update links

Author: aofarrel

README.md

@@ -4,7 +4,7 @@
 This is a work-in-progress project to implement some components of the University of Washington [TOPMed pipeline](https://github.com/UW-GAC/analysis_pipeline) into Workflow Description Lauange (WDL) in a way that closely mimics [the CWL version of the UW Pipeline](https://github.com/UW-GAC/analysis_pipeline_cwl). In other words, this is a WDL that mimics a CWL that mimics a Python pipeline. All three pipelines use the same underlying R scripts which do most of the heavy lifting, making their results directly comparable.
 
 ## Features
-* This pipeline is very similiar to the CWL version, and while the main differences between the two [are documented](https://github.com/DataBiosphere/analysis_pipeline_WDL/blob/main/documentation/cwl-vs-wdl.md), testing indicates they are functionally equivalent -- so much so that files generated by the CWL are used as truth files for the WDL   
+* This pipeline is very similiar to the CWL version, and while the main differences between the two [are documented](https://github.com/DataBiosphere/analysis_pipeline_WDL/blob/main/_documentation_/for%20users/cwl-vs-wdl-user.md), testing indicates they are functionally equivalent -- so much so that files generated by the CWL are used as truth files for the WDL   
 * As it works in a Docker container, it does not have any external dependencies other than the usual setup required for [WDL](https://software.broadinstitute.org/wdl/documentation/quickstart) and [Cromwell](http://cromwell.readthedocs.io/en/develop/)
 * Contains a checker workflow for validating a set of known inputs and expected outputs
 
@@ -15,10 +15,10 @@ The original pipeline had arguments relating to runtime such as `ncores` and `cl
 ### Terra users
 For Terra users, it is recommended to import via Dockstore. Importing the correct JSON file for your workflow at the workflow field entry page will fill in test data and recommended runtime attributes for said test data. For example, load `vcf-to-gds-terra.json` for `vcf-to-gds.wfl`. If you are using your own data, please be sure to increase your runtime attributes appropriately.  
 ### Local users
-Running these workflows locally is technically possible, but this is not officially supported due to how the local version of Cromwell handles local resources. Please see [this document](https://github.com/DataBiosphere/analysis_pipeline_WDL/blob/main/documentation/running-locally.md) for specifics on running locally.
+Running these workflows locally is technically possible, but this is not officially supported due to how the local version of Cromwell handles local resources. Please see [this document](https://github.com/DataBiosphere/analysis_pipeline_WDL/blob/main/_documentation_/for%20users/running-locally.md) for specifics on running locally.
 
 ## Further reading
-* [checker workflows](https://github.com/DataBiosphere/analysis_pipeline_WDL/blob/main/_documentation_/checker.md)
+* [checker workflows](https://github.com/DataBiosphere/analysis_pipeline_WDL/blob/main/_documentation_/for%20users/checker.md)
 * [ld-pruning](https://github.com/DataBiosphere/analysis_pipeline_WDL/blob/main/ld-pruning/README.md)
 * [null-model](https://github.com/DataBiosphere/analysis_pipeline_WDL/blob/main/null-model/README.md)
 * [vcf-to-gds](https://github.com/DataBiosphere/analysis_pipeline_WDL/blob/main/vcf-to-gds/README.md)