From b0fb84e0aaee98cc3a1d9f45d307c564e01aca8c Mon Sep 17 00:00:00 2001
From: buehlere <buehlere@mskcc.org>
Date: Tue, 20 Jan 2026 10:13:10 -0500
Subject: [PATCH 01/32] Update gitbook-sync.yml

---
 .github/workflows/gitbook-sync.yml | 43 +++++++++++++++++++++++++-----
 1 file changed, 36 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/gitbook-sync.yml b/.github/workflows/gitbook-sync.yml
index 1b97bf1a..37fe2c4b 100644
--- a/.github/workflows/gitbook-sync.yml
+++ b/.github/workflows/gitbook-sync.yml
@@ -48,7 +48,34 @@ jobs:
 
       - name: Combine all tags.yml files
         id: get_tags
-        run: find . -name "tags.yml" -not -path "./.github/*" -exec cat {} + > .github/tags.yml
+        run: |
+          echo "{}" > .github/tags.yml
+
+          for f in $(find . -name "tags.yml" -not -path "./.github/*"); do
+            # Determine feature type from path
+            if [[ "$f" == *"/modules/"* ]]; then
+              PREFIX="modules"
+            elif [[ "$f" == *"/subworkflows/"* ]]; then
+              PREFIX="subworkflows"
+            else
+              echo "Unknown feature type for $f"
+              exit 1
+            fi
+
+            # Rewrite keys to be namespaced
+            yq eval "
+              with_entries(
+                .key = \"${PREFIX}/\" + .key
+              )
+            " "$f" > /tmp/tags.prefixed.yml
+
+            # Merge into final tags.yml
+            yq eval-all '. as \$item ireduce ({}; . *+ \$item)' \
+              .github/tags.yml /tmp/tags.prefixed.yml > /tmp/tags.merged.yml
+
+            mv /tmp/tags.merged.yml .github/tags.yml
+          done
+
 
       - name: debug
         run: cat .github/tags.yml
@@ -85,6 +112,8 @@ jobs:
         uses: actions/setup-python@v4
         with:
           python-version: "3.10" # install the python version needed
+      - name: Install yq
+        run: sudo apt-get update && sudo apt-get install -y yq
       - uses: actions/checkout@v4
         with:
           ref: docs
@@ -156,18 +185,18 @@ jobs:
         run: |
           echo ${{ matrix.tags }}
           python ${{ github.workspace }}/yaml_to_md.py all --yaml-file ${{ github.workspace }}/temp.yml --output-file ./${{ env.FEATURE_TYPE }}/${{ env.MD_NAME }}.md --schema-url https://raw.githubusercontent.com/mskcc-omics-workflows/yaml_to_md/0.0.3/nextflow_schema/${{ env.FEATURE_TYPE }}/meta-schema.json ${{ env.SUBWORKFLOW }}
-      - name: Check file existence for modules
-        id: check_files
-        uses: andstor/file-existence-action@v1
-        with:
-          branch: docs
-          files: ${{ env.FEATURE_TYPE}}/${{ env.MD_NAME }}.md
       - name: Add to SUMMARY for new features
         run: |
           curl -o ${{ github.workspace }}/update_summary.py https://raw.githubusercontent.com/mskcc-omics-workflows/modules/develop/.github/workflows/update_summary.py
           python ${{ github.workspace }}/update_summary.py SUMMARY.md "* [${{ env.MD_NAME }}](${{ env.FEATURE_TYPE }}/${{ env.MD_NAME }}.md)" ${{ env.SUMMARY_TYPE }} > tmp_summary.md
           mv tmp_summary.md SUMMARY.md
+      - name: Check for changes
+        run: |
+          if git diff --quiet; then
+            echo "NO_CHANGES=true" >> $GITHUB_ENV
+          fi
       - uses: EndBug/add-and-commit@v9
+        if: env.NO_CHANGES != 'true'
         with:
           default_author: github_actions
           message: "add doc for ${{ matrix.tags }}"

From c3c6b0dec177731bdaa7558db8dce426c4317534 Mon Sep 17 00:00:00 2001
From: buehlere <buehlere@mskcc.org>
Date: Tue, 20 Jan 2026 10:20:47 -0500
Subject: [PATCH 02/32] Update gitbook-sync.yml

---
 .github/workflows/gitbook-sync.yml | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/.github/workflows/gitbook-sync.yml b/.github/workflows/gitbook-sync.yml
index 37fe2c4b..cc951468 100644
--- a/.github/workflows/gitbook-sync.yml
+++ b/.github/workflows/gitbook-sync.yml
@@ -47,12 +47,10 @@ jobs:
           fetch-depth: 2 # To retrieve the preceding commit.
 
       - name: Combine all tags.yml files
-        id: get_tags
         run: |
           echo "{}" > .github/tags.yml
 
           for f in $(find . -name "tags.yml" -not -path "./.github/*"); do
-            # Determine feature type from path
             if [[ "$f" == *"/modules/"* ]]; then
               PREFIX="modules"
             elif [[ "$f" == *"/subworkflows/"* ]]; then
@@ -62,15 +60,13 @@ jobs:
               exit 1
             fi
 
-            # Rewrite keys to be namespaced
             yq eval "
               with_entries(
                 .key = \"${PREFIX}/\" + .key
               )
             " "$f" > /tmp/tags.prefixed.yml
 
-            # Merge into final tags.yml
-            yq eval-all '. as \$item ireduce ({}; . *+ \$item)' \
+            yq eval-all '. as $item ireduce ({}; . *+ $item)' \
               .github/tags.yml /tmp/tags.prefixed.yml > /tmp/tags.merged.yml
 
             mv /tmp/tags.merged.yml .github/tags.yml

From 862efb5e11d033537340cb407700f024d6a31b53 Mon Sep 17 00:00:00 2001
From: buehlere <buehlere@mskcc.org>
Date: Tue, 20 Jan 2026 11:15:40 -0500
Subject: [PATCH 03/32] yml formatting

---
 modules/msk/calculatenoise/environment.yml         | 2 +-
 modules/msk/calculatenoise/meta.yml                | 4 ++--
 modules/msk/fgbio/collectduplexseqmetrics/meta.yml | 6 +++---
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/modules/msk/calculatenoise/environment.yml b/modules/msk/calculatenoise/environment.yml
index 4b3c9d37..4c59b932 100644
--- a/modules/msk/calculatenoise/environment.yml
+++ b/modules/msk/calculatenoise/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "YOUR-TOOL-HERE"
+  - "YOUR-TOOL=HERE"
diff --git a/modules/msk/calculatenoise/meta.yml b/modules/msk/calculatenoise/meta.yml
index 54568d25..a2a51b94 100644
--- a/modules/msk/calculatenoise/meta.yml
+++ b/modules/msk/calculatenoise/meta.yml
@@ -12,7 +12,7 @@ tools:
       tool_dev_url: "https://github.com/msk-access/sequence_qc"
       doi: ""
       licence: ["MIT"]
-      identifier: null
+      identifier: ""
 
 input:
   - - meta:
@@ -141,4 +141,4 @@ output:
 authors:
   - "@mikefeixu"
 maintainers:
-  - "@mikefeixu"
\ No newline at end of file
+  - "@mikefeixu"
diff --git a/modules/msk/fgbio/collectduplexseqmetrics/meta.yml b/modules/msk/fgbio/collectduplexseqmetrics/meta.yml
index 5219fc6f..60c76972 100644
--- a/modules/msk/fgbio/collectduplexseqmetrics/meta.yml
+++ b/modules/msk/fgbio/collectduplexseqmetrics/meta.yml
@@ -8,9 +8,9 @@ keywords:
 tools:
   - "fgbio":
       description: "A set of tools for working with genomic and high throughput sequencing data, including UMIs"
-      homepage: "None"
-      documentation: "None"
-      tool_dev_url: "None"
+      homepage: "https://github.com/fulcrumgenomics/fgbio"
+      documentation: "https://github.com/fulcrumgenomics/fgbio"
+      tool_dev_url: "https://github.com/fulcrumgenomics/fgbio"
       doi: ""
       licence: ["MIT"]
       identifier: biotools:fgbio

From 99ac7ea0ea662e91635797d9f83b3d57810e6c9f Mon Sep 17 00:00:00 2001
From: buehlere <buehlere@mskcc.org>
Date: Tue, 20 Jan 2026 11:20:50 -0500
Subject: [PATCH 04/32] yml formatting

---
 modules/msk/calculatenoise/meta.yml                | 2 +-
 modules/msk/fgbio/collectduplexseqmetrics/meta.yml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/msk/calculatenoise/meta.yml b/modules/msk/calculatenoise/meta.yml
index a2a51b94..714dbaf7 100644
--- a/modules/msk/calculatenoise/meta.yml
+++ b/modules/msk/calculatenoise/meta.yml
@@ -10,7 +10,7 @@ tools:
       homepage: "https://github.com/msk-access/sequence_qc"
       documentation: "https://github.com/msk-access/sequence_qc"
       tool_dev_url: "https://github.com/msk-access/sequence_qc"
-      doi: ""
+      doi: "no DOI available"
       licence: ["MIT"]
       identifier: ""
 
diff --git a/modules/msk/fgbio/collectduplexseqmetrics/meta.yml b/modules/msk/fgbio/collectduplexseqmetrics/meta.yml
index 60c76972..97c772bb 100644
--- a/modules/msk/fgbio/collectduplexseqmetrics/meta.yml
+++ b/modules/msk/fgbio/collectduplexseqmetrics/meta.yml
@@ -11,7 +11,7 @@ tools:
       homepage: "https://github.com/fulcrumgenomics/fgbio"
       documentation: "https://github.com/fulcrumgenomics/fgbio"
       tool_dev_url: "https://github.com/fulcrumgenomics/fgbio"
-      doi: ""
+      doi: "no DOI available"
       licence: ["MIT"]
       identifier: biotools:fgbio
 

From 78662a54695e2b99c4d033f11d435ba38146d5a4 Mon Sep 17 00:00:00 2001
From: buehlere <buehlere@mskcc.org>
Date: Tue, 20 Jan 2026 11:24:49 -0500
Subject: [PATCH 05/32] Update gitbook-sync.yml

---
 .github/workflows/gitbook-sync.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/gitbook-sync.yml b/.github/workflows/gitbook-sync.yml
index cc951468..ec4e7829 100644
--- a/.github/workflows/gitbook-sync.yml
+++ b/.github/workflows/gitbook-sync.yml
@@ -198,3 +198,6 @@ jobs:
           message: "add doc for ${{ matrix.tags }}"
           add: '["*/*.md --force", "SUMMARY.md --force"]'
           cwd: "./"
+          pull: "--rebase"
+          push: true
+

From a9967df53bb53b369e78b5c21476e5c903b60a4b Mon Sep 17 00:00:00 2001
From: buehlere <buehlere@mskcc.org>
Date: Tue, 20 Jan 2026 11:31:36 -0500
Subject: [PATCH 06/32] Update gitbook-sync.yml

---
 .github/workflows/gitbook-sync.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/gitbook-sync.yml b/.github/workflows/gitbook-sync.yml
index ec4e7829..d45c5c34 100644
--- a/.github/workflows/gitbook-sync.yml
+++ b/.github/workflows/gitbook-sync.yml
@@ -191,6 +191,8 @@ jobs:
           if git diff --quiet; then
             echo "NO_CHANGES=true" >> $GITHUB_ENV
           fi
+      - name: Stage all changes
+        run: git add -A
       - uses: EndBug/add-and-commit@v9
         if: env.NO_CHANGES != 'true'
         with:
@@ -200,4 +202,3 @@ jobs:
           cwd: "./"
           pull: "--rebase"
           push: true
-

From f8de3d1a02bc49a675f2198929b93f006afd9d60 Mon Sep 17 00:00:00 2001
From: buehlere <buehlere@mskcc.org>
Date: Tue, 20 Jan 2026 11:34:03 -0500
Subject: [PATCH 07/32] Update gitbook-sync.yml

---
 .github/workflows/gitbook-sync.yml | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/.github/workflows/gitbook-sync.yml b/.github/workflows/gitbook-sync.yml
index d45c5c34..727ca5ba 100644
--- a/.github/workflows/gitbook-sync.yml
+++ b/.github/workflows/gitbook-sync.yml
@@ -191,8 +191,6 @@ jobs:
           if git diff --quiet; then
             echo "NO_CHANGES=true" >> $GITHUB_ENV
           fi
-      - name: Stage all changes
-        run: git add -A
       - uses: EndBug/add-and-commit@v9
         if: env.NO_CHANGES != 'true'
         with:
@@ -200,5 +198,4 @@ jobs:
           message: "add doc for ${{ matrix.tags }}"
           add: '["*/*.md --force", "SUMMARY.md --force"]'
           cwd: "./"
-          pull: "--rebase"
-          push: true
+          push: --force

From f190c26e24fdabd146b83ef5f3d5ac273668ef87 Mon Sep 17 00:00:00 2001
From: buehlere <buehlere@mskcc.org>
Date: Tue, 20 Jan 2026 11:59:30 -0500
Subject: [PATCH 08/32] Update gitbook-sync.yml

---
 .github/workflows/gitbook-sync.yml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/gitbook-sync.yml b/.github/workflows/gitbook-sync.yml
index 727ca5ba..d8d0f3e9 100644
--- a/.github/workflows/gitbook-sync.yml
+++ b/.github/workflows/gitbook-sync.yml
@@ -123,9 +123,8 @@ jobs:
         id: replace_slash
         run: |
           FRAGMENT="${{ env.SW_NAME }}"
-          MD_NAME=$(echo $FRAGMENT | sed 's/\//_/g')
-          echo "MD_NAME=$MD_NAME" >> $GITHUB_ENV
-          echo "${MD_NAME}"
+          MD_PATH="${FRAGMENT}"   # Keep subfolders
+          echo "MD_PATH=$MD_PATH" >> $GITHUB_ENV
       - uses: EndBug/add-and-commit@v9
         with:
           default_author: github_actions
@@ -180,11 +179,12 @@ jobs:
       - name: Run convertor to generate md file for new module
         run: |
           echo ${{ matrix.tags }}
-          python ${{ github.workspace }}/yaml_to_md.py all --yaml-file ${{ github.workspace }}/temp.yml --output-file ./${{ env.FEATURE_TYPE }}/${{ env.MD_NAME }}.md --schema-url https://raw.githubusercontent.com/mskcc-omics-workflows/yaml_to_md/0.0.3/nextflow_schema/${{ env.FEATURE_TYPE }}/meta-schema.json ${{ env.SUBWORKFLOW }}
+          mkdir -p ./${{ env.FEATURE_TYPE }}/$(dirname $MD_PATH)
+          python ${{ github.workspace }}/yaml_to_md.py all --yaml-file ${{ github.workspace }}/temp.yml --output-file ./${{ env.FEATURE_TYPE }}/${{ env.MD_PATH }}.md --schema-url https://raw.githubusercontent.com/mskcc-omics-workflows/yaml_to_md/0.0.3/nextflow_schema/${{ env.FEATURE_TYPE }}/meta-schema.json ${{ env.SUBWORKFLOW }}
       - name: Add to SUMMARY for new features
         run: |
           curl -o ${{ github.workspace }}/update_summary.py https://raw.githubusercontent.com/mskcc-omics-workflows/modules/develop/.github/workflows/update_summary.py
-          python ${{ github.workspace }}/update_summary.py SUMMARY.md "* [${{ env.MD_NAME }}](${{ env.FEATURE_TYPE }}/${{ env.MD_NAME }}.md)" ${{ env.SUMMARY_TYPE }} > tmp_summary.md
+          python ${{ github.workspace }}/update_summary.py SUMMARY.md "* [${{ env.MD_PATH }}](${{ env.FEATURE_TYPE }}/${{ env.MD_PATH }}.md)" ${{ env.SUMMARY_TYPE }} > tmp_summary.md
           mv tmp_summary.md SUMMARY.md
       - name: Check for changes
         run: |
@@ -196,6 +196,6 @@ jobs:
         with:
           default_author: github_actions
           message: "add doc for ${{ matrix.tags }}"
-          add: '["*/*.md --force", "SUMMARY.md --force"]'
+          add: '["**/*.md --force", "SUMMARY.md --force"]'
           cwd: "./"
           push: --force

From 82ae92055b8481992868eb14f8f22b49ca39cf6e Mon Sep 17 00:00:00 2001
From: buehlere <buehlere@mskcc.org>
Date: Tue, 20 Jan 2026 12:16:35 -0500
Subject: [PATCH 09/32] Update gitbook-sync.yml

---
 .github/workflows/gitbook-sync.yml | 15 +++++++++++----
 1 file changed, 11 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/gitbook-sync.yml b/.github/workflows/gitbook-sync.yml
index d8d0f3e9..436f542a 100644
--- a/.github/workflows/gitbook-sync.yml
+++ b/.github/workflows/gitbook-sync.yml
@@ -123,8 +123,10 @@ jobs:
         id: replace_slash
         run: |
           FRAGMENT="${{ env.SW_NAME }}"
-          MD_PATH="${FRAGMENT}"   # Keep subfolders
+          MD_PATH="${FRAGMENT}"   # keep subfolders for output file
+          MD_NAME="${MD_PATH}"    # <-- key change: preserve nested folder for display text
           echo "MD_PATH=$MD_PATH" >> $GITHUB_ENV
+          echo "MD_NAME=$MD_NAME" >> $GITHUB_ENV
       - uses: EndBug/add-and-commit@v9
         with:
           default_author: github_actions
@@ -176,15 +178,20 @@ jobs:
           echo "FEATURE_TYPE=$FEATURE_TYPE" >> $GITHUB_ENV
           echo "SUMMARY_TYPE=$SUMMARY_TYPE" >> $GITHUB_ENV
           echo "SUBWORKFLOW=$SUBWORKFLOW" >> $GITHUB_ENV
+
       - name: Run convertor to generate md file for new module
         run: |
           echo ${{ matrix.tags }}
           mkdir -p ./${{ env.FEATURE_TYPE }}/$(dirname $MD_PATH)
-          python ${{ github.workspace }}/yaml_to_md.py all --yaml-file ${{ github.workspace }}/temp.yml --output-file ./${{ env.FEATURE_TYPE }}/${{ env.MD_PATH }}.md --schema-url https://raw.githubusercontent.com/mskcc-omics-workflows/yaml_to_md/0.0.3/nextflow_schema/${{ env.FEATURE_TYPE }}/meta-schema.json ${{ env.SUBWORKFLOW }}
+          python ${{ github.workspace }}/yaml_to_md.py all \
+            --yaml-file ${{ github.workspace }}/temp.yml \
+            --output-file ./${{ env.FEATURE_TYPE }}/${{ env.MD_PATH }}.md \
+            --schema-url https://raw.githubusercontent.com/mskcc-omics-workflows/yaml_to_md/0.0.3/nextflow_schema/${{ env.FEATURE_TYPE }}/meta-schema.json \
+            ${{ env.SUBWORKFLOW }}
       - name: Add to SUMMARY for new features
         run: |
           curl -o ${{ github.workspace }}/update_summary.py https://raw.githubusercontent.com/mskcc-omics-workflows/modules/develop/.github/workflows/update_summary.py
-          python ${{ github.workspace }}/update_summary.py SUMMARY.md "* [${{ env.MD_PATH }}](${{ env.FEATURE_TYPE }}/${{ env.MD_PATH }}.md)" ${{ env.SUMMARY_TYPE }} > tmp_summary.md
+          python ${{ github.workspace }}/update_summary.py SUMMARY.md "* [${{ env.MD_NAME }}](${{ env.FEATURE_TYPE }}/${{ env.MD_PATH }}.md)" ${{ env.SUMMARY_TYPE }} > tmp_summary.md
           mv tmp_summary.md SUMMARY.md
       - name: Check for changes
         run: |
@@ -196,6 +203,6 @@ jobs:
         with:
           default_author: github_actions
           message: "add doc for ${{ matrix.tags }}"
-          add: '["**/*.md --force", "SUMMARY.md --force"]'
+          add: '["**/*.md", "SUMMARY.md"]'
           cwd: "./"
           push: --force

From ecec9801b212ae03f67ee8a8b5f1a5768b8437a6 Mon Sep 17 00:00:00 2001
From: buehlere <buehlere@mskcc.org>
Date: Tue, 20 Jan 2026 13:38:30 -0500
Subject: [PATCH 10/32] Update gitbook-sync.yml

---
 .github/workflows/gitbook-sync.yml | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/gitbook-sync.yml b/.github/workflows/gitbook-sync.yml
index 436f542a..add43467 100644
--- a/.github/workflows/gitbook-sync.yml
+++ b/.github/workflows/gitbook-sync.yml
@@ -198,11 +198,14 @@ jobs:
           if git diff --quiet; then
             echo "NO_CHANGES=true" >> $GITHUB_ENV
           fi
+      - name: Stage new files
+        run: |
+          git add "./${{ env.FEATURE_TYPE }}/${{ env.MD_PATH }}.md"
+          git add SUMMARY.md
       - uses: EndBug/add-and-commit@v9
-        if: env.NO_CHANGES != 'true'
         with:
           default_author: github_actions
           message: "add doc for ${{ matrix.tags }}"
-          add: '["**/*.md", "SUMMARY.md"]'
+          add: '["*/*.md --force", "SUMMARY.md --force"]'
           cwd: "./"
           push: --force

From 2ee566faa3ba57b6e4288f9ec07f1aa199c6f55f Mon Sep 17 00:00:00 2001
From: buehlere <buehlere@mskcc.org>
Date: Tue, 20 Jan 2026 13:52:39 -0500
Subject: [PATCH 11/32] Update update_summary.py

---
 .github/workflows/update_summary.py | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/update_summary.py b/.github/workflows/update_summary.py
index 8dc679cd..131321a5 100644
--- a/.github/workflows/update_summary.py
+++ b/.github/workflows/update_summary.py
@@ -35,24 +35,26 @@ def add_new_feature(sections: dict, new_feature: str, feature_type: str):
     new_list = []
     found = False
     if feature_type == "module":
-        # Check if the new feature is already in current summary file
         if new_feature.replace("\\", "") in [line.strip().replace("\\", "") for line in sections["Modules"]]:
             return sections
-        # Get module name from [] and remove the _ part.
-        # Check if the first part of the module name exists
-        new_feature_category = new_feature.split("]")[0].split("_")[0].replace("* [", "").replace("\\", "").strip()
+
+        # Use folder as category (first part before /)
+        if "/" in new_feature:
+            new_feature_category = new_feature.split("]")[0].split("/")[0].replace("* [", "").strip()
+        else:
+            new_feature_category = new_feature.split("]")[0].split("_")[0].replace("* [", "").strip()
+
         for line in sections["Modules"]:
             new_list.append(line)
             if f"[{new_feature_category}]" in line:
                 found = True
-                new_list.append(f"  {new_feature}\n")
+                new_list.append(f"  {new_feature}\n")  # two spaces indent for submodules
         if not found:
-            # If not found, put the new feature to the last
+            # If no parent exists, add at the end
             new_list.append(new_feature + "\n\n")
         sections["Modules"] = new_list
 
     if feature_type == "subworkflow" and new_feature not in sections["Subworkflows"]:
-        # There is no subset of subworkflow, so put the new feature to the last
         sections["Subworkflows"].append(new_feature + "\n")
     return sections
 

From 223e3de2828a55f414505e5476f935f8dbef13ce Mon Sep 17 00:00:00 2001
From: buehlere <buehlere@mskcc.org>
Date: Tue, 20 Jan 2026 14:00:43 -0500
Subject: [PATCH 12/32] Update update_summary.py

---
 .github/workflows/update_summary.py | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/update_summary.py b/.github/workflows/update_summary.py
index 131321a5..7fe90198 100644
--- a/.github/workflows/update_summary.py
+++ b/.github/workflows/update_summary.py
@@ -49,9 +49,15 @@ def add_new_feature(sections: dict, new_feature: str, feature_type: str):
             if f"[{new_feature_category}]" in line:
                 found = True
                 new_list.append(f"  {new_feature}\n")  # two spaces indent for submodules
-        if not found:
-            # If no parent exists, add at the end
-            new_list.append(new_feature + "\n\n")
+            if not found:
+                # If no parent exists, add parent + new feature at the end
+                if "/" in new_feature:
+                    parent_name = new_feature.split("]")[0].split("/")[0].replace("* [", "").strip()
+                    parent_line = f"* [{parent_name}](modules/{parent_name}/README.md)"
+                    new_list.append(parent_line + "\n")
+                    new_list.append(f"  {new_feature}\n")
+                else:
+                    new_list.append(new_feature + "\n\n")
         sections["Modules"] = new_list
 
     if feature_type == "subworkflow" and new_feature not in sections["Subworkflows"]:

From 63ef113085963093236f537f5965fbcb2d9ad974 Mon Sep 17 00:00:00 2001
From: buehlere <buehlere@mskcc.org>
Date: Tue, 20 Jan 2026 14:07:42 -0500
Subject: [PATCH 13/32] Update update_summary.py

---
 .github/workflows/update_summary.py | 19 ++++++++++---------
 1 file changed, 10 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/update_summary.py b/.github/workflows/update_summary.py
index 7fe90198..64472f92 100644
--- a/.github/workflows/update_summary.py
+++ b/.github/workflows/update_summary.py
@@ -49,15 +49,16 @@ def add_new_feature(sections: dict, new_feature: str, feature_type: str):
             if f"[{new_feature_category}]" in line:
                 found = True
                 new_list.append(f"  {new_feature}\n")  # two spaces indent for submodules
-            if not found:
-                # If no parent exists, add parent + new feature at the end
-                if "/" in new_feature:
-                    parent_name = new_feature.split("]")[0].split("/")[0].replace("* [", "").strip()
-                    parent_line = f"* [{parent_name}](modules/{parent_name}/README.md)"
-                    new_list.append(parent_line + "\n")
-                    new_list.append(f"  {new_feature}\n")
-                else:
-                    new_list.append(new_feature + "\n\n")
+
+        if not found:
+            if "/" in new_feature:
+                parent_name = new_feature.split("]")[0].split("/")[0].replace("* [", "").strip()
+                parent_line = f"* [{parent_name}](modules/{parent_name}/README.md)"
+                new_list.append(parent_line + "\n")
+                new_list.append(f"  {new_feature}\n")
+            else:
+                new_list.append(new_feature + "\n\n")
+
         sections["Modules"] = new_list
 
     if feature_type == "subworkflow" and new_feature not in sections["Subworkflows"]:

From a4559b90d80df94614d14f2070f9b5b5a482fa5e Mon Sep 17 00:00:00 2001
From: buehlere <buehlere@mskcc.org>
Date: Tue, 20 Jan 2026 14:45:58 -0500
Subject: [PATCH 14/32] Update update_summary.py

---
 .github/workflows/update_summary.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/update_summary.py b/.github/workflows/update_summary.py
index 64472f92..efc8061c 100644
--- a/.github/workflows/update_summary.py
+++ b/.github/workflows/update_summary.py
@@ -40,7 +40,10 @@ def add_new_feature(sections: dict, new_feature: str, feature_type: str):
 
         # Use folder as category (first part before /)
         if "/" in new_feature:
-            new_feature_category = new_feature.split("]")[0].split("/")[0].replace("* [", "").strip()
+            new_feature_category = (new_feature.split("]")[0]
+                            .replace("* [", "")
+                            .rsplit("/", 1)[0]
+                            .strip())
         else:
             new_feature_category = new_feature.split("]")[0].split("_")[0].replace("* [", "").strip()
 

From 0ce574ba799abec28ca75bfcb1b8eff4e16cd9e8 Mon Sep 17 00:00:00 2001
From: buehlere <buehlere@mskcc.org>
Date: Tue, 20 Jan 2026 15:21:23 -0500
Subject: [PATCH 15/32] Update update_summary.py

---
 .github/workflows/update_summary.py | 26 +++++++++++---------------
 1 file changed, 11 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/update_summary.py b/.github/workflows/update_summary.py
index efc8061c..db5fed76 100644
--- a/.github/workflows/update_summary.py
+++ b/.github/workflows/update_summary.py
@@ -38,14 +38,13 @@ def add_new_feature(sections: dict, new_feature: str, feature_type: str):
         if new_feature.replace("\\", "") in [line.strip().replace("\\", "") for line in sections["Modules"]]:
             return sections
 
-        # Use folder as category (first part before /)
-        if "/" in new_feature:
-            new_feature_category = (new_feature.split("]")[0]
-                            .replace("* [", "")
-                            .rsplit("/", 1)[0]
-                            .strip())
+        full_name = new_feature.split("]")[0].replace("* [", "").strip()
+
+        if "/" in full_name:
+            new_feature_category, display_name = full_name.split("/", 1)
+            new_feature = new_feature.replace(full_name, display_name)
         else:
-            new_feature_category = new_feature.split("]")[0].split("_")[0].replace("* [", "").strip()
+            new_feature_category = full_name
 
         for line in sections["Modules"]:
             new_list.append(line)
@@ -53,14 +52,11 @@ def add_new_feature(sections: dict, new_feature: str, feature_type: str):
                 found = True
                 new_list.append(f"  {new_feature}\n")  # two spaces indent for submodules
 
-        if not found:
-            if "/" in new_feature:
-                parent_name = new_feature.split("]")[0].split("/")[0].replace("* [", "").strip()
-                parent_line = f"* [{parent_name}](modules/{parent_name}/README.md)"
-                new_list.append(parent_line + "\n")
-                new_list.append(f"  {new_feature}\n")
-            else:
-                new_list.append(new_feature + "\n\n")
+        if not found and "/" in full_name:
+            parent_name = new_feature_category
+            parent_line = f"* [{parent_name}](modules/{parent_name}/README.md)"
+            new_list.append(parent_line + "\n")
+            new_list.append(f"  {new_feature}\n")
 
         sections["Modules"] = new_list
 

From 68aa0e8312cc0d58f530a195ec2a64206335be5b Mon Sep 17 00:00:00 2001
From: buehlere <buehlere@mskcc.org>
Date: Tue, 20 Jan 2026 15:35:25 -0500
Subject: [PATCH 16/32] fixing update summary

---
 .github/workflows/gitbook-sync.yml  | 10 +++--
 .github/workflows/update_summary.py | 60 +++++++++++++++++++----------
 2 files changed, 47 insertions(+), 23 deletions(-)

diff --git a/.github/workflows/gitbook-sync.yml b/.github/workflows/gitbook-sync.yml
index add43467..693043f8 100644
--- a/.github/workflows/gitbook-sync.yml
+++ b/.github/workflows/gitbook-sync.yml
@@ -123,8 +123,12 @@ jobs:
         id: replace_slash
         run: |
           FRAGMENT="${{ env.SW_NAME }}"
-          MD_PATH="${FRAGMENT}"   # keep subfolders for output file
-          MD_NAME="${MD_PATH}"    # <-- key change: preserve nested folder for display text
+          DIR="$(dirname "$FRAGMENT")"
+          BASE="$(basename "$FRAGMENT")"
+
+          MD_PATH="${DIR}/${DIR}_${BASE}"
+          MD_NAME="${FRAGMENT}"
+
           echo "MD_PATH=$MD_PATH" >> $GITHUB_ENV
           echo "MD_NAME=$MD_NAME" >> $GITHUB_ENV
       - uses: EndBug/add-and-commit@v9
@@ -191,7 +195,7 @@ jobs:
       - name: Add to SUMMARY for new features
         run: |
           curl -o ${{ github.workspace }}/update_summary.py https://raw.githubusercontent.com/mskcc-omics-workflows/modules/develop/.github/workflows/update_summary.py
-          python ${{ github.workspace }}/update_summary.py SUMMARY.md "* [${{ env.MD_NAME }}](${{ env.FEATURE_TYPE }}/${{ env.MD_PATH }}.md)" ${{ env.SUMMARY_TYPE }} > tmp_summary.md
+          python ${{ github.workspace }}/update_summary.py SUMMARY.md "[${{ env.MD_NAME }}](${{ env.FEATURE_TYPE }}/${{ env.MD_PATH }}.md)" ${{ env.SUMMARY_TYPE }} > tmp_summary.md
           mv tmp_summary.md SUMMARY.md
       - name: Check for changes
         run: |
diff --git a/.github/workflows/update_summary.py b/.github/workflows/update_summary.py
index db5fed76..58824d8e 100644
--- a/.github/workflows/update_summary.py
+++ b/.github/workflows/update_summary.py
@@ -1,6 +1,23 @@
 import sys
 from collections import defaultdict
 
+def build_module_entry(module_id: str):
+    """
+    module_id: fgbio/collectduplexseqmetrics
+    """
+    if "/" in module_id:
+        namespace, name = module_id.split("/", 1)
+        path = f"modules/{namespace}/{namespace}_{name}.md"
+        display = name
+        parent = namespace
+    else:
+        path = f"modules/{module_id}.md"
+        display = module_id
+        parent = None
+
+    entry = f"* [{display}]({path})"
+    return entry, parent
+
 
 def update_summary_old(origin: str, new_feature: str, feature_type: str):
     out_summary = ""
@@ -32,36 +49,39 @@ def load_summary_file(origin: str):
 
 
 def add_new_feature(sections: dict, new_feature: str, feature_type: str):
-    new_list = []
-    found = False
     if feature_type == "module":
-        if new_feature.replace("\\", "") in [line.strip().replace("\\", "") for line in sections["Modules"]]:
-            return sections
+        entry, parent = build_module_entry(new_feature)
 
-        full_name = new_feature.split("]")[0].replace("* [", "").strip()
+        # Avoid duplicates (exact match)
+        existing = [line.strip() for line in sections["Modules"]]
+        if entry in existing or f"  {entry}" in existing:
+            return sections
 
-        if "/" in full_name:
-            new_feature_category, display_name = full_name.split("/", 1)
-            new_feature = new_feature.replace(full_name, display_name)
-        else:
-            new_feature_category = full_name
+        new_list = []
+        inserted = False
 
         for line in sections["Modules"]:
             new_list.append(line)
-            if f"[{new_feature_category}]" in line:
-                found = True
-                new_list.append(f"  {new_feature}\n")  # two spaces indent for submodules
 
-        if not found and "/" in full_name:
-            parent_name = new_feature_category
-            parent_line = f"* [{parent_name}](modules/{parent_name}/README.md)"
-            new_list.append(parent_line + "\n")
-            new_list.append(f"  {new_feature}\n")
+            if parent and not inserted and line.startswith(f"* [{parent}]("):
+                new_list.append(f"  {entry}\n")
+                inserted = True
+
+        # Parent section doesn't exist yet
+        if parent and not inserted:
+            new_list.append(f"* [{parent}](modules/{parent}/README.md)\n")
+            new_list.append(f"  {entry}\n")
+
+        # Top-level module (no namespace)
+        if not parent:
+            new_list.append(entry + "\n")
 
         sections["Modules"] = new_list
 
-    if feature_type == "subworkflow" and new_feature not in sections["Subworkflows"]:
-        sections["Subworkflows"].append(new_feature + "\n")
+    elif feature_type == "subworkflow":
+        if new_feature + "\n" not in sections["Subworkflows"]:
+            sections["Subworkflows"].append(new_feature + "\n")
+
     return sections
 
 

From 2e8428b7dcf2be5c0b0155bcf8b784a9974eadf9 Mon Sep 17 00:00:00 2001
From: buehlere <buehlere@mskcc.org>
Date: Tue, 20 Jan 2026 15:47:34 -0500
Subject: [PATCH 17/32] Update gitbook-sync.yml

---
 .github/workflows/gitbook-sync.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/gitbook-sync.yml b/.github/workflows/gitbook-sync.yml
index 693043f8..b2bc2ea9 100644
--- a/.github/workflows/gitbook-sync.yml
+++ b/.github/workflows/gitbook-sync.yml
@@ -195,7 +195,7 @@ jobs:
       - name: Add to SUMMARY for new features
         run: |
           curl -o ${{ github.workspace }}/update_summary.py https://raw.githubusercontent.com/mskcc-omics-workflows/modules/develop/.github/workflows/update_summary.py
-          python ${{ github.workspace }}/update_summary.py SUMMARY.md "[${{ env.MD_NAME }}](${{ env.FEATURE_TYPE }}/${{ env.MD_PATH }}.md)" ${{ env.SUMMARY_TYPE }} > tmp_summary.md
+          python ${{ github.workspace }}/update_summary.py SUMMARY.md "${{ env.SW_NAME }}" ${{ env.SUMMARY_TYPE }} > tmp_summary.md
           mv tmp_summary.md SUMMARY.md
       - name: Check for changes
         run: |

From 80956132bfd5d83b1c05491398afc8650c42d866 Mon Sep 17 00:00:00 2001
From: buehlere <buehlere@mskcc.org>
Date: Tue, 20 Jan 2026 16:24:24 -0500
Subject: [PATCH 18/32] fixing summary

---
 .github/workflows/gitbook-sync.yml  | 6 ++++++
 .github/workflows/update_summary.py | 7 ++-----
 2 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/gitbook-sync.yml b/.github/workflows/gitbook-sync.yml
index b2bc2ea9..7ec18b22 100644
--- a/.github/workflows/gitbook-sync.yml
+++ b/.github/workflows/gitbook-sync.yml
@@ -137,6 +137,12 @@ jobs:
           message: "pull changes before adding doc for ${{ matrix.tags }}"
           pull: "--rebase"
           cwd: "./"
+      - name: Ensure output folder exists and debug
+        run: |
+          echo "MD_PATH=${MD_PATH}"
+          echo "Creating folder: ./modules/$(dirname ${MD_PATH})"
+          mkdir -p ./modules/$(dirname ${MD_PATH})
+          ls -la ./modules
       - name: Download convertor from yml to md
         run: |
           curl -o ${{ github.workspace }}/yaml_to_md.py https://raw.githubusercontent.com/mskcc-omics-workflows/yaml_to_md/0.0.3/yaml_to_md.py
diff --git a/.github/workflows/update_summary.py b/.github/workflows/update_summary.py
index 58824d8e..ba5c6a5c 100644
--- a/.github/workflows/update_summary.py
+++ b/.github/workflows/update_summary.py
@@ -2,17 +2,14 @@
 from collections import defaultdict
 
 def build_module_entry(module_id: str):
-    """
-    module_id: fgbio/collectduplexseqmetrics
-    """
     if "/" in module_id:
         namespace, name = module_id.split("/", 1)
+        display = f"{namespace}_{name}"
         path = f"modules/{namespace}/{namespace}_{name}.md"
-        display = name
         parent = namespace
     else:
-        path = f"modules/{module_id}.md"
         display = module_id
+        path = f"modules/{module_id}.md"
         parent = None
 
     entry = f"* [{display}]({path})"

From 45c1795b82ccebca9f82b266f7ff42d9eae3c7c5 Mon Sep 17 00:00:00 2001
From: buehlere <buehlere@mskcc.org>
Date: Tue, 20 Jan 2026 16:39:43 -0500
Subject: [PATCH 19/32] generate READMEs

---
 .github/workflows/gitbook-sync.yml  | 6 ++++++
 .github/workflows/update_summary.py | 4 ++--
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/gitbook-sync.yml b/.github/workflows/gitbook-sync.yml
index 7ec18b22..e0f89390 100644
--- a/.github/workflows/gitbook-sync.yml
+++ b/.github/workflows/gitbook-sync.yml
@@ -143,6 +143,12 @@ jobs:
           echo "Creating folder: ./modules/$(dirname ${MD_PATH})"
           mkdir -p ./modules/$(dirname ${MD_PATH})
           ls -la ./modules
+      - name: Ensure parent README exists
+        run: |
+          DIR="$(dirname "$MD_PATH")"
+          if [ ! -f "./modules/$DIR/README.md" ]; then
+            echo "# $DIR" > "./modules/$DIR/README.md"
+          fi
       - name: Download convertor from yml to md
         run: |
           curl -o ${{ github.workspace }}/yaml_to_md.py https://raw.githubusercontent.com/mskcc-omics-workflows/yaml_to_md/0.0.3/yaml_to_md.py
diff --git a/.github/workflows/update_summary.py b/.github/workflows/update_summary.py
index ba5c6a5c..a85677a7 100644
--- a/.github/workflows/update_summary.py
+++ b/.github/workflows/update_summary.py
@@ -60,9 +60,9 @@ def add_new_feature(sections: dict, new_feature: str, feature_type: str):
         for line in sections["Modules"]:
             new_list.append(line)
 
-            if parent and not inserted and line.startswith(f"* [{parent}]("):
+            if parent and not inserted:
+                new_list.append(f"* [{parent}](modules/{parent}/README.md)\n")
                 new_list.append(f"  {entry}\n")
-                inserted = True
 
         # Parent section doesn't exist yet
         if parent and not inserted:

From 8b19b9c0b3a842024c80def56c2f92b99880df6d Mon Sep 17 00:00:00 2001
From: buehlere <buehlere@mskcc.org>
Date: Tue, 20 Jan 2026 16:52:25 -0500
Subject: [PATCH 20/32] update summary

---
 .github/workflows/gitbook-sync.yml  |  2 +-
 .github/workflows/update_summary.py | 11 ++---------
 2 files changed, 3 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/gitbook-sync.yml b/.github/workflows/gitbook-sync.yml
index e0f89390..9e1a51a3 100644
--- a/.github/workflows/gitbook-sync.yml
+++ b/.github/workflows/gitbook-sync.yml
@@ -117,7 +117,7 @@ jobs:
         run: |
           MATRIX_FRAGMENT="${{ matrix.tags }}"
           TEMP_NAME=$(echo $MATRIX_FRAGMENT | sed 's/subworkflows\///g')
-          SW_NAME=$(echo $TEMP_NAME | sed 's/modules\///g')
+          SW_NAME=$(echo $TEMP_NAME | sed 's/modules\///g' | sed 's/\//\//')
           echo "SW_NAME=$SW_NAME" >> $GITHUB_ENV
       - name: Rename md file
         id: replace_slash
diff --git a/.github/workflows/update_summary.py b/.github/workflows/update_summary.py
index a85677a7..ba6b4cf6 100644
--- a/.github/workflows/update_summary.py
+++ b/.github/workflows/update_summary.py
@@ -15,7 +15,6 @@ def build_module_entry(module_id: str):
     entry = f"* [{display}]({path})"
     return entry, parent
 
-
 def update_summary_old(origin: str, new_feature: str, feature_type: str):
     out_summary = ""
     with open(origin, 'r') as f:
@@ -48,8 +47,6 @@ def load_summary_file(origin: str):
 def add_new_feature(sections: dict, new_feature: str, feature_type: str):
     if feature_type == "module":
         entry, parent = build_module_entry(new_feature)
-
-        # Avoid duplicates (exact match)
         existing = [line.strip() for line in sections["Modules"]]
         if entry in existing or f"  {entry}" in existing:
             return sections
@@ -59,17 +56,14 @@ def add_new_feature(sections: dict, new_feature: str, feature_type: str):
 
         for line in sections["Modules"]:
             new_list.append(line)
-
-            if parent and not inserted:
-                new_list.append(f"* [{parent}](modules/{parent}/README.md)\n")
+            if parent and not inserted and line.startswith(f"* [{parent}]("):
                 new_list.append(f"  {entry}\n")
+                inserted = True
 
-        # Parent section doesn't exist yet
         if parent and not inserted:
             new_list.append(f"* [{parent}](modules/{parent}/README.md)\n")
             new_list.append(f"  {entry}\n")
 
-        # Top-level module (no namespace)
         if not parent:
             new_list.append(entry + "\n")
 
@@ -81,7 +75,6 @@ def add_new_feature(sections: dict, new_feature: str, feature_type: str):
 
     return sections
 
-
 def rebuild_summary(origin: str, new_feature: str, feature_type: str):
     # Load current summary file to dictionary
     sections = load_summary_file(origin=origin)

From b2ac3a4222d66569d9f9574f1d21527e64434539 Mon Sep 17 00:00:00 2001
From: buehlere <buehlere@mskcc.org>
Date: Tue, 20 Jan 2026 16:57:11 -0500
Subject: [PATCH 21/32] Update update_summary.py

---
 .github/workflows/update_summary.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/update_summary.py b/.github/workflows/update_summary.py
index ba6b4cf6..4ed70faf 100644
--- a/.github/workflows/update_summary.py
+++ b/.github/workflows/update_summary.py
@@ -48,19 +48,21 @@ def add_new_feature(sections: dict, new_feature: str, feature_type: str):
     if feature_type == "module":
         entry, parent = build_module_entry(new_feature)
         existing = [line.strip() for line in sections["Modules"]]
+
         if entry in existing or f"  {entry}" in existing:
             return sections
 
         new_list = []
+        parent_exists = any(line.startswith(f"* [{parent}](") for line in existing)
         inserted = False
 
         for line in sections["Modules"]:
             new_list.append(line)
-            if parent and not inserted and line.startswith(f"* [{parent}]("):
+            if parent and parent_exists and not inserted and line.startswith(f"* [{parent}]("):
                 new_list.append(f"  {entry}\n")
                 inserted = True
 
-        if parent and not inserted:
+        if parent and not parent_exists:
             new_list.append(f"* [{parent}](modules/{parent}/README.md)\n")
             new_list.append(f"  {entry}\n")
 
@@ -75,6 +77,7 @@ def add_new_feature(sections: dict, new_feature: str, feature_type: str):
 
     return sections
 
+
 def rebuild_summary(origin: str, new_feature: str, feature_type: str):
     # Load current summary file to dictionary
     sections = load_summary_file(origin=origin)

From 0eff8d2e6de0d0e7fd132143954d2a6c55ee4f25 Mon Sep 17 00:00:00 2001
From: buehlere <buehlere@mskcc.org>
Date: Tue, 20 Jan 2026 17:03:59 -0500
Subject: [PATCH 22/32] Update update_summary.py

---
 .github/workflows/update_summary.py | 88 ++++++++++++-----------------
 1 file changed, 35 insertions(+), 53 deletions(-)

diff --git a/.github/workflows/update_summary.py b/.github/workflows/update_summary.py
index 4ed70faf..c7586f61 100644
--- a/.github/workflows/update_summary.py
+++ b/.github/workflows/update_summary.py
@@ -15,87 +15,69 @@ def build_module_entry(module_id: str):
     entry = f"* [{display}]({path})"
     return entry, parent
 
-def update_summary_old(origin: str, new_feature: str, feature_type: str):
-    out_summary = ""
-    with open(origin, 'r') as f:
-        for line in f.readlines():
-            if feature_type == "module" and line.startswith("## Subworkflows") and new_feature not in out_summary:
-                out_summary += new_feature + '\n\n'
-            if line.strip():
-                out_summary += line
-    if feature_type == "subworkflow" and new_feature not in out_summary:
-        out_summary += new_feature
-    return out_summary
-
-
 def load_summary_file(origin: str):
-    # Read the summary file to dict
-    # keys, "Table of contents", "Modules", "Subworkflows"
-    # values are list of lines
     sections = defaultdict(list)
     current_section = None
-    with open(origin, "r") as file_read:
-        for row in file_read:
+    with open(origin, "r") as f:
+        for row in f:
             if row.startswith("#"):
                 current_section = row.replace("#", "").strip()
                 continue
             if row.strip():
-                sections[current_section].append(row)
+                sections[current_section].append(row.rstrip("\n"))
     return sections
 
-
 def add_new_feature(sections: dict, new_feature: str, feature_type: str):
     if feature_type == "module":
         entry, parent = build_module_entry(new_feature)
-        existing = [line.strip() for line in sections["Modules"]]
+        existing = sections["Modules"]
 
-        if entry in existing or f"  {entry}" in existing:
-            return sections
-
-        new_list = []
-        parent_exists = any(line.startswith(f"* [{parent}](") for line in existing)
-        inserted = False
+        parent_header = f"* [{parent}](modules/{parent}/README.md)" if parent else None
+        child_entry = f"  {entry}" if parent else entry
 
-        for line in sections["Modules"]:
-            new_list.append(line)
-            if parent and parent_exists and not inserted and line.startswith(f"* [{parent}]("):
-                new_list.append(f"  {entry}\n")
-                inserted = True
+        parent_exists = parent and any(line.strip() == parent_header for line in existing)
+        child_exists = any(line.strip() == child_entry.strip() for line in existing)
 
-        if parent and not parent_exists:
-            new_list.append(f"* [{parent}](modules/{parent}/README.md)\n")
-            new_list.append(f"  {entry}\n")
+        if child_exists:
+            return sections
 
-        if not parent:
-            new_list.append(entry + "\n")
+        new_list = []
+        if parent:
+            inserted = False
+            for line in existing:
+                new_list.append(line)
+                if not inserted and line.strip() == parent_header:
+                    new_list.append(child_entry)
+                    inserted = True
+            if not parent_exists:
+                new_list.append(parent_header)
+                new_list.append(child_entry)
+        else:
+            new_list = existing + [entry]
 
         sections["Modules"] = new_list
 
     elif feature_type == "subworkflow":
-        if new_feature + "\n" not in sections["Subworkflows"]:
-            sections["Subworkflows"].append(new_feature + "\n")
+        if new_feature not in sections["Subworkflows"]:
+            sections["Subworkflows"].append(new_feature)
 
     return sections
 
-
 def rebuild_summary(origin: str, new_feature: str, feature_type: str):
-    # Load current summary file to dictionary
-    sections = load_summary_file(origin=origin)
-    # Add the new feature to summary file dict
-    updated_sections = add_new_feature(
-        sections=sections, new_feature=new_feature, feature_type=feature_type)
-    # Output the updated summary file to string
+    sections = load_summary_file(origin)
+    sections = add_new_feature(sections, new_feature, feature_type)
+
     out_summary = "# Table of contents\n\n"
-    for line in updated_sections["Table of contents"]:
-        out_summary += line
+    for line in sections["Table of contents"]:
+        out_summary += f"{line}\n"
     out_summary += "\n## Modules\n\n"
-    for line in updated_sections["Modules"]:
-        out_summary += line
+    for line in sections["Modules"]:
+        out_summary += f"{line}\n"
     out_summary += "\n## Subworkflows\n\n"
-    for line in updated_sections["Subworkflows"]:
-        out_summary += line
-    return out_summary
+    for line in sections["Subworkflows"]:
+        out_summary += f"{line}\n"
 
+    return out_summary
 
 if __name__ == "__main__":
     origin_summary = sys.argv[1]

From fcf4fe93979318723fc32a4a15c198859add068f Mon Sep 17 00:00:00 2001
From: buehlere <buehlere@mskcc.org>
Date: Tue, 20 Jan 2026 17:11:21 -0500
Subject: [PATCH 23/32] Update update_summary.py

---
 .github/workflows/update_summary.py | 44 ++++++++++++++---------------
 1 file changed, 22 insertions(+), 22 deletions(-)

diff --git a/.github/workflows/update_summary.py b/.github/workflows/update_summary.py
index c7586f61..e0a01524 100644
--- a/.github/workflows/update_summary.py
+++ b/.github/workflows/update_summary.py
@@ -30,38 +30,38 @@ def load_summary_file(origin: str):
 def add_new_feature(sections: dict, new_feature: str, feature_type: str):
     if feature_type == "module":
         entry, parent = build_module_entry(new_feature)
-        existing = sections["Modules"]
+        module_lines = sections["Modules"]
+        existing_lines = [line.rstrip("\n") for line in module_lines]
 
-        parent_header = f"* [{parent}](modules/{parent}/README.md)" if parent else None
-        child_entry = f"  {entry}" if parent else entry
-
-        parent_exists = parent and any(line.strip() == parent_header for line in existing)
-        child_exists = any(line.strip() == child_entry.strip() for line in existing)
-
-        if child_exists:
+        if entry in existing_lines or f"  {entry}" in existing_lines:
             return sections
 
-        new_list = []
         if parent:
+            parent_line = f"* [{parent}](modules/{parent}/README.md)"
+            parent_present = any(line.strip() == parent_line for line in existing_lines)
+            new_module_lines = []
             inserted = False
-            for line in existing:
-                new_list.append(line)
-                if not inserted and line.strip() == parent_header:
-                    new_list.append(child_entry)
+
+            for line in module_lines:
+                new_module_lines.append(line)
+                if parent_present and not inserted and line.strip() == parent_line:
+                    new_module_lines.append(f"  {entry}\n")
                     inserted = True
-            if not parent_exists:
-                new_list.append(parent_header)
-                new_list.append(child_entry)
-        else:
-            new_list = existing + [entry]
 
-        sections["Modules"] = new_list
+            if not parent_present:
+                new_module_lines.append(f"{parent_line}\n")
+                new_module_lines.append(f"  {entry}\n")
+
+            sections["Modules"] = new_module_lines
+
+        else:
+            module_lines.append(f"{entry}\n")
+            sections["Modules"] = module_lines
 
     elif feature_type == "subworkflow":
-        if new_feature not in sections["Subworkflows"]:
-            sections["Subworkflows"].append(new_feature)
+        if new_feature + "\n" not in sections["Subworkflows"]:
+            sections["Subworkflows"].append(new_feature + "\n")
 
-    return sections
 
 def rebuild_summary(origin: str, new_feature: str, feature_type: str):
     sections = load_summary_file(origin)

From b8c64426e09e854f37034136a6965b0b3afada09 Mon Sep 17 00:00:00 2001
From: buehlere <buehlere@mskcc.org>
Date: Tue, 20 Jan 2026 17:17:46 -0500
Subject: [PATCH 24/32] Update update_summary.py

---
 .github/workflows/update_summary.py | 44 +++++++++++++----------------
 1 file changed, 19 insertions(+), 25 deletions(-)

diff --git a/.github/workflows/update_summary.py b/.github/workflows/update_summary.py
index e0a01524..4ed08673 100644
--- a/.github/workflows/update_summary.py
+++ b/.github/workflows/update_summary.py
@@ -11,7 +11,6 @@ def build_module_entry(module_id: str):
         display = module_id
         path = f"modules/{module_id}.md"
         parent = None
-
     entry = f"* [{display}]({path})"
     return entry, parent
 
@@ -31,37 +30,33 @@ def add_new_feature(sections: dict, new_feature: str, feature_type: str):
     if feature_type == "module":
         entry, parent = build_module_entry(new_feature)
         module_lines = sections["Modules"]
-        existing_lines = [line.rstrip("\n") for line in module_lines]
 
-        if entry in existing_lines or f"  {entry}" in existing_lines:
+        # Check if entry already exists
+        existing_entries = [line.strip() for line in module_lines]
+        if entry in existing_entries or f"  {entry}" in existing_entries:
             return sections
 
         if parent:
+            # Check if parent already exists
             parent_line = f"* [{parent}](modules/{parent}/README.md)"
-            parent_present = any(line.strip() == parent_line for line in existing_lines)
-            new_module_lines = []
-            inserted = False
-
-            for line in module_lines:
-                new_module_lines.append(line)
-                if parent_present and not inserted and line.strip() == parent_line:
-                    new_module_lines.append(f"  {entry}\n")
-                    inserted = True
-
-            if not parent_present:
-                new_module_lines.append(f"{parent_line}\n")
-                new_module_lines.append(f"  {entry}\n")
-
-            sections["Modules"] = new_module_lines
-
+            parent_indices = [i for i, line in enumerate(module_lines) if line.strip() == parent_line]
+            if parent_indices:
+                # Insert under existing parent
+                index = parent_indices[-1] + 1
+                module_lines.insert(index, f"  {entry}")
+            else:
+                # Add parent at end if missing, then child
+                module_lines.append(parent_line)
+                module_lines.append(f"  {entry}")
         else:
-            module_lines.append(f"{entry}\n")
-            sections["Modules"] = module_lines
+            module_lines.append(entry)
 
-    elif feature_type == "subworkflow":
-        if new_feature + "\n" not in sections["Subworkflows"]:
-            sections["Subworkflows"].append(new_feature + "\n")
+        sections["Modules"] = module_lines
 
+    elif feature_type == "subworkflow":
+        if new_feature not in sections["Subworkflows"]:
+            sections["Subworkflows"].append(new_feature)
+    return sections
 
 def rebuild_summary(origin: str, new_feature: str, feature_type: str):
     sections = load_summary_file(origin)
@@ -76,7 +71,6 @@ def rebuild_summary(origin: str, new_feature: str, feature_type: str):
     out_summary += "\n## Subworkflows\n\n"
     for line in sections["Subworkflows"]:
         out_summary += f"{line}\n"
-
     return out_summary
 
 if __name__ == "__main__":

From 7c5e35cd0517428c3377289d09a21f8ed6ac854c Mon Sep 17 00:00:00 2001
From: buehlere <buehlere@mskcc.org>
Date: Tue, 20 Jan 2026 17:31:07 -0500
Subject: [PATCH 25/32] Update gitbook-sync.yml

---
 .github/workflows/gitbook-sync.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/gitbook-sync.yml b/.github/workflows/gitbook-sync.yml
index 9e1a51a3..f59ae7d8 100644
--- a/.github/workflows/gitbook-sync.yml
+++ b/.github/workflows/gitbook-sync.yml
@@ -206,7 +206,7 @@ jobs:
             ${{ env.SUBWORKFLOW }}
       - name: Add to SUMMARY for new features
         run: |
-          curl -o ${{ github.workspace }}/update_summary.py https://raw.githubusercontent.com/mskcc-omics-workflows/modules/develop/.github/workflows/update_summary.py
+          cp .github/workflows/update_summary.py /home/runner/work/modules/modules/update_summary.py
           python ${{ github.workspace }}/update_summary.py SUMMARY.md "${{ env.SW_NAME }}" ${{ env.SUMMARY_TYPE }} > tmp_summary.md
           mv tmp_summary.md SUMMARY.md
       - name: Check for changes

From 3a20429d7c0e2caa3b686dceb43fa025fe833001 Mon Sep 17 00:00:00 2001
From: buehlere <buehlere@mskcc.org>
Date: Tue, 20 Jan 2026 17:39:07 -0500
Subject: [PATCH 26/32] Update gitbook-sync.yml

---
 .github/workflows/gitbook-sync.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/gitbook-sync.yml b/.github/workflows/gitbook-sync.yml
index f59ae7d8..a08434d9 100644
--- a/.github/workflows/gitbook-sync.yml
+++ b/.github/workflows/gitbook-sync.yml
@@ -206,7 +206,7 @@ jobs:
             ${{ env.SUBWORKFLOW }}
       - name: Add to SUMMARY for new features
         run: |
-          cp .github/workflows/update_summary.py /home/runner/work/modules/modules/update_summary.py
+          curl -o ${{ github.workspace }}/update_summary.py https://raw.githubusercontent.com/mskcc-omics-workflows/modules/release/0.2.4/.github/workflows/update_summary.py
           python ${{ github.workspace }}/update_summary.py SUMMARY.md "${{ env.SW_NAME }}" ${{ env.SUMMARY_TYPE }} > tmp_summary.md
           mv tmp_summary.md SUMMARY.md
       - name: Check for changes

From 9b9742425ba3066baa903fa43dcafd4b1b5a9a99 Mon Sep 17 00:00:00 2001
From: buehlere <buehlere@mskcc.org>
Date: Wed, 21 Jan 2026 10:07:00 -0500
Subject: [PATCH 27/32] sub-tools vs no sub-tools

---
 .github/workflows/gitbook-sync.yml | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/gitbook-sync.yml b/.github/workflows/gitbook-sync.yml
index a08434d9..726a8990 100644
--- a/.github/workflows/gitbook-sync.yml
+++ b/.github/workflows/gitbook-sync.yml
@@ -123,10 +123,15 @@ jobs:
         id: replace_slash
         run: |
           FRAGMENT="${{ env.SW_NAME }}"
-          DIR="$(dirname "$FRAGMENT")"
-          BASE="$(basename "$FRAGMENT")"
+          if [[ "$FRAGMENT" == *"/"* ]]; then
+            DIR="$(dirname "$FRAGMENT")"
+            BASE="$(basename "$FRAGMENT")"
+            MD_PATH="${DIR}/${DIR}_${BASE}"
+          else
+            MD_PATH="$FRAGMENT"
+          fi
 
-          MD_PATH="${DIR}/${DIR}_${BASE}"
+          echo "MD_PATH=$MD_PATH" >> $GITHUB_ENV
           MD_NAME="${FRAGMENT}"
 
           echo "MD_PATH=$MD_PATH" >> $GITHUB_ENV

From 384c73224c26ac3c226d8bdf4db78708ed9e8174 Mon Sep 17 00:00:00 2001
From: buehlere <buehlere@mskcc.org>
Date: Wed, 21 Jan 2026 10:38:46 -0500
Subject: [PATCH 28/32] Update gitbook-sync.yml

---
 .github/workflows/gitbook-sync.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/gitbook-sync.yml b/.github/workflows/gitbook-sync.yml
index 726a8990..08faec64 100644
--- a/.github/workflows/gitbook-sync.yml
+++ b/.github/workflows/gitbook-sync.yml
@@ -227,6 +227,5 @@ jobs:
         with:
           default_author: github_actions
           message: "add doc for ${{ matrix.tags }}"
-          add: '["*/*.md --force", "SUMMARY.md --force"]'
           cwd: "./"
           push: --force

From 7e3492115f933c0fa77eb1b3b1b8cff4b341f581 Mon Sep 17 00:00:00 2001
From: buehlere <buehlere@mskcc.org>
Date: Wed, 21 Jan 2026 10:56:59 -0500
Subject: [PATCH 29/32] Update gitbook-sync.yml

---
 .github/workflows/gitbook-sync.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/gitbook-sync.yml b/.github/workflows/gitbook-sync.yml
index 08faec64..6825c2e3 100644
--- a/.github/workflows/gitbook-sync.yml
+++ b/.github/workflows/gitbook-sync.yml
@@ -90,6 +90,7 @@ jobs:
     needs: [pytest-changes, nf-test-changes]
     strategy:
       fail-fast: false
+      max-parallel: 1
       matrix:
         tags:
           [

From 83e2dc87cf4d5975920c98c6dc8971d03c0dd6b7 Mon Sep 17 00:00:00 2001
From: John Orgera <65687576+johnoooh@users.noreply.github.com>
Date: Fri, 6 Feb 2026 16:12:06 -0500
Subject: [PATCH 30/32] Fix FASTA header to preserve mutation identity through
 netMHCpan

Prepend identifier_key (e.g. 2CAE_MC) to MUT and WT FASTA headers so
that netMHCpan Identity column retains the encoded mutation type needed
by generate_input.py for downstream neoantigen input generation.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
---
 .../1.2/resources/usr/bin/generateMutFasta.py                 | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/msk/generatemutfasta/1.2/resources/usr/bin/generateMutFasta.py b/modules/msk/generatemutfasta/1.2/resources/usr/bin/generateMutFasta.py
index ed576e38..6d309efe 100755
--- a/modules/msk/generatemutfasta/1.2/resources/usr/bin/generateMutFasta.py
+++ b/modules/msk/generatemutfasta/1.2/resources/usr/bin/generateMutFasta.py
@@ -131,9 +131,9 @@ def main():
                     + " Alt:"
                     + str(mut.maf_row["Tumor_Seq_Allele2"])
                 )
-                out_fa.write(">" + id_string + "\n")
+                out_fa.write(">" + mut.identifier_key + " " + id_string + "\n")
                 out_fa.write(mut.mt_altered_aa + "\n")
-                out_WT_fa.write(">" + id_string + "\n")
+                out_WT_fa.write(">" + mut.identifier_key + " " + id_string + "\n")
                 out_WT_fa.write(mut.wt_altered_aa + "\n")
 
                 ### write out WT/MT CDS + AA for debugging purposes

From 81acf713656392b60b394c9e549389c3fa622f6b Mon Sep 17 00:00:00 2001
From: John Orgera <65687576+johnoooh@users.noreply.github.com>
Date: Fri, 6 Feb 2026 16:24:55 -0500
Subject: [PATCH 31/32] Update generatemutfasta/1.2 test snapshots for
 identifier_key header

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
---
 .../generatemutfasta/1.2/tests/main.nf.test.snap   | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/modules/msk/generatemutfasta/1.2/tests/main.nf.test.snap b/modules/msk/generatemutfasta/1.2/tests/main.nf.test.snap
index 60c19112..ee0f19e9 100644
--- a/modules/msk/generatemutfasta/1.2/tests/main.nf.test.snap
+++ b/modules/msk/generatemutfasta/1.2/tests/main.nf.test.snap
@@ -10,7 +10,7 @@
                         "id": "test",
                         "single_end": false
                     },
-                    "test.MUT.sequences.fa:md5,dff338ec438ac75aa674b64ea8e26544"
+                    "test.MUT.sequences.fa:md5,5c86389b9b56eaa6f9aeb9391c7dea9d"
                 ]
             ],
             [
@@ -19,16 +19,16 @@
                         "id": "test",
                         "single_end": false
                     },
-                    "test.WT.sequences.fa:md5,51415a40a725a16eaa8f5c51fa43799e"
+                    "test.WT.sequences.fa:md5,02e4c68d88d856416b40cef391049211"
                 ]
             ],
             "test_generate_mut_fasta.log"
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.10.2"
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2026-01-28T15:30:02.572804474"
+        "timestamp": "2026-02-06T16:24:15.454193"
     },
     "generatemutfasta_1.2 - maf - fasta - stub": {
         "content": [
@@ -96,9 +96,9 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2025-12-18T16:08:27.448965"
+        "timestamp": "2026-02-06T16:24:30.641252"
     }
 }
\ No newline at end of file

From 0e81776d00ecd79b6cc5edd8f6b607d1a6b21c91 Mon Sep 17 00:00:00 2001
From: John Orgera <65687576+johnoooh@users.noreply.github.com>
Date: Mon, 9 Feb 2026 15:25:32 -0500
Subject: [PATCH 32/32] Use identifier_key with _M/_W suffix as sole FASTA
 header

netMHCpan concatenates the entire FASTA header (replacing spaces with
underscores) and truncates to 15 characters. The previous commit
included transcript and variant info after identifier_key, producing
truncated Identity values that didn't match generate_input.py's
mutation_dict keys. Restore the original format of >identifier_key_M
and >identifier_key_W to keep identities under 15 chars.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
---
 .../1.2/resources/usr/bin/generateMutFasta.py   | 17 ++---------------
 .../1.2/tests/main.nf.test.snap                 |  8 ++++----
 2 files changed, 6 insertions(+), 19 deletions(-)

diff --git a/modules/msk/generatemutfasta/1.2/resources/usr/bin/generateMutFasta.py b/modules/msk/generatemutfasta/1.2/resources/usr/bin/generateMutFasta.py
index 6d309efe..1afc95ce 100755
--- a/modules/msk/generatemutfasta/1.2/resources/usr/bin/generateMutFasta.py
+++ b/modules/msk/generatemutfasta/1.2/resources/usr/bin/generateMutFasta.py
@@ -118,22 +118,9 @@ def main():
                 n_missing_tx_id += 1
 
             if len(mut.mt_altered_aa) > 5:
-                id_string = (
-                    str(mut.maf_row["Transcript_ID"])
-                    + " Variant "
-                    + str(mut.maf_row["Chromosome"])
-                    + ":"
-                    + str(mut.maf_row["Start_Position"])
-                    + "-"
-                    + str(mut.maf_row["End_Position"])
-                    + " Ref:"
-                    + str(mut.maf_row["Reference_Allele"])
-                    + " Alt:"
-                    + str(mut.maf_row["Tumor_Seq_Allele2"])
-                )
-                out_fa.write(">" + mut.identifier_key + " " + id_string + "\n")
+                out_fa.write(">" + mut.identifier_key + "_M\n")
                 out_fa.write(mut.mt_altered_aa + "\n")
-                out_WT_fa.write(">" + mut.identifier_key + " " + id_string + "\n")
+                out_WT_fa.write(">" + mut.identifier_key + "_W\n")
                 out_WT_fa.write(mut.wt_altered_aa + "\n")
 
                 ### write out WT/MT CDS + AA for debugging purposes
diff --git a/modules/msk/generatemutfasta/1.2/tests/main.nf.test.snap b/modules/msk/generatemutfasta/1.2/tests/main.nf.test.snap
index ee0f19e9..cc9060bc 100644
--- a/modules/msk/generatemutfasta/1.2/tests/main.nf.test.snap
+++ b/modules/msk/generatemutfasta/1.2/tests/main.nf.test.snap
@@ -10,7 +10,7 @@
                         "id": "test",
                         "single_end": false
                     },
-                    "test.MUT.sequences.fa:md5,5c86389b9b56eaa6f9aeb9391c7dea9d"
+                    "test.MUT.sequences.fa:md5,3d2ff66590a4329f9a24e03bdf84e0ab"
                 ]
             ],
             [
@@ -19,7 +19,7 @@
                         "id": "test",
                         "single_end": false
                     },
-                    "test.WT.sequences.fa:md5,02e4c68d88d856416b40cef391049211"
+                    "test.WT.sequences.fa:md5,4bfcfc4d29d01ddc4108f39350936228"
                 ]
             ],
             "test_generate_mut_fasta.log"
@@ -28,7 +28,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.5"
         },
-        "timestamp": "2026-02-06T16:24:15.454193"
+        "timestamp": "2026-02-09T15:03:37.884362"
     },
     "generatemutfasta_1.2 - maf - fasta - stub": {
         "content": [
@@ -99,6 +99,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.5"
         },
-        "timestamp": "2026-02-06T16:24:30.641252"
+        "timestamp": "2026-02-09T15:03:51.569621"
     }
 }
\ No newline at end of file