added refs for galaxy and nextflow

Author: aleidel

paper/paper.bib

@@ -123,3 +123,38 @@ @article{gustafsson_workflowhub_2025
   pages         = {837},
   file          = {Full Text PDF:C\:\\Users\\krumsieck\\Zotero\\storage\\K83GDZ2U\\Gustafsson et al. - 2025 - WorkflowHub a registry for computational workflows.pdf:application/pdf}
 }
+@article{di_tommaso_nextflow_2017,
+	title = {Nextflow enables reproducible computational workflows},
+	volume = {35},
+	copyright = {2017 Springer Nature America, Inc.},
+	issn = {1546-1696},
+	url = {https://www.nature.com/articles/nbt.3820},
+	doi = {10.1038/nbt.3820},
+	language = {en},
+	number = {4},
+	urldate = {2026-04-22},
+	journal = {Nature Biotechnology},
+	author = {Di Tommaso, Paolo and Chatzou, Maria and Floden, Evan W. and Barja, Pablo Prieto and Palumbo, Emilio and Notredame, Cedric},
+	month = apr,
+	year = {2017},
+	keywords = {Computational biology and bioinformatics, Data publication and archiving},
+	pages = {316--319},
+}
+@article{goecks_galaxy_2010,
+	title = {Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences},
+	volume = {11},
+	issn = {1474-760X},
+	shorttitle = {Galaxy},
+	url = {https://doi.org/10.1186/gb-2010-11-8-r86},
+	doi = {10.1186/gb-2010-11-8-r86},
+	abstract = {Increased reliance on computational approaches in the life sciences has revealed grave concerns about how accessible and reproducible computation-reliant results truly are. Galaxy http://usegalaxy.org, an open web-based platform for genomic research, addresses these problems. Galaxy automatically tracks and manages data provenance and provides support for capturing the context and intent of computational methods. Galaxy Pages are interactive, web-based documents that provide users with a medium to communicate a complete computational analysis.},
+	language = {en},
+	number = {8},
+	urldate = {2026-04-22},
+	journal = {Genome Biology},
+	author = {Goecks, Jeremy and Nekrutenko, Anton and Taylor, James and {The Galaxy Team}},
+	month = aug,
+	year = {2010},
+	keywords = {Analysis Workspace, Galaxy Server, Phylogenetic Profile, Public Repository, User Metadata},
+	pages = {R86},
+}

paper/paper.md

@@ -58,7 +58,7 @@ CWL therefore is predestined to be written by machines rather than humans, which
 SciWIn-Client provides an intuitive command-line interface that automates CWL generation and management. It translates typical research computing tasks into structured, version-controlled workflow definitions, effectively allowing scientists to “write CWL by doing science.”
 
 # State of the field
-The landscape of scientific workflow management is broad and fragmented. Numerous patforms and languages have emerged to adress the need for reproducible, automated data analysis pipeline. Tools such as Nextflow[@ref] and Galaxy[@ref] have achieved significant adoption within the scientific community. Both offer powerful execution environments and rich graphical or scripting environments. Both platforms put significant effort in providing a broad set of scripts especially for the OMICS-community (e.g. nf-core), however lacking in the agro-community where individual scripting plays a key part. 
+The landscape of scientific workflow management is broad and fragmented. Numerous patforms and languages have emerged to adress the need for reproducible, automated data analysis pipeline. Tools such as Nextflow[@di_tommaso_nextflow_2017] and Galaxy[@goecks_galaxy_2010] have achieved significant adoption within the scientific community. Both offer powerful execution environments and rich graphical or scripting environments. Both platforms put significant effort in providing a broad set of scripts especially for the OMICS-community (e.g. nf-core), however lacking in the agro-community where individual scripting plays a key part. 
 Bringing individual scripts into the platform in both cases has a hurdle to overcome. For nextflow researchers need to learn the Groovy-based DSL, for Galaxy a curation process needs to be passed to get tools onto the platform. Workflows authored for Galaxy are typically bound to a specific Galaxy instance, and portability across infrastructures can require substantial re-engineering effort.
 CWL was introduced as a vendor-neutral, platform agnostic standard to address fragmentation. CWL workflows are portable by design as they in principle can run on any compliant execution engine. They are even efforts to make Galaxy and Nextflow compliant to this standard [@ref]. One big downside however is the lack of tooling especially in the creation process. CWLs adoption is comparable smaller than Nextflow and Galaxy. Its verbose, YAML-based syntax demands familiarity with structured data formats and workflow abstractions that many domain researchers lack. The result is a paradox: a universal standard that remains inaccessible to a large share of its intended users.
 The CWL ecosystem further compounds this problem. While a number of great runner implementations exist (e.g. cwltool, Toil, REANA, ........), the space of authoring tools is sparse. Rabix offered a graphical editor (Rabix Composer) which was made closed-source and moved into the seven-bridges Platform. The open-sourced version has been unmaintained for over 5 years and is significantly outdated. Many generators are outdated as well meaning there is no actively developed open and lightweight CWL generator that integrates naturally into a researchers existing command-line-driven "workflow". (Planemo einbauen??!?)