Galaxy Workflow Testing

This repository runs automated tests of several workflows against various Galaxy servers.

Testing

We are automatically running these workflows against UseGalaxy.eu, and we can test against your server too!

Workflow	UseGalaxy.EU
GraphClust2/GC-lite.ga
example1/wf3-shed-tools.ga
example2/wf4-shed-tools.ga
raceid3/raceid3_workflow.ga
sklearn/adaboost/adaboost.ga
sklearn/ard/ard.ga
training/assembly/general-introduction/assembly-general-introduction.ga
training/assembly/unicycler-assembly/unicycler.ga
training/chip-seq/formation_of_super-structures_on_xi/formation_of_super_structures_on_xi.ga
training/epigenetics/hicexplorer/hicexplorer.ga
training/epigenetics/methylation-seq/methylation-seq.ga
training/metagenomics/general-tutorial/amplicon.ga
training/proteomics/metaproteomics/metaproteomics.ga
training/proteomics/protein-id-sg-ps/protein-id-sg-ps.ga
training/proteomics/protein_quant_sil/protein_quant_sil.ga
training/sequence-analysis/mapping/mapping.ga
training/sequence-analysis/quality-control/quality_control.ga
training/sequence-analysis/ref-based-rad-seq/rad_seq_ref_based.ga
training/statistics/machine_learning/classification/linear_SVC_classification.ga
training/statistics/machine_learning/regression/gradient_boosting_regression.ga
training/transcriptomics/ref-based/ref_based.ga
training/transcriptomics/small_ncrna_clustering/blockclust_workflow.ga
training/variant-analysis/dip/diploid.ga
training/variant-analysis/mapping-by-sequencing/mapping_by_sequencing.ga
training/variant-analysis/microbial-variants/microbial_variant_calling.ga
training/proteomics/F1000_Metaproteomics_QueryTabular/F1000_Metaproteomics_QueryTabular.ga
training/proteomics/F1000_Proteogenomics_QueryTabular/F1000_Proteogenomics_QueryTabular.ga
training/transcriptomics/rna-seq-viz-with-volcanoplot/rna-seq-viz-with-volcanoplot.ga
training/transcriptomics/rna-seq-viz-with-heatmap2/rna-seq-viz-with-heatmap2.ga
training/computational-chemistry/bio3danalysis/MD_Analysis_using_Bio3D.ga
training/computational-chemistry/bio3danalysis/gromacs.ga
training/metabolomics/F1000_Metabolomics_Query_Tabular_Mass_Adjustment.ga

Contributing

An introduction to workflow testing and a tutorial can be found at the Galaxy Training Network.

About

Based off of jmchilton's template, except running tests against UseGalaxy.eu

Pretty-printing Worfklow JSON

You can use the command line tool jq to pretty-print the workflow .ga files:

cat wf.ga | jq . -S > out.ga

or this webservice: https://jsonformatter.org/