Updating formatting for public listing page

.github/generate_readme.sh

@@ -5,39 +5,15 @@ Greetings! This repositiory contains an automatically updated listing (in the fo
 logical organization of all repositiories owned/mainteined by CGDS. You can discovery more information
 on what's being worked on within the organization through a quick review of this document or navigate
 to a specific section if you know what type of tool, software, analysis, workflow, etc. you're looking
-for in specific.
+for in specific. You can learn more about how this repo was setup and how it's automagically populated
+by checking out the [setup instructions](setup.md). The setup instructions also contain details on
+customizing the setup of this README and how repos are queried and listed.
 
 [![Generation Status](https://github.com/uab-cgds-worthey/CGDS-Repo-Discovery/actions/workflows/organize-readme.yml/badge.svg)](https://github.com/uab-cgds-worthey/CGDS-Repo-Discovery/actions/workflows/organize-readme.yml)
 
 ## Software Development
 $(gh repo list --limit 10000 uab-cgds-worthey --topic software --json description,name,url,repositoryTopics --jq 'sort_by(.name) | .[] | .repositoryTopics = [.repositoryTopics[]?.name] | .repositoryTopics = (.repositoryTopics | join(", ")) | "  - [\(.name)](\(.url)) - \(.description) -  _Repo Topics_: \(.repositoryTopics)"')
 
-## Project-based Analysis
-
-### Cystic Fibrosis (CF)
-$(gh repo list --limit 10000 uab-cgds-worthey --topic cystic-fibrosis --json description,name,url,repositoryTopics --jq 'sort_by(.name) | .[] | .repositoryTopics = [.repositoryTopics[]?.name] | .repositoryTopics = (.repositoryTopics | join(", ")) | "  - [\(.name)](\(.url)) - \(.description) -  _Repo Topics_: \(.repositoryTopics)"')
-
-### Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)
-$(gh repo list --limit 10000 uab-cgds-worthey --topic mecfs --json description,name,url,repositoryTopics --jq 'sort_by(.name) | .[] | .repositoryTopics = [.repositoryTopics[]?.name] | .repositoryTopics = (.repositoryTopics | join(", ")) | "  - [\(.name)](\(.url)) - \(.description) -  _Repo Topics_: \(.repositoryTopics)"')
-
-### Neurofibromatosis type 1 (NF1)
-$(gh repo list --limit 10000 uab-cgds-worthey --topic nf1 --json description,name,url,repositoryTopics --jq 'sort_by(.name) | .[] | .repositoryTopics = [.repositoryTopics[]?.name] | .repositoryTopics = (.repositoryTopics | join(", ")) | "  - [\(.name)](\(.url)) - \(.description) -  _Repo Topics_: \(.repositoryTopics)"')
-
-### Pediatric Thyroid Cancer (PTC)
-$(gh repo list --limit 10000 uab-cgds-worthey --topic ptc --json description,name,url,repositoryTopics --jq 'sort_by(.name) | .[] | .repositoryTopics = [.repositoryTopics[]?.name] | .repositoryTopics = (.repositoryTopics | join(", ")) | "  - [\(.name)](\(.url)) - \(.description) -  _Repo Topics_: \(.repositoryTopics)"')
-
-### Placental Vascular Pathology (PVP)
-$(gh repo list --limit 10000 uab-cgds-worthey --topic pvp --json description,name,url,repositoryTopics --jq 'sort_by(.name) | .[] | .repositoryTopics = [.repositoryTopics[]?.name] | .repositoryTopics = (.repositoryTopics | join(", ")) | "  - [\(.name)](\(.url)) - \(.description) -  _Repo Topics_: \(.repositoryTopics)"')
-
-### Pulmonary Arterial Hypertension (PAH)
-$(gh repo list --limit 10000 uab-cgds-worthey --topic pah --json description,name,url,repositoryTopics --jq 'sort_by(.name) | .[] | .repositoryTopics = [.repositoryTopics[]?.name] | .repositoryTopics = (.repositoryTopics | join(", ")) | "  - [\(.name)](\(.url)) - \(.description) -  _Repo Topics_: \(.repositoryTopics)"')
-
-### Undiagnosed Diseases Network (UDN)
-$(gh repo list --limit 10000 uab-cgds-worthey --topic udn --json description,name,url,repositoryTopics --jq 'sort_by(.name) | .[] | .repositoryTopics = [.repositoryTopics[]?.name] | .repositoryTopics = (.repositoryTopics | join(", ")) | "  - [\(.name)](\(.url)) - \(.description) -  _Repo Topics_: \(.repositoryTopics)"')
-
-### Prader-Willi Syndrome
-$(gh repo list --limit 10000 uab-cgds-worthey --topic pws --json description,name,url,repositoryTopics --jq 'sort_by(.name) | .[] | .repositoryTopics = [.repositoryTopics[]?.name] | .repositoryTopics = (.repositoryTopics | join(", ")) | "  - [\(.name)](\(.url)) - \(.description) -  _Repo Topics_: \(.repositoryTopics)"')
-
 ## DevOps
 $(gh repo list --limit 10000 uab-cgds-worthey --topic devops --json description,name,url,repositoryTopics --jq 'sort_by(.name) | .[] | .repositoryTopics = [.repositoryTopics[]?.name] | .repositoryTopics = (.repositoryTopics | join(", ")) | "  - [\(.name)](\(.url)) - \(.description) -  _Repo Topics_: \(.repositoryTopics)"')
 
@@ -50,9 +26,6 @@ $(gh repo list --limit 10000 uab-cgds-worthey --topic pipeline --json descriptio
 ### Support
 $(gh repo list --limit 10000 uab-cgds-worthey --topic support --json description,name,url,repositoryTopics --jq 'sort_by(.name) | .[] | .repositoryTopics = [.repositoryTopics[]?.name] | .repositoryTopics = (.repositoryTopics | join(", ")) | "  - [\(.name)](\(.url)) - \(.description) -  _Repo Topics_: \(.repositoryTopics)"')
 
-### Workflow Management
-$(gh repo list --limit 10000 uab-cgds-worthey --topic workflow --json description,name,url,repositoryTopics --jq 'sort_by(.name) | .[] | .repositoryTopics = [.repositoryTopics[]?.name] | .repositoryTopics = (.repositoryTopics | join(", ")) | "  - [\(.name)](\(.url)) - \(.description) -  _Repo Topics_: \(.repositoryTopics)"')
-
 ## Miscellaneous
 $(gh repo list --limit 10000 uab-cgds-worthey --json description,name,url,repositoryTopics --jq '["support","pipeline", "software", "devops", "sciops", "workflow", "cystic-fibrosis", "mecfs", "nf1", "ptc", "pvp", "pah", "udn", "pws"] as $blacklist | sort_by(.name) | .[] | .repositoryTopics = [.repositoryTopics[]?.name] | (.repositoryTopics | length) as $origlen | select((.repositoryTopics - $blacklist | length) == $origlen) | .repositoryTopics = (.repositoryTopics | join(", ")) | "  - [\(.name)](\(.url)) - \(.description) -  _Repo Topics_: \(.repositoryTopics)"')
 

.github/workflows/organize-readme.yml

@@ -26,7 +26,7 @@ jobs:
         run: bash .github/generate_readme.sh
 
         env:
-          GITHUB_TOKEN: ${{ secrets.REPO_FINE_GRAIN_TOKEN }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
       - uses: stefanzweifel/git-auto-commit-action@v4
         with:

README.md

@@ -4,6 +4,9 @@ Greetings! This repositiory contains an automatically updated listing (in the fo
 logical organization of all repositiories owned/mainteined by CGDS. You can discovery more information
 on what's being worked on within the organization through a quick review of this document or navigate
 to a specific section if you know what type of tool, software, analysis, workflow, etc. you're looking
-for in specific.
+for in specific. You can learn more about how this repo was setup and how it's automagically populated
+by checking out the [setup instructions](setup.md). The setup instructions also contain details on
+customizing the setup of this README and how repos are queried and listed.
 
 [![Generation Status](https://github.com/uab-cgds-worthey/CGDS-Repo-Discovery/actions/workflows/organize-readme.yml/badge.svg)](https://github.com/uab-cgds-worthey/CGDS-Repo-Discovery/actions/workflows/organize-readme.yml)
+