta \\\n        --use-apptainer \\\n        --apptainer-prefix ~/.sequana/apptainers\n\nThen run as usual::\n\n    cd bioconvert\n    sh bioconvert.sh\n\n\nRequirements\n------------\n\n- **bioconvert** ≥ 1.1.0 — the underlying conversion tool\n- **graphviz** — for pipeline DAG rendering (available via apptainer)\n\nInstall dependencies via conda/mamba::\n\n    mamba env create -f environment.yml\n\nRules and configuration details\n--------------------------------\n\nThe latest configuration file is available at:\n`config.yaml \u003chttps://raw.githubusercontent.com/sequana/bioconvert/main/sequana_pipelines/bioconvert/config.yaml\u003e`_\n\nEach rule used in the pipeline has a corresponding section in ``config.yaml``.\n\nChangelog\n---------\n\n========= ====================================================================\nVersion   Description\n========= ====================================================================\n1.2.0     * Update apptainer image to bioconvert 1.1.0\n          * Switch to ``manager.get_shell()`` — no longer uses sequana_wrappers\n          * Remove ``sequana_wrappers`` field from config and schema\n          * Use ``importlib.metadata`` for version (fixes ``\u003e=x.y.z`` display\n            in HTML reports)\n          * ``--input-pattern`` now optional (default ``*``); combined with\n            ``--input-ext`` to form the actual glob pattern\n          * Add ``md5_output.txt`` alongside ``md5_input.txt``\n          * Improved HTML report: method display, bioconvert doc link,\n            cleaner table labels\n          * Early exit with clear error if no input files are found\n          * Fix fragile sample name extraction for multi-dot filenames\n1.1.0     * Update apptainer image to bioconvert 1.1.0\n          * CI: update to Python 3.10/3.11/3.12 and actions/checkout@v4\n1.0.0     Uses bioconvert 1.0.0\n0.10.0    Add container\n0.9.0     Version using new sequana/sequana_pipetools framework\n0.8.1     **Working version**\n0.8.0     **First release**\n========= ====================================================================\n\n\nContribute \u0026 Code of Conduct\n-----------------------------\n\nTo contribute to this project, please take a look at the\n`Contributing Guidelines \u003chttps://github.com/sequana/sequana/blob/main/CONTRIBUTING.rst\u003e`_ first. Please note that this project is released with a\n`Code of Conduct \u003chttps://github.com/sequana/sequana/blob/main/CONDUCT.md\u003e`_. By contributing to this project, you agree to abide by its terms.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsequana%2Fbioconvert","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsequana%2Fbioconvert","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsequana%2Fbioconvert/lists"}