fix broken links

docs/docs/documentation/modular_workflow_execution.md

@@ -17,7 +17,7 @@ The pipeline is designed into three independent modules:
 2. **Module 2: Local Ancestry Inference** (using RFMix2, G-Nomix, FLARE)
 3. **Module 3: Tractor GWAS**
 
-The whole workflow can be run together, as we discussed in [Launching an NXF Workflow](https://atkinson-lab.github.io/TractorWorkflow/docs/docs/documentation/launching_nxf_workflow.html), but these modules can also be run indepdendently or two at a time.
+The whole workflow can be run together, as we discussed in [Launching an NXF Workflow](https://atkinson-lab.github.io/TractorWorkflow/docs/documentation/launching_nxf_workflow.html), but these modules can also be run indepdendently or two at a time.
 
 Here we discuss the scripts to be able to independently run these modules:
 

docs/docs/faq.md

@@ -26,7 +26,7 @@ Tractor currently supports several Local Ancestry Inference (LAI) tools, includi
 
 If the LAI tool you are using generates an `*.msp` file, you can use `extract_tracts.py` to generate the necessary inputs and then run Tractor GWAS. For FLARE, which outputs a VCF file with both ancestry calls and genotypes, we have created a new script, `extract_tracts_flare.py`, to support this process.
 
-If you want to experiment with a new LAI tool, you can run the workflow modularly (one module at a time) and test the tool out. Check [here](https://atkinson-lab.github.io/NextflowWorkflow/docs/docs/documentation/modular_workflow_execution.html) for modular workflow runs.
+If you want to experiment with a new LAI tool, you can run the workflow modularly (one module at a time) and test the tool out. Check [here](https://atkinson-lab.github.io/TractorWorkflow/docs/documentation/modular_workflow_execution.html) for modular workflow runs.
 
 **5. If I want to run additional phenotypes on the same dataset I've previously used with Tractor, do I need to rerun the entire pipeline?**
 

docs/index.md

@@ -18,12 +18,13 @@ The Tractor Nextflow (NXF) Workflow is designed to simplify this process for use
 **Tractor Nextflow (NXF) Workflow: v0.0.0.TBD.** See the [TBD-CHANGELOG](tbd) for details. -->
 
 {: .new }
-**Tractor GWAS: v1.4.0.** See the [CHANGELOG](https://atkinson-lab.github.io/TractorWorkflow/docs/docs/CHANGELOG.html) for details.
+**Tractor GWAS: v1.4.0.** See the [CHANGELOG](https://atkinson-lab.github.io/TractorWorkflow/docs/CHANGELOG.html) for details.
 
 ## Description
 The goal of creating a Tractor Nextflow (NXF) workflow was threefold:
 * **Lowering the barrier of adoption:** We wanted to streamline the process by simplifying the numerous steps involved while offering support for most commonly used tools for each of the steps.
-* **Enable customization:** We wanted to give users the flexibility to customize the workflow, allowing them to run specific steps via Nextflow based on their needs. We have the split the workflow into <u><b>three modules</b></u> which allows for this. Please see [Documentation](https://atkinson-lab.github.io/TractorWorkflow/docs/docs/documentation/documentation_home.html)
+* **Enable customization:** We wanted to give users the flexibility to customize the workflow, allowing them to run specific steps via Nextflow based on their needs. We have the split the workflow into <u><b>three modules</b></u> which allows for this. Please see [Documentation](https://atkinson-lab.github.io/TractorWorkflow/docs/documentation/documentation_home.html)
+
 * **Tutorial:** We also wanted to provide a clear tutorial of what a Tractor run typically looks like, to guide users through the process
 
 ## Citation