{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,3]],"date-time":"2026-04-03T00:15:32Z","timestamp":1775175332987,"version":"3.50.1"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"19","license":[{"start":{"date-parts":[[2021,3,27]],"date-time":"2021-03-27T00:00:00Z","timestamp":1616803200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100006108","name":"National Center for Advancing Translational Sciences","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100006108","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["UL1TR0012-05"],"award-info":[{"award-number":["UL1TR0012-05"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["U24CA232979"],"award-info":[{"award-number":["U24CA232979"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["U24180996"],"award-info":[{"award-number":["U24180996"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000051","name":"National Human Genome Research Institute","doi-asserted-by":"publisher","award":["U41HG004059"],"award-info":[{"award-number":["U41HG004059"]}],"id":[{"id":"10.13039\/100000051","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,10,11]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>The Common Workflow Language (CWL) is used to provide portable and reproducible data analysis workflows across different tools and computing environments. We have developed Rcwl, an R interface to CWL, to provide easier development, use and maintenance of CWL pipelines from within R. We have also collected more than 100 pre-built tools and pipelines in RcwlPipelines, ready to be queried and used by researchers in their own analysis. A single-cell RNA sequencing preprocessing pipeline demonstrates use of the software.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Project website: https:\/\/rcwl.org (Rcwl: https:\/\/bioconductor.org\/packages\/Rcwl; RcwlPipelines: https:\/\/bioconductor.org\/packages\/RcwlPipelines).<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab208","type":"journal-article","created":{"date-parts":[[2021,3,26]],"date-time":"2021-03-26T02:09:37Z","timestamp":1616724577000},"page":"3351-3352","source":"Crossref","is-referenced-by-count":6,"title":["<i>Bioconductor<\/i> toolchain for reproducible bioinformatics pipelines using <i>Rcwl<\/i> and <i>RcwlPipelines<\/i>"],"prefix":"10.1093","volume":"37","author":[{"given":"Qiang","family":"Hu","sequence":"first","affiliation":[{"name":"Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center , Buffalo, NY 14203, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alan","family":"Hutson","sequence":"additional","affiliation":[{"name":"Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center , Buffalo, NY 14203, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Song","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center , Buffalo, NY 14203, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Martin","family":"Morgan","sequence":"additional","affiliation":[{"name":"Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center , Buffalo, NY 14203, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1456-5099","authenticated-orcid":false,"given":"Qian","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center , Buffalo, NY 14203, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,3,27]]},"reference":[{"key":"2023051608261351900_btab208-B1","doi-asserted-by":"crossref","first-page":"W537","DOI":"10.1093\/nar\/gky379","article-title":"The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update","volume":"46","author":"Afgan","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2023051608261351900_btab208-B2","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1038\/s41592-019-0654-x","article-title":"Orchestrating single-cell analysis with Bioconductor","volume":"17","author":"Amezquita","year":"2020","journal-title":"Nat. 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