🎉 moved old workflows to deprecated folder

kids-first · Sep 10, 2020 · 2fc3086 · 2fc3086
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diff --git a/README.md b/README.md
@@ -3,7 +3,7 @@ Kids First Data Resource Center Joint Genotyping Workflow (cram-to-deNovoGVCF).
 
 Using existing gVCFs, likely from GATK Haplotype Caller, we follow this workflow: [Germline short variant discovery (SNPs + Indels)](https://software.broadinstitute.org/gatk/best-practices/workflow?id=11145), to create family joint calling and joint trios (typically mother-father-child) variant calls. Peddy is run to raise any potential issues in family relation definitions and sex assignment.
 
-Inputs from this can be used later on for further analysis in joint trio genotyping and subsequent refinement and deNovo variant analysis. If you would like to run this workflow using the cavatica public app, a basic primer on running public apps can be found [here](https://www.notion.so/d3b/Starting-From-Scratch-Running-Cavatica-af5ebb78c38a4f3190e32e67b4ce12bb).
+If you would like to run this workflow using the cavatica public app, a basic primer on running public apps can be found [here](https://www.notion.so/d3b/Starting-From-Scratch-Running-Cavatica-af5ebb78c38a4f3190e32e67b4ce12bb).
 Alternatively, if you'd like to run it locally using `cwltool`, a basic primer on that can be found [here](https://www.notion.so/d3b/Starting-From-Scratch-Running-CWLtool-b8dbbde2dc7742e4aff290b0a878344d) and combined with app-specific info from the readme below.
 This workflow is the current production workflow, equivalent to this [Cavatica public app](https://cavatica.sbgenomics.com/public/apps#cavatica/apps-publisher/kfdrc-jointgenotyping-refinement-workflow).
 

diff --git a/workflow/kfdrc-jointgenotyping-refinement-workflow.cwl b/workflow/kfdrc-jointgenotyping-refinement-workflow.cwl
@@ -8,7 +8,7 @@ doc: |
 
   Using existing gVCFs, likely from GATK Haplotype Caller, we follow this workflow: [Germline short variant discovery (SNPs + Indels)](https://software.broadinstitute.org/gatk/best-practices/workflow?id=11145), to create family joint calling and joint trios (typically mother-father-child) variant calls. Peddy is run to raise any potential issues in family relation definitions and sex assignment.
 
-  Inputs from this can be used later on for further analysis in joint trio genotyping and subsequent refinement and deNovo variant analysis. If you would like to run this workflow using the cavatica public app, a basic primer on running public apps can be found [here](https://www.notion.so/d3b/Starting-From-Scratch-Running-Cavatica-af5ebb78c38a4f3190e32e67b4ce12bb).
+  If you would like to run this workflow using the cavatica public app, a basic primer on running public apps can be found [here](https://www.notion.so/d3b/Starting-From-Scratch-Running-Cavatica-af5ebb78c38a4f3190e32e67b4ce12bb).
   Alternatively, if you'd like to run it locally using `cwltool`, a basic primer on that can be found [here](https://www.notion.so/d3b/Starting-From-Scratch-Running-CWLtool-b8dbbde2dc7742e4aff290b0a878344d) and combined with app-specific info from the readme below.
 
   ![data service logo](https://github.com/d3b-center/d3b-research-workflows/raw/master/doc/kfdrc-logo-sm.png)

diff --git a/...c_jointgenotyping_refinement_workflow.cwl → ...c_jointgenotyping_refinement_workflow.cwl b/...c_jointgenotyping_refinement_workflow.cwl → ...c_jointgenotyping_refinement_workflow.cwl
diff --git a/...drc_single_sample_genotyping_workflow.cwl → ...drc_single_sample_genotyping_workflow.cwl b/...drc_single_sample_genotyping_workflow.cwl → ...drc_single_sample_genotyping_workflow.cwl