update data

book/workflow_frameworks/data/wf_aggregated_scores.csv

@@ -1,36 +1,50 @@
 "name","framework","mean_score"
 "Community","Argo Workflows",0.125
+"Community","Cromwell + WDL",NA
 "Community","Galaxy",0.75
 "Community","Nextflow",1
 "Community","Snakemake",0.75
+"Community","Toil + WDL",0.5
 "Community","Viash + Nextflow",0.75
 "Maintainability","Argo Workflows",0.5
+"Maintainability","Cromwell + WDL",0.7
 "Maintainability","Galaxy",0.6
 "Maintainability","Nextflow",0.5
 "Maintainability","Snakemake",0.7
+"Maintainability","Toil + WDL",0.6
 "Maintainability","Viash + Nextflow",1
 "Modularity","Argo Workflows",0.8
+"Modularity","Cromwell + WDL",0.7
 "Modularity","Galaxy",0.9
 "Modularity","Nextflow",0.5
 "Modularity","Snakemake",1
+"Modularity","Toil + WDL",0.4
 "Modularity","Viash + Nextflow",1
 "Polyglot","Argo Workflows",0.666666666666667
+"Polyglot","Cromwell + WDL",0.333333333333333
 "Polyglot","Galaxy",0.333333333333333
 "Polyglot","Nextflow",0.666666666666667
 "Polyglot","Snakemake",0.666666666666667
+"Polyglot","Toil + WDL",0.333333333333333
 "Polyglot","Viash + Nextflow",0.666666666666667
 "Portability","Argo Workflows",0.5
+"Portability","Cromwell + WDL",0.611111111111111
 "Portability","Galaxy",0.666666666666667
 "Portability","Nextflow",0.944444444444444
 "Portability","Snakemake",0.888888888888889
+"Portability","Toil + WDL",0.472222222222222
 "Portability","Viash + Nextflow",0.944444444444444
 "Reproducibility","Argo Workflows",0.7
+"Reproducibility","Cromwell + WDL",0.3
 "Reproducibility","Galaxy",0.8
 "Reproducibility","Nextflow",0.5
 "Reproducibility","Snakemake",0.7
+"Reproducibility","Toil + WDL",0.3
 "Reproducibility","Viash + Nextflow",0.8
 "Scalability","Argo Workflows",0.5
+"Scalability","Cromwell + WDL",0.833333333333333
 "Scalability","Galaxy",0.333333333333333
 "Scalability","Nextflow",0.833333333333333
 "Scalability","Snakemake",0.833333333333333
+"Scalability","Toil + WDL",0.666666666666667
 "Scalability","Viash + Nextflow",0.833333333333333

book/workflow_frameworks/data/wf_metadata.csv

@@ -3,6 +3,14 @@
 "Snakemake","J/M","https://snakemake.github.io/","A workflow management system that uses Python-based rules to define dependencies and execute tasks.","https://github.com/snakemake/snakemake","https://snakemake.readthedocs.io/en/stable/","https://doi.org/10.12688/f1000research.29032.2","https://snakemake-wrappers.readthedocs.io/en/stable/","https://github.com/snakemake-workflows
 https://github.com/snakemake/snakemake-wrappers","snakemake"
 "Galaxy","R","https://galaxyproject.org/","A web-based platform for creating, running, and sharing data analysis workflows without the need for programming expertise.","https://github.com/galaxyproject/galaxy","https://docs.galaxyproject.org/en/master/","https://doi.org/10.1093/nar/gkae410","https://galaxyproject.org/iuc/","https://github.com/galaxyproject/tools-iuc","galaxy"
+"Cromwell + WDL","J","https://cromwell.readthedocs.io/","An execution engine (Cromwell) that uses a workflow description language (WDL) for defining and running scientific workflows, particularly in genomics and bioinformatics.","https://github.com/broadinstitute/cromwell","https://cromwell.readthedocs.io/","https://doi.org/10.7490/f1000research.1114634.1
+https://doi.org/10.4230/OASIcs.SLATE.2014.77","https://broadinstitute.github.io/warp/
+https://biowdl.github.io/tasks/v0.1/index.html","https://github.com/broadinstitute/warp
+https://github.com/biowdl/tasks","cromwell_wdl"
+"Toil + WDL","J","http://toil.ucsc-cgl.org/","A workflow engine (Toil) that leverages WDL to define and execute scientific workflows with a focus on scalability and fault tolerance.","https://github.com/DataBiosphere/toil","https://toil.readthedocs.io/en/latest/","http://doi.org/10.1038/nbt.3772
+https://doi.org/10.1145/3486897","https://broadinstitute.github.io/warp/
+https://biowdl.github.io/tasks/v0.1/index.html","https://github.com/broadinstitute/warp
+https://github.com/biowdl/tasks","toil_wdl"
+"Argo Workflows","T","https://argoproj.github.io/workflows/","A Kubernetes-native workflow engine for orchestrating containerized tasks and automating complex workflows.","https://github.com/argoproj/argo-workflows","https://argo-workflows.readthedocs.io",NA,NA,NA,"argo_workflows"
 "Viash + Nextflow","R","https://viash.io/","A combination of Viash, a tool for defining bioinformatics workflow components, and Nextflow for scalable and reproducible execution.","https://github.com/viash-io/viash","https://viash.io/guide/
 https://www.nextflow.io/docs/latest/index.html","https://joss.theoj.org/papers/10.21105/joss.06089","https://web.viash-hub.com/packages","https://github.com/viash-hub","viash_nextflow"
-"Argo Workflows","T","https://argoproj.github.io/workflows/","A Kubernetes-native workflow engine for orchestrating containerized tasks and automating complex workflows.","https://github.com/argoproj/argo-workflows","https://argo-workflows.readthedocs.io",NA,NA,NA,"argo_workflows"

book/workflow_frameworks/quality_assessment.qmd

@@ -36,7 +36,10 @@ for (i in seq(2, nrow(wf_qc2), by = 1)) {
 
 # remove incomplete frameworks and unused questions
 wf_qc2 <- wf_qc2 |>
- select(name, aspect, item, Nextflow, Snakemake, Galaxy, `Viash + Nextflow`, `Argo Workflows`) %>%
+ select(
+ name, aspect, item,
+ Nextflow, Snakemake, Galaxy, `Cromwell + WDL`,
+ `Toil + WDL`, `Argo Workflows`, `Viash + Nextflow`) %>%
  filter(!is.na(Nextflow)) %>%
  filter(item != "The framework provides clear error messages and debugging tools.")
 
@@ -84,9 +87,9 @@ agg <- scores |>
  summarize(mean_score = mean(score), .groups = "drop")
 
 # write to file
-write.csv(meta, "notebooks/workflows/data/wf_metadata.csv", row.names = FALSE)
-write.csv(criteria, "notebooks/workflows/data/criteria.csv", row.names = FALSE)
-write.csv(agg, "notebooks/workflows/data/wf_aggregated_scores.csv", row.names = FALSE)
+write.csv(meta, "book/workflow_frameworks/data/wf_metadata.csv", row.names = FALSE)
+write.csv(criteria, "book/workflow_frameworks/data/criteria.csv", row.names = FALSE)
+write.csv(agg, "book/workflow_frameworks/data/wf_aggregated_scores.csv", row.names = FALSE)
 ```
 
 Given the abovementioned limitations, we decided to conduct our own quality assessment of workflow frameworks. This assessment is still largely in the works, but we're happy to share the preliminary results with you.