{"id":461,"date":"2022-10-24T13:38:53","date_gmt":"2022-10-24T13:38:53","guid":{"rendered":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/workflows-combining-tools-for-data-analysis\/snakemake\/"},"modified":"2022-10-26T14:27:36","modified_gmt":"2022-10-26T14:27:36","slug":"snakemake","status":"publish","type":"page","link":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/workflows-combining-tools-for-data-analysis\/why-create-workflows\/snakemake\/","title":{"rendered":"SnakeMake"},"content":{"rendered":"\n<p class=\"wp-block-paragraph\">SnakeMake is an open source <a rel=\"noreferrer noopener\" href=\"https:\/\/snakemake.readthedocs.io\/en\/stable\/\" target=\"_blank\">workflow management system<\/a> used to create reproducible and scalable data analyses. <\/p>\n\n\n\n<p class=\"wp-block-paragraph\">With SnakeMake, workflows are described via a human readable, Python-based language. SnakeMake and its related documentation is made available under an MIT licence detailed <a rel=\"noreferrer noopener\" href=\"https:\/\/snakemake.readthedocs.io\/en\/stable\/project_info\/license.html\" target=\"_blank\">here<\/a>.<sup><a href=\"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/workflows-combining-tools-for-data-analysis\/references\/\">3<\/a><a href=\"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/workflows-combining-tools-for-data-analysis\/references\/\"><\/a><\/sup> <\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Some other advantages of SnakeMake:<sup><a href=\"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/workflows-combining-tools-for-data-analysis\">3,4<\/a><\/sup><\/p>\n\n\n\n<ul class=\"wp-block-list\"><li>It is scalable without modifying how workflows are defined <\/li><li>It can be integrated with Conda and Docker<\/li><li>It provides an introductory tutorial <\/li><li>It has a community of users in Discord<\/li><\/ul>\n\n\n\n<p class=\"wp-block-paragraph\">There are also many published SnakeMake workflows in the <a rel=\"noreferrer noopener\" href=\"https:\/\/snakemake.github.io\/snakemake-workflow-catalog\/\" target=\"_blank\">public catalog<\/a> that you can deploy, configure and run yourself. <\/p>\n\n\n\n<p class=\"wp-block-paragraph\">To get started with SnakeMake try the <a rel=\"noreferrer noopener\" href=\"https:\/\/snakemake.readthedocs.io\/en\/stable\/tutorial\/tutorial.html#tutorial\" target=\"_blank\">introductory tutorial<\/a>, part of <a rel=\"noreferrer noopener\" href=\"https:\/\/snakemake.readthedocs.io\/en\/stable\/#\" target=\"_blank\">SnakeMake&#8217;s ReadTheDocs<\/a>. <sup><a href=\"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/workflows-combining-tools-for-data-analysis\/references\/\"><\/a><\/sup><\/p>\n","protected":false},"excerpt":{"rendered":"<p>SnakeMake is an open source workflow management system used to create reproducible and scalable data analyses. With SnakeMake, workflows are described via a human readable, Python-based language. SnakeMake and its related documentation is made available under an MIT licence detailed here.3 Some other advantages of SnakeMake:3,4 It is scalable without modifying how workflows are defined&#8230;<\/p>\n","protected":false},"author":30,"featured_media":0,"parent":8,"menu_order":2,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-461","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/workflows-combining-tools-for-data-analysis\/wp-json\/wp\/v2\/pages\/461","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/workflows-combining-tools-for-data-analysis\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/workflows-combining-tools-for-data-analysis\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/workflows-combining-tools-for-data-analysis\/wp-json\/wp\/v2\/users\/30"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/workflows-combining-tools-for-data-analysis\/wp-json\/wp\/v2\/comments?post=461"}],"version-history":[{"count":18,"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/workflows-combining-tools-for-data-analysis\/wp-json\/wp\/v2\/pages\/461\/revisions"}],"predecessor-version":[{"id":625,"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/workflows-combining-tools-for-data-analysis\/wp-json\/wp\/v2\/pages\/461\/revisions\/625"}],"up":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/workflows-combining-tools-for-data-analysis\/wp-json\/wp\/v2\/pages\/8"}],"wp:attachment":[{"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/workflows-combining-tools-for-data-analysis\/wp-json\/wp\/v2\/media?parent=461"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}