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Argo workflows

Readme.txt

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+Release notes for v2.5 of Argo Based Dynamic Workflow Generator
+==============================================================
+
+Features:
+1. Generation of templates and workflow steps for multiple steps in a WGS and WES Pipeline
+2. Any template file and Any workflow-steps-file can be provided in the configuration file
+3. Support extended to implement scatter-gather from bwa-mem through mark-duplicates for a single sample (upto 4 lanes)
+4. Generation of templates from bwa-mem through ApplyBQSR provided
+5. Upto 13 intervals supported for BQSR and ApplyBQSR 
+6. Additional validation of argo configuration file added
+
+Steps to compile:
+Run the ant build.xml cleanall, build, jar
+This creates a jar ArgoDynamicWorkflowGenerator.jar
+Note: Make sure that the referenced libs commons-io-2.6.jar is on the classpath
+
+Steps to run:
+1) java -cp lib:commons-io-2.6.jar:<all template directories>:<configuration file> Jar-file-from-previous-step configfilename 
+2) All the template files and configuration files must be on the class path 
+c) The output file name is <configfile name>.workflow.yaml
+
+Validate the yaml:
+1) Install Argo locally
+2) Run argo lint <workflow file>
+3) If access to GKE cluster is available, argo submit <workflow file>
+
+