From f4447c1a7c1d882bd44b7ba6e9aa5f2a88babe11 Mon Sep 17 00:00:00 2001 From: Stian Soiland-Reyes Date: Wed, 7 Aug 2024 15:42:23 +0100 Subject: [PATCH 1/4] More publications/posters for the README --- README.md | 32 ++++++++++++++++++++++++++++++-- 1 file changed, 30 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index df1ce874..e72c50ea 100644 --- a/README.md +++ b/README.md @@ -31,9 +31,37 @@ Additional present and future documentation is hosted at [development-docs](deve ### Presentations and outreach -Fernández JM, Rodríguez-Navas L and Capella-Gutiérrez S. Secured and annotated execution of workflows with WfExS-backend [version 1; not peer reviewed]. F1000Research 2022, 11:1318 (poster) (https://doi.org/10.7490/f1000research.1119198.1) +Paula Iborra, José M. Fernández, Salvador Capella-Gutierrez (2024): +[**Onboarding Snakemake: Progress towards WfExS-backend integration**](https://doi.org/10.7490/f1000research.1119725.1). +_F1000Research_ **13**(ELIXIR):551 (poster) + + +Eugenio Gonzalo1, Laia Codó, Jose María Fernandez, Stian Soiland-Reyes, Salvador Capella-Gutierrez, Emily Jefferson, Carole Goble, Tim Beck, Phil Quinlan, Tom Giles (2024): +[**Five safes workflow RO-Crate and WfExS**. Closing the gap of federated analysis and Trusted Research Enviroments (TREs) in the health data context](https://doi.org/10.7490/f1000research.1119724.1). +_F1000Research_ **13**(ELIXIR):550 (poster) + + +José M. Fernández, Paula Iborra, Sébastien Moretti, Arun Isaac, Paul De Geest, Stian Soiland-Reyes (2024): +[**BioHackEU23: FAIR Workflow Execution with WfExS and Workflow Run Crate**](https://doi.org/10.37044/osf.io/7f94w). +_BioHackrXiv_ + + +Simone Leo, Michael R. Crusoe, Laura Rodríguez-Navas, Raül Sirvent, Alexander Kanitz, Paul De Geest, Rudolf Wittner, Luca Pireddu, Daniel Garijo, José M. Fernández, Iacopo Colonnelli, Matej Gallo, Tazro Ohta, Hirotaka Suetake, Salvador Capella-Gutierrez, Renske de Wit, Bruno de Paula Kinoshita, Stian Soiland-Reyes (2024): +[**Recording provenance of workflow runs with RO-Crate**](https://doi.org/10.48550/arXiv.2312.07852). +_arXiv_:2312.07852 + + +José M. Fernández1, Laura Rodriguez-Navas, Salvador Capella-Gutiérrez (2023): +[**WfExS-backend in the WRROC world**?](https://doi.org/10.7490/f1000research.1119457.1) +_F1000Research_ **12**(ELIXIR):616 (poster) + + +Fernández JM, Rodríguez-Navas L and Capella-Gutiérrez S. +[**Secured and annotated execution of workflows with WfExS-backend**](https://doi.org/10.7490/f1000research.1119198.1) [version 1; not peer reviewed]. +_F1000Research_ 2022, 11:1318 (poster) + -Laura Rodríguez-Navas (2021): +Laura Rodríguez-Navas (2021): [**WfExS: a software component to enable the use of RO-Crate in the EOSC-Life collaboratory**](https://osf.io/tb5ku/). _FAIR Digital Object Forum_, [CWFR & FDO SEM meeting](https://osf.io/v8xjz/), 2021-07-02 [[video recording](https://osf.io/wna42/)], [[slides](https://osf.io/tb5ku/)] From 1860d6b79a39fd4509732ddf6411324668d5b17c Mon Sep 17 00:00:00 2001 From: Stian Soiland-Reyes Date: Wed, 7 Aug 2024 15:43:18 +0100 Subject: [PATCH 2/4] Markdown typo fixed --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index e72c50ea..7d1ebcfd 100644 --- a/README.md +++ b/README.md @@ -70,7 +70,7 @@ Laura Rodríguez-Navas (2021): [**WfExS: a software component to enable the use of RO-Crate in the EOSC-Life tools collaboratory**](https://repository.eoscsecretariat.eu/index.php/s/ERebmpJcyjFRqcx/download?path=%2F17%20June%2F1400%20-%20Technical%20challenges%20on%20EOSC%2FBreakout%203%20-%20Interoperability%20challenges%20for%20thematic%20communities&files=05%20-%20Laura%20Rodr%C3%ADguez-Navas%20-%20WfExS.pdf&downloadStartSecret=zwwx23xrow). _[EOSC Symposium 2021](https://www.eoscsecretariat.eu/eosc-symposium-2021-programme)_, 2021-06-17 [[video recording](https://youtu.be/x5lLEym-gug?list=PLbISfqJh3Tstmx6CgrBmYI7lyyVXiY5VE&t=3238)] -[[slides](https://drive.google.com/file/d/1LJkmI_gyl9VnuQ2_ZHBGeFkt_QTWFieg/view) +[[slides](https://drive.google.com/file/d/1LJkmI_gyl9VnuQ2_ZHBGeFkt_QTWFieg/view)] Salvador Capella-Gutierrez (2021): [**Demonstrator 7: Accessing human sensitive data from analytical workflows available to everyone in EOSC-Life**](https://www.eosc-life.eu/d7/) From 366b90a6bbbf59ce10dbbb9ab7f14d20d9d72dbe Mon Sep 17 00:00:00 2001 From: Stian Soiland-Reyes Date: Wed, 7 Aug 2024 15:48:48 +0100 Subject: [PATCH 3/4] software and ro-crate citations --- README.md | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/README.md b/README.md index 7d1ebcfd..b3193f00 100644 --- a/README.md +++ b/README.md @@ -29,6 +29,15 @@ and [cwltool](https://github.com/common-workflow-language/cwltool)). Additional present and future documentation is hosted at [development-docs](development-docs/index.md) subfolder, until it is migrated to a proper documentation service. +## Cite as + +José María Fernández, Laura Rodríguez-Navas, Adrián Muñoz-Cívico, Paula Iborra, Daniel Lea (2024): +**WfExS-backend**. +_Zenodo_ + + +Visit the [Zenodo record](https://doi.org/10.5281/zenodo.6567591) for the latest versioned DOI and author list. + ### Presentations and outreach Paula Iborra, José M. Fernández, Salvador Capella-Gutierrez (2024): @@ -83,6 +92,11 @@ Bietrix, Florence; Carazo, José Maria; Capella-Gutierrez, Salvador; Coppens, Fr EOSC-Life deliverable D8.1, _Zenodo_ +## Example RO-Crate outputs + +* -- execution of [WOMBAT-Pipelines](https://github.com/wombat-p/WOMBAT-Pipelines) Nextflow workflow +* -- execution of [Wetlab2Variations](https://github.com/inab/Wetlab2Variations/) CWL workflow + ## WfExS-backend Usage From 9df2680d77956dfb91a6c2fef8723542032528a7 Mon Sep 17 00:00:00 2001 From: Stian Soiland-Reyes Date: Wed, 7 Aug 2024 15:49:29 +0100 Subject: [PATCH 4/4] Version-less DOI --- CITATION.cff | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CITATION.cff b/CITATION.cff index f0604254..811677b0 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -18,7 +18,7 @@ cff-version: 1.2.0 identifiers: - description: WfExS-backend release in Zenodo type: doi - value: "10.5281/zenodo.6567592" + value: "10.5281/zenodo.6567591" keywords: - workflows - ro-crate