Fixing broken link and updating badges in README's (#289)

tefirman · web-flow · commit 575d3e5c7111 · 2026-03-23T21:32:17.000-07:00
* Fixing broken PROOF How To link in README's

* Updating badges for the overarching repo and select resources
diff --git a/README.md b/README.md
@@ -9,7 +9,7 @@
 </table>
 
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
-[![Project Status: Prototype – Useable, some support, open to feedback, unstable API.](https://getwilds.org/badges/badges/prototype.svg)](https://getwilds.org/badges/#prototype)
+[![Project Status: Stable – Useable, full support, open to feedback, stable API.](https://getwilds.org/badges/badges/stable.svg)](https://getwilds.org/badges/#stable)
 [![WDL Executors](https://img.shields.io/badge/WDL-Cromwell%20%7C%20miniWDL%20%7C%20Sprocket-blue.svg)](https://github.com/getwilds/wilds-wdl-library)
 [![WDL](https://img.shields.io/badge/WDL-1.0-orange.svg)](https://openwdl.org/)<br>
 [![Module Tests](https://github.com/getwilds/wilds-wdl-library/actions/workflows/modules-testrun.yml/badge.svg)](https://github.com/getwilds/wilds-wdl-library/actions/workflows/modules-testrun.yml)
@@ -104,7 +104,7 @@ All components are tested with multiple WDL executors:
 
 ## For Fred Hutch Users
 
-Fred Hutch researchers can use [PROOF](https://sciwiki.fredhutch.org/dasldemos/proof-how-to/) to submit workflows directly to the on-premise HPC cluster. This provides a user-friendly interface for researchers unfamiliar with command-line tools while leveraging the power of the institutional computing resources.
+Fred Hutch researchers can use [PROOF](https://sciwiki.fredhutch.org/datademos/proof-how-to/) to submit workflows directly to the on-premise HPC cluster. This provides a user-friendly interface for researchers unfamiliar with command-line tools while leveraging the power of the institutional computing resources.
 
 **Cromwell Configuration**: PROOF users can customize workflow execution using Cromwell options. See [cromwell-options.json](cromwell-options.json) for example configurations including call caching, output directories, and more. For detailed information, refer to the [Cromwell workflow options documentation](https://cromwell.readthedocs.io/en/stable/wf_options/Overview/).
 
diff --git a/modules/ww-annovar/README.md b/modules/ww-annovar/README.md
@@ -1,5 +1,7 @@
 # ww-annovar
 
+[![Project Status: Experimental – Useable, some support, not open to feedback, unstable API.](https://getwilds.org/badges/badges/experimental.svg)](https://getwilds.org/badges/#experimental)
+
 A WILDS WDL module for variant annotation using Annovar. This module provides comprehensive annotation of genetic variants with customizable protocols and operations.
 
 ## Overview
diff --git a/modules/ww-bcftools/README.md b/modules/ww-bcftools/README.md
@@ -1,5 +1,5 @@
 # ww-bcftools
-[![Project Status: Experimental – Useable, some support, not open to feedback, unstable API.](https://getwilds.org/badges/badges/experimental.svg)](https://getwilds.org/badges/#experimental)
+[![Project Status: Stable – Useable, full support, open to feedback, stable API.](https://getwilds.org/badges/badges/stable.svg)](https://getwilds.org/badges/#stable)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 
 A WILDS WDL module for variant calling and manipulation using bcftools.
diff --git a/modules/ww-bedtools/README.md b/modules/ww-bedtools/README.md
@@ -1,5 +1,5 @@
 # ww-bedtools
-[![Project Status: Experimental – Useable, some support, not open to feedback, unstable API.](https://getwilds.org/badges/badges/experimental.svg)](https://getwilds.org/badges/#experimental)
+[![Project Status: Stable – Useable, full support, open to feedback, stable API.](https://getwilds.org/badges/badges/stable.svg)](https://getwilds.org/badges/#stable)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 
 A WILDS WDL module for working with genomic intervals using BEDTools.
diff --git a/modules/ww-bwa/README.md b/modules/ww-bwa/README.md
@@ -1,5 +1,5 @@
 # ww-bwa
-[![Project Status: Experimental – Useable, some support, not open to feedback, unstable API.](https://getwilds.org/badges/badges/experimental.svg)](https://getwilds.org/badges/#experimental)
+[![Project Status: Stable – Useable, full support, open to feedback, stable API.](https://getwilds.org/badges/badges/stable.svg)](https://getwilds.org/badges/#stable)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 
 A WILDS WDL module for sequence alignment using the Burrows-Wheeler Aligner (BWA).
diff --git a/modules/ww-gatk/README.md b/modules/ww-gatk/README.md
@@ -1,5 +1,5 @@
 # ww-gatk
-[![Project Status: Experimental – Useable, some support, not open to feedback, unstable API.](https://getwilds.org/badges/badges/experimental.svg)](https://getwilds.org/badges/#experimental)
+[![Project Status: Stable – Useable, full support, open to feedback, stable API.](https://getwilds.org/badges/badges/stable.svg)](https://getwilds.org/badges/#stable)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 
 A WILDS WDL module for GATK variant calling and analysis tasks with automated parallelization.
diff --git a/modules/ww-samtools/README.md b/modules/ww-samtools/README.md
@@ -1,5 +1,5 @@
 # ww-samtools
-[![Project Status: Experimental – Useable, some support, not open to feedback, unstable API.](https://getwilds.org/badges/badges/experimental.svg)](https://getwilds.org/badges/#experimental)
+[![Project Status: Stable – Useable, full support, open to feedback, stable API.](https://getwilds.org/badges/badges/stable.svg)](https://getwilds.org/badges/#stable)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 
 A WILDS WDL module for processing genomic files with [Samtools](http://www.htslib.org/).
diff --git a/modules/ww-sra/README.md b/modules/ww-sra/README.md
@@ -1,5 +1,5 @@
 # ww-sra
-[![Project Status: Experimental – Useable, some support, not open to feedback, unstable API.](https://getwilds.org/badges/badges/experimental.svg)](https://getwilds.org/badges/#experimental)
+[![Project Status: Stable – Useable, full support, open to feedback, stable API.](https://getwilds.org/badges/badges/stable.svg)](https://getwilds.org/badges/#stable)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 
 A WILDS WDL module for downloading genomic data from the NCBI Sequence Read Archive (SRA).
diff --git a/modules/ww-star/README.md b/modules/ww-star/README.md
@@ -1,5 +1,5 @@
 # ww-star
-[![Project Status: Experimental – Useable, some support, not open to feedback, unstable API.](https://getwilds.org/badges/badges/experimental.svg)](https://getwilds.org/badges/#experimental)
+[![Project Status: Stable – Useable, full support, open to feedback, stable API.](https://getwilds.org/badges/badges/stable.svg)](https://getwilds.org/badges/#stable)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 
 A WILDS WDL module for RNA-seq alignment using STAR's two-pass methodology.
diff --git a/modules/ww-strelka/README.md b/modules/ww-strelka/README.md
@@ -1,5 +1,7 @@
 # ww-strelka
 
+[![Project Status: Experimental – Useable, some support, not open to feedback, unstable API.](https://getwilds.org/badges/badges/experimental.svg)](https://getwilds.org/badges/#experimental)
+
 A WILDS WDL module for germline and somatic variant calling using Strelka, a fast and accurate small variant caller optimized for analysis of germline variation in small cohorts and somatic variation in tumor/normal sample pairs.
 
 ## Overview
diff --git a/pipelines/ww-bwa-gatk/README.md b/pipelines/ww-bwa-gatk/README.md
@@ -1,5 +1,5 @@
 # ww-bwa-gatk Pipeline
-[![Project Status: Experimental – Useable, some support, not open to feedback, unstable API.](https://getwilds.org/badges/badges/experimental.svg)](https://getwilds.org/badges/#experimental)
+[![Project Status: Stable – Useable, full support, open to feedback, stable API.](https://getwilds.org/badges/badges/stable.svg)](https://getwilds.org/badges/#stable)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 
 A WILDS WDL pipeline demonstrating read alignment and initial quality control using modular WILDS components.
@@ -80,7 +80,7 @@ sprocket run ww-bwa-gatk.wdl inputs.json
 
 ### For Fred Hutch Users
 
-Fred Hutch users can use [PROOF](https://sciwiki.fredhutch.org/dasldemos/proof-how-to/) to submit this pipeline directly to the on-premise HPC cluster:
+Fred Hutch users can use [PROOF](https://sciwiki.fredhutch.org/datademos/proof-how-to/) to submit this pipeline directly to the on-premise HPC cluster:
 
 1. Ensure your input files are accessible by the cluster
 2. Update the inputs JSON
diff --git a/pipelines/ww-ena-star/README.md b/pipelines/ww-ena-star/README.md
@@ -1,5 +1,5 @@
 # ww-ena-star Pipeline
-[![Project Status: Experimental – Useable, some support, not open to feedback, unstable API.](https://getwilds.org/badges/badges/experimental.svg)](https://getwilds.org/badges/#experimental)
+[![Project Status: Stable – Useable, full support, open to feedback, stable API.](https://getwilds.org/badges/badges/stable.svg)](https://getwilds.org/badges/#stable)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 
 A WILDS WDL pipeline demonstrating RNA-seq analysis from ENA download to alignment using modular WILDS components.
@@ -84,7 +84,7 @@ sprocket run ww-ena-star.wdl inputs.json
 
 ### For Fred Hutch Users
 
-Fred Hutch users can use [PROOF](https://sciwiki.fredhutch.org/dasldemos/proof-how-to/) to submit this pipeline directly to the on-premise HPC cluster:
+Fred Hutch users can use [PROOF](https://sciwiki.fredhutch.org/datademos/proof-how-to/) to submit this pipeline directly to the on-premise HPC cluster:
 
 1. Update the inputs JSON with your desired ENA accessions
 2. Ensure reference genome files are accessible to the cluster
diff --git a/pipelines/ww-imputation/README.md b/pipelines/ww-imputation/README.md
@@ -103,7 +103,7 @@ sprocket run ww-imputation.wdl inputs.json
 
 ### For Fred Hutch Users
 
-Fred Hutch users can use [PROOF](https://sciwiki.fredhutch.org/dasldemos/proof-how-to/) to submit this pipeline directly to the cluster:
+Fred Hutch users can use [PROOF](https://sciwiki.fredhutch.org/datademos/proof-how-to/) to submit this pipeline directly to the cluster:
 
 1. Ensure your input files are accessible by the cluster
 2. Update the inputs JSON
diff --git a/pipelines/ww-jetlag/README.md b/pipelines/ww-jetlag/README.md
@@ -86,7 +86,7 @@ sprocket run ww-jetlag.wdl inputs.json
 
 ### For Fred Hutch Users
 
-Fred Hutch users can use [PROOF](https://sciwiki.fredhutch.org/dasldemos/proof-how-to/) to submit this pipeline directly to the on-premise HPC cluster.
+Fred Hutch users can use [PROOF](https://sciwiki.fredhutch.org/datademos/proof-how-to/) to submit this pipeline directly to the on-premise HPC cluster.
 
 ## Input Parameters
 
diff --git a/pipelines/ww-leukemia/README.md b/pipelines/ww-leukemia/README.md
@@ -178,7 +178,7 @@ The pipeline produces comprehensive outputs from each analysis step:
 
 ## For Fred Hutch Users
 
-Fred Hutch users can use [PROOF](https://sciwiki.fredhutch.org/dasldemos/proof-how-to/) to submit this pipeline to the on-premise HPC cluster:
+Fred Hutch users can use [PROOF](https://sciwiki.fredhutch.org/datademos/proof-how-to/) to submit this pipeline to the on-premise HPC cluster:
 
 1. Clone or download this repository
 2. Update `inputs.json` with your sample paths and reference files
diff --git a/pipelines/ww-saturation/README.md b/pipelines/ww-saturation/README.md
@@ -131,7 +131,7 @@ sprocket run testrun.wdl
 
 ### For Fred Hutch Users
 
-Fred Hutch users can use [PROOF](https://sciwiki.fredhutch.org/dasldemos/proof-how-to/) to submit this pipeline directly to the on-premise HPC cluster:
+Fred Hutch users can use [PROOF](https://sciwiki.fredhutch.org/datademos/proof-how-to/) to submit this pipeline directly to the on-premise HPC cluster:
 
 1. Ensure your input files are accessible by the cluster
 2. Update the inputs JSON
diff --git a/pipelines/ww-splicing-proteomics/README.md b/pipelines/ww-splicing-proteomics/README.md
@@ -121,7 +121,7 @@ sprocket run ww-splicing-proteomics.wdl inputs.json
 
 ### For Fred Hutch Users
 
-Fred Hutch users can use [PROOF](https://sciwiki.fredhutch.org/dasldemos/proof-how-to/) to submit this pipeline directly to the on-premise HPC cluster:
+Fred Hutch users can use [PROOF](https://sciwiki.fredhutch.org/datademos/proof-how-to/) to submit this pipeline directly to the on-premise HPC cluster:
 
 1. Ensure your input files are accessible by the cluster
 2. Update the inputs JSON with sample information and group assignments
diff --git a/pipelines/ww-sra-salmon/README.md b/pipelines/ww-sra-salmon/README.md
@@ -84,7 +84,7 @@ sprocket run ww-sra-salmon.wdl inputs.json
 
 ### For Fred Hutch Users
 
-Fred Hutch users can use [PROOF](https://sciwiki.fredhutch.org/dasldemos/proof-how-to/) to submit this pipeline directly to the on-premise HPC cluster:
+Fred Hutch users can use [PROOF](https://sciwiki.fredhutch.org/datademos/proof-how-to/) to submit this pipeline directly to the on-premise HPC cluster:
 
 1. Update the inputs JSON with your desired SRA accessions
 2. Ensure transcriptome reference file is accessible to the cluster
diff --git a/pipelines/ww-sra-star/README.md b/pipelines/ww-sra-star/README.md
@@ -1,5 +1,5 @@
 # ww-sra-star Pipeline
-[![Project Status: Experimental – Useable, some support, not open to feedback, unstable API.](https://getwilds.org/badges/badges/experimental.svg)](https://getwilds.org/badges/#experimental)
+[![Project Status: Stable – Useable, full support, open to feedback, stable API.](https://getwilds.org/badges/badges/stable.svg)](https://getwilds.org/badges/#stable)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 
 A WILDS WDL pipeline demonstrating RNA-seq analysis from SRA download to alignment using modular WILDS components.
@@ -80,7 +80,7 @@ sprocket run ww-sra-star.wdl inputs.json
 
 ### For Fred Hutch Users
 
-Fred Hutch users can use [PROOF](https://sciwiki.fredhutch.org/dasldemos/proof-how-to/) to submit this pipeline directly to the on-premise HPC cluster:
+Fred Hutch users can use [PROOF](https://sciwiki.fredhutch.org/datademos/proof-how-to/) to submit this pipeline directly to the on-premise HPC cluster:
 
 1. Update the inputs JSON with your desired SRA accessions
 2. Ensure reference genome files are accessible to the cluster
diff --git a/pipelines/ww-star-deseq2/README.md b/pipelines/ww-star-deseq2/README.md
@@ -108,7 +108,7 @@ sprocket run ww-star-deseq2.wdl inputs.json
 
 ### For Fred Hutch Users
 
-Fred Hutch users can use [PROOF](https://sciwiki.fredhutch.org/dasldemos/proof-how-to/) to submit this pipeline directly to the on-premise HPC cluster:
+Fred Hutch users can use [PROOF](https://sciwiki.fredhutch.org/datademos/proof-how-to/) to submit this pipeline directly to the on-premise HPC cluster:
 
 1. Ensure your input files are accessible by the cluster
 2. Update the inputs JSON with sample information and conditions
