. 2021 Nov 4;11:21680. doi: 10.1038/s41598-021-99288-8

Table 4.

The WfMSs examined in this study.

WfMS		Use case I: Variant calling pipeline	Use case II: Scalability evaluation
Language	Engine	Use case I: Variant calling pipeline	Use case II: Scalability evaluation
Swift/T		GATK3; multi-sample; single-step if needed¹⁷; https://swift-t-variant-calling.readthedocs.io/en/latest/	–
Nextflow		GATK 4; multi-sample; https://github.com/ncsa/Genomics_MGC_VariantCalling_Nextflow/tree/dev-gatk^‡	Same repository for these three WfMSs (https://github.com/azzaea/scalability-tst)
CWL^a	Cromwell, Toil^†	–
WDL^a	Cromwell^†	GATK4; single sample; https://github.com/ncsa/MayomicsVC/tree/dev-gatk‡

^†Other engines were limited in portability, conformance to language specification, or setup (Table 2).

^‡Repositories with identical code structure, which facilitated comparison of results (Supplementary note 1).

^aCommon Workflow Languagen (CWL); Workflow Description Language (WDL).