{"id":18448870,"url":"https://github.com/sequana/sequana_merge_flowcells","last_synced_at":"2025-04-15T11:27:24.744Z","repository":{"id":115175098,"uuid":"313598580","full_name":"sequana/sequana_merge_flowcells","owner":"sequana","description":"merge 2 or more flowcells (with identical design) into a single set of FastQ files","archived":false,"fork":false,"pushed_at":"2020-11-17T12:11:32.000Z","size":60,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":3,"default_branch":"master","last_synced_at":"2024-12-25T02:42:14.678Z","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":"2020-11-17T11:30:20.000Z","updated_at":"2020-11-17T12:11:34.000Z","dependencies_parsed_at":null,"dependency_job_id":"6e2b18ce-c583-49e2-a59e-fb101282611a","html_url":"https://github.com/sequana/sequana_merge_flowcells","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sequana%2Fsequana_merge_flowcells","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sequana%2Fsequana_merge_flowcells/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sequana%2Fsequana_merge_flowcells/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sequana%2Fsequana_merge_flowcells/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/sequana","download_url":"https://codeload.github.com/sequana/sequana_merge_flowcells/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":239132704,"owners_count":19587107,"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":[],"created_at":"2024-11-06T07:17:31.526Z","updated_at":"2025-02-16T13:23:06.575Z","avatar_url":"https://github.com/sequana.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"This is is the **merge_flowcells** pipeline from the `Sequana \u003chttps://sequana.readthedocs.org\u003e`_ project\n\n:Overview: Merge gzipped FastQ files from several flowcells\n:Input: set of identically named FastQ files from several directories\n:Output: merged FastQ files stored in an output directory. \n:Status: mature\n:Citation: Cokelaer et al, (2017), ‘Sequana’: a Set of Snakemake NGS pipelines, Journal of Open Source Software, 2(16), 352, JOSS DOI doi:10.21105/joss.00352\n\n\nInstallation\n~~~~~~~~~~~~\n\nYou must install Sequana first::\n\n    pip install sequana\n\nThen, just install this package::\n\n    pip install sequana_merge_flowcells\n\n\nUsage\n~~~~~\n\n::\n\n    sequana_pipelines_merge_flowcells --help\n    sequana_pipelines_merge_flowcells --input-directory DATAPATH \n\nThis creates a directory with the pipeline and configuration file. You will then need \nto execute the pipeline::\n\n    cd merge_flowcells\n    sh merge_flowcells.sh  # for a local run\n\nThis launch a snakemake pipeline. If you are familiar with snakemake, you can \nretrieve the pipeline itself and its configuration files and then execute the pipeline yourself with specific parameters::\n\n    snakemake -s merge_flowcells.rules -c config.yaml --cores 4 --stats stats.txt\n\nOr use `sequanix \u003chttps://sequana.readthedocs.io/en/master/sequanix.html\u003e`_ interface.\n\nRequirements\n~~~~~~~~~~~~\n\nThis pipelines requires the following executable(s):\n\n- sequana\n- pigz\n- zcat\n\n.. image:: https://raw.githubusercontent.com/sequana/sequana_merge_flowcells/master/sequana_pipelines/merge_flowcells/dag.png\n\n\nDetails\n~~~~~~~~~\n\nThis pipeline runs **merge_flowcells** in parallel on the input fastq files (paired or not). \nYou have to provide at least two subdirectories. You may provide more. \nThe input FastQ files must be zipped in the current version. The input FastQ\nfiles found in the first directory muts be found in all subsequent directories.\n\n\nRules and configuration details\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\nHere is the `latest documented configuration file \u003chttps://raw.githubusercontent.com/sequana/sequana_merge_flowcells/master/sequana_pipelines/merge_flowcells/config.yaml\u003e`_\nto be used with the pipeline. Each rule used in the pipeline may have a section in the configuration file. \n\nChangelog\n~~~~~~~~~\n\n========= ====================================================================\nVersion   Description\n========= ====================================================================\n0.0.1     **First release.**\n========= ====================================================================\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsequana%2Fsequana_merge_flowcells","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsequana%2Fsequana_merge_flowcells","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsequana%2Fsequana_merge_flowcells/lists"}