iedb workflow #9
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Also on this branch add the workflow graph call from project.xml to do alignments on cluster and load results. |
… MakeEpitopeMappingNextflowConfig.pm to make the nextflow confing and the mapEpitopeNextflow.xml for the epitope mapping
jbrestel
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Apr 5, 2024
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in project.xml ... you don't need a datasetTemplate. We want to run these steps for EVERY reference strain.
Instead of dataset template use the "includeIf" syntax to run the subgraph when appropriate
Make sure this subgraph depends on the componentGlobal iedb step
In mapEpitopeNextflow.xml ... I think you only need to run the "mirrorToCluster" step 1 time. Do this after you make the nextflow config. Copy everything over at that point
… the mapEpitopeNextflow.xml
…ect xml and moved the iedb_epitope nextflow mapping subgraph into the organism template. Updated the mapEpitopeNextflow.xml and remove the loading step that is already done in project.xml
… modules in the WorkflowSteps to load the epitope results
… into iedbWorkflow
… ID. Need to confirm that with John
…itopeNextflow.xml and InsertAaSequenceEpitope.pm
…fig.pm script to correct file paths
…GlobalGraph.xml and mapEpitopeNextflow.xml xml graphs
…ding the epitope peptide match result
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