{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,28]],"date-time":"2026-03-28T19:51:56Z","timestamp":1774727516224,"version":"3.50.1"},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2026,2,24]],"date-time":"2026-02-24T00:00:00Z","timestamp":1771891200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002347","name":"Federal Ministry of Research, Technology and Space","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100002347","id-type":"DOI","asserted-by":"crossref"}]},{"name":"NBI\/ELIXIR-DE","award":["W-de.NBI-001"],"award-info":[{"award-number":["W-de.NBI-001"]}]},{"name":"Heidelberg Center for Human Bioinformatics"},{"DOI":"10.13039\/501100018929","name":"German Network for Bioinformatics Infrastructure","doi-asserted-by":"publisher","award":["031A537A"],"award-info":[{"award-number":["031A537A"]}],"id":[{"id":"10.13039\/501100018929","id-type":"DOI","asserted-by":"publisher"}]},{"name":"BMFTR"},{"name":"German Center for Child and Adolescent Health","award":["01GL2401A"],"award-info":[{"award-number":["01GL2401A"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,2,28]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>In biomedical research, managing computational workflows across numerous projects\u2014with varying parameters, tools, and environments\u2014creates major challenges in scalability, reproducibility, and collaboration. Here, we present WESkit, an implementation of the Global Alliance for Genomics and Health (GA4GH) Workflow Execution Service (WES) interface, designed to streamline the execution, monitoring, and documentation of data processing workflows. It addresses the complexities involved in managing numerous executions with varying parameters across diverse research projects. Supporting both Snakemake and Nextflow, the system enables consistent automation and centralized monitoring, which benefits research groups aiming for long-term reproducibility and scalable collaboration. Its suitability for larger teams and service units is further enhanced by seamless integration into cloud environments, contributing to the GA4GH cloud framework.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The software WESkit is available under MIT license at the GitLab repository (https:\/\/gitlab.com\/one-touch-pipeline\/weskit). The WESkit main repository is archived at Software Heritage (https:\/\/archive.softwareheritage.org\/browse\/origin\/directory\/?origin_url=https:\/\/gitlab.com\/one-touch-pipeline\/weskit\/api.git) and can be found using \u201cone-touch-pipeline\/weskit\u201d term in the search section.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag091","type":"journal-article","created":{"date-parts":[[2026,2,20]],"date-time":"2026-02-20T12:39:30Z","timestamp":1771591170000},"source":"Crossref","is-referenced-by-count":0,"title":["Managing workflow executions with WESkit"],"prefix":"10.1093","volume":"42","author":[{"given":"Valentin","family":"Schneider-Lunitz","sequence":"first","affiliation":[{"name":"Berlin Institute of Health at Charit\u00e9\u2014Universit\u00e4tsmedizin Berlin, Center of Digital Health , Berlin 10117,","place":["Germany"]}]},{"given":"Philip R","family":"Kensche","sequence":"additional","affiliation":[{"name":"German Cancer Research Center (DKFZ) Heidelberg, Division Omics IT and Data Management Core Facility (ODCF), Im Neuenheimer Feld 280, 69120 Heidelberg,","place":["Germany"]}]},{"given":"Landfried","family":"Kraatz","sequence":"additional","affiliation":[{"name":"Berlin Institute of Health at Charit\u00e9\u2014Universit\u00e4tsmedizin Berlin, Center of Digital Health , Berlin 10117,","place":["Germany"]}]},{"given":"Philipp","family":"Strubel","sequence":"additional","affiliation":[{"name":"Berlin Institute of Health at Charit\u00e9\u2014Universit\u00e4tsmedizin Berlin, Center of Digital Health , Berlin 10117,","place":["Germany"]}]},{"given":"Stefan","family":"Borufka","sequence":"additional","affiliation":[{"name":"German Cancer Research Center (DKFZ) Heidelberg, Division Omics IT and Data Management Core Facility (ODCF), Im Neuenheimer Feld 280, 69120 Heidelberg,","place":["Germany"]}]},{"given":"Gurudeep","family":"Parala","sequence":"additional","affiliation":[{"name":"German Cancer Research Center (DKFZ) Heidelberg, Division Omics IT and Data Management Core Facility (ODCF), Im Neuenheimer Feld 280, 69120 Heidelberg,","place":["Germany"]},{"name":"BotCraft GmbH , M\u00fcnchen 80807,","place":["Germany"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3468-0652","authenticated-orcid":false,"given":"Alexander","family":"Kanitz","sequence":"additional","affiliation":[{"name":"Biozentrum, University of Basel , Basel 4056,","place":["Switzerland"]},{"name":"Swiss Institute of Bioinformatics, Amphip\u00f4le, Quartier UNIL-Sorge , Lausanne 1015,","place":["Switzerland"]}]},{"given":"Roland","family":"Eils","sequence":"additional","affiliation":[{"name":"Berlin Institute of Health at Charit\u00e9\u2014Universit\u00e4tsmedizin Berlin, Center of Digital Health , Berlin 10117,","place":["Germany"]},{"name":"German Center for Mental Health (DZPG), Partner Site Berlin\/Potsdam ,","place":["Germany"]},{"name":"German Center for Child and Adolescent Health (DZKJ), Partner Site Berlin 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