From 5f9a3f259d9fb92d8430b390e9ebe9fd4531b67e Mon Sep 17 00:00:00 2001
From: znorgaard <zach@fulcrumgenomics.com>
Date: Wed, 27 May 2026 14:03:19 -0700
Subject: [PATCH] docs: regenerate nf-fgsv example for fg-labs org move
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

The nf-fgsv repository moved from the `fulcrumgenomics` org to `fg-labs`, so
the example's repository and source links pointed at the old (now-redirected)
location. Regenerate the example with current nf-docs against
`fg-labs/nf-fgsv` so the links are correct and the output reflects the
pipeline's current docs (typed records, expanded `--input` schema, workflow
docstring). The `fulcrumgenomics/fgsv` tool links are unchanged — that
repository did not move.
---
 docs/examples/nf-fgsv/index.html             | 338 +++++++------------
 docs/examples/nf-fgsv/json/pipeline-api.json | 128 ++++---
 docs/examples/nf-fgsv/markdown/index.md      |   4 +-
 docs/examples/nf-fgsv/markdown/inputs.md     |   9 +-
 docs/examples/nf-fgsv/markdown/processes.md  |  42 +--
 docs/examples/nf-fgsv/markdown/workflows.md  |  15 +-
 docs/examples/nf-fgsv/table/README.md        |  44 +--
 docs/examples/nf-fgsv/yaml/pipeline-api.yaml | 151 +++++----
 8 files changed, 326 insertions(+), 405 deletions(-)

diff --git a/docs/examples/nf-fgsv/index.html b/docs/examples/nf-fgsv/index.html
index 0b8b4e3..a98636b 100644
--- a/docs/examples/nf-fgsv/index.html
+++ b/docs/examples/nf-fgsv/index.html
@@ -922,6 +922,7 @@
       class="fixed top-0 left-0 right-0 h-14 bg-white border-b border-slate-200 z-50 flex items-center px-4 md:px-6"
     >
       <!-- Mobile menu button -->
+      
       <button
         id="mobile-menu-btn"
         class="md:hidden mr-3 p-1.5 rounded hover:bg-slate-100 transition-colors"
@@ -936,6 +937,7 @@
           ></path>
         </svg>
       </button>
+      
 
       <!-- Left: Organization/user avatar (GitHub only) and pipeline name -->
       <a
@@ -946,7 +948,7 @@
         
         <img
           id="repo-avatar"
-          src="data:image/png;base64,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"
+          src="data:image/png;base64,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"
           alt="Organization avatar"
           class="w-6 h-6 rounded mr-2"
         />
@@ -962,6 +964,7 @@ <h1 class="text-lg font-bold text-primary">nf-fgsv workflow parameters</h1>
       <!-- Right: Search and GitHub link -->
       <div class="ml-auto flex items-center gap-4">
         <!-- Search (hidden on mobile, shown in mobile menu) -->
+        
         <div class="relative hidden md:block">
           <input
             type="text"
@@ -984,6 +987,7 @@ <h1 class="text-lg font-bold text-primary">nf-fgsv workflow parameters</h1>
             </svg>
           </button>
         </div>
+        
 
         <!-- Dark mode toggle -->
         <button
@@ -1015,7 +1019,7 @@ <h1 class="text-lg font-bold text-primary">nf-fgsv workflow parameters</h1>
         <!-- Repository link -->
         
         <a
-          href="https://github.com/fulcrumgenomics/nf-fgsv"
+          href="https://github.com/fg-labs/nf-fgsv"
           target="_blank"
           rel="noopener noreferrer"
           class="flex items-center gap-1.5 text-sm text-slate-600 hover:text-primary transition-colors"
@@ -1037,6 +1041,7 @@ <h1 class="text-lg font-bold text-primary">nf-fgsv workflow parameters</h1>
       </div>
     </header>
 
+    
     <!-- Mobile Navigation Drawer -->
     <div
       id="mobile-menu-overlay"
@@ -1066,6 +1071,7 @@ <h1 class="text-lg font-bold text-primary">nf-fgsv workflow parameters</h1>
       </div>
 
       <!-- Mobile Navigation Links -->
+      
       <div id="mobile-main-nav">
         <nav class="p-4 border-b border-slate-200">
           <!-- Search link for mobile -->
@@ -1147,7 +1153,7 @@ <h1 class="text-lg font-bold text-primary">nf-fgsv workflow parameters</h1>
           
           <div class="mt-6 pt-4 border-t border-slate-200">
             <a
-              href="https://github.com/fulcrumgenomics/nf-fgsv"
+              href="https://github.com/fg-labs/nf-fgsv"
               target="_blank"
               rel="noopener noreferrer"
               class="flex items-center gap-2 px-3 py-2 text-sm text-slate-600 hover:text-primary transition-colors"
@@ -1166,6 +1172,7 @@ <h1 class="text-lg font-bold text-primary">nf-fgsv workflow parameters</h1>
           
         </nav>
       </div>
+      
 
       <!-- Mobile Table of Contents (hidden by default) -->
       <div id="mobile-toc-nav" class="hidden h-full flex flex-col">
@@ -1192,8 +1199,10 @@ <h1 class="text-lg font-bold text-primary">nf-fgsv workflow parameters</h1>
         </nav>
       </div>
     </aside>
+    
 
     <div class="flex min-h-screen pt-14">
+      
       <!-- Left Sidebar - Main Navigation -->
       <aside
         id="left-nav"
@@ -1241,10 +1250,15 @@ <h1 class="text-lg font-bold text-primary">nf-fgsv workflow parameters</h1>
           </ul>
         </nav>
       </aside>
+      
 
       <!-- Main content -->
-      <main class="md:ml-56 lg:mr-64 flex-1 p-4 md:p-8 lg:p-12">
+      <main
+        class="md:ml-56 lg:mr-64 flex-1 p-4 md:p-8 lg:p-12"
+      >
+        
         <!-- Search Results Section (hidden by default) -->
+        
         <section id="search-results" class="section hidden">
           <h1 class="text-3xl font-bold mb-4 text-slate-800">Search Results</h1>
 
@@ -1305,7 +1319,7 @@ <h1 class="text-3xl font-bold mb-4 text-slate-800">Search Results</h1>
             <p class="text-sm mt-2">Try a different search term</p>
           </div>
         </section>
-
+         
         <!-- Overview Section -->
         <section id="overview" class="section">
           <h1 class="text-3xl font-bold mb-4 text-slate-800">nf-fgsv workflow parameters</h1>
@@ -1316,7 +1330,7 @@ <h1 class="text-3xl font-bold mb-4 text-slate-800">nf-fgsv workflow parameters</
           <div class="flex flex-wrap gap-4 mb-6">
              
             <a
-              href="https://github.com/fulcrumgenomics/nf-fgsv"
+              href="https://github.com/fg-labs/nf-fgsv"
               target="_blank"
               class="inline-flex items-center gap-1.5 text-sm text-primary hover:underline"
             >
@@ -1328,7 +1342,7 @@ <h1 class="text-3xl font-bold mb-4 text-slate-800">nf-fgsv workflow parameters</
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                 ></path>
               </svg>
-               https://github.com/fulcrumgenomics/nf-fgsv
+               https://github.com/fg-labs/nf-fgsv
             </a>
             
           </div>
@@ -1336,6 +1350,19 @@ <h1 class="text-3xl font-bold mb-4 text-slate-800">nf-fgsv workflow parameters</
           <div id="readme-content" class="prose max-w-none text-slate-600">
             <div class="alert alert-note"><div class="alert-title"><svg class="alert-icon" viewBox="0 0 16 16" width="16" height="16"><path d="M0 8a8 8 0 1 1 16 0A8 8 0 0 1 0 8Zm8-6.5a6.5 6.5 0 1 0 0 13 6.5 6.5 0 0 0 0-13ZM6.5 7.75A.75.75 0 0 1 7.25 7h1a.75.75 0 0 1 .75.75v2.75h.25a.75.75 0 0 1 0 1.5h-2a.75.75 0 0 1 0-1.5h.25v-2h-.25a.75.75 0 0 1-.75-.75ZM8 6a1 1 0 1 1 0-2 1 1 0 0 1 0 2Z"></path></svg><span>Note</span></div><div class="alert-content"><p>This repository is primarily for testing the latest Nextflow features and the workflow is relatively simple.</p></div></div>
 <p>This is a Nextflow workflow for running <a href="https://github.com/fulcrumgenomics/fgsv">fgsv</a> on a BAM file to gather evidence for structural variation via breakpoint detection.</p>
+<p>
+<a href="https://fulcrumgenomics.com">
+<picture>
+  <source media="(prefers-color-scheme: dark)" srcset="https://raw.githubusercontent.com/fg-labs/nf-fgsv/main/.github/logos/fulcrumgenomics-dark.svg">
+  <source media="(prefers-color-scheme: light)" srcset="https://raw.githubusercontent.com/fg-labs/nf-fgsv/main/.github/logos/fulcrumgenomics-light.svg">
+  <img alt="Fulcrum Genomics" src="https://raw.githubusercontent.com/fg-labs/nf-fgsv/main/.github/logos/fulcrumgenomics-light.svg" height="100" width="25%">
+</picture>
+</a>
+</p>
+
+<p><a href="https://www.fulcrumgenomics.com">Visit us at Fulcrum Genomics</a> to learn more about how we can power your Bioinformatics with nf-fgsv and beyond.</p>
+<p><a href="mailto:contact@fulcrumgenomics.com?subject=[GitHub inquiry]"><img src="https://img.shields.io/badge/Email_us-%2338b44a.svg?&style=for-the-badge&logo=gmail&logoColor=white"/></a>
+<a href="https://www.fulcrumgenomics.com"><img src="https://img.shields.io/badge/Visit_Us-%2326a8e0.svg?&style=for-the-badge&logo=wordpress&logoColor=white"/></a></p>
 <h2 id="readme-set-up-environment" class="heading-anchor">Set up Environment<a href="#readme-set-up-environment" class="paragraph-link">¶</a></h2>
 <p>Make sure <a href="https://pixi.sh/latest/#installation">Pixi</a> and <a href="https://docs.docker.com/engine/install/">Docker</a> are installed.</p>
 <p>The environment for this analysis is in <a href="pixi.toml">pixi.toml</a> and is named <code>nf-fgsv</code>.</p>
@@ -1463,8 +1490,10 @@ <h2 class="text-2xl font-semibold mt-8 mb-4 pb-2 border-b border-slate-200">Auth
           </ul>
           
         </section>
+        
 
         <!-- Inputs Section -->
+        
         <section id="inputs" class="section hidden">
           <h1 class="text-3xl font-bold mb-4 text-slate-800">Pipeline Inputs</h1>
           <p class="mb-4 text-slate-600">
@@ -1516,22 +1545,27 @@ <h1 class="text-3xl font-bold mb-4 text-slate-800">Pipeline Inputs</h1>
               
             </div>
             
-            <div class="prose mb-2 text-slate-600"><p>Path to tab-separated file containing information about the samples in the experiment.</p></div>
+            <div class="prose mb-2 text-slate-600"><p>Path to a tab-separated values (TSV) sample sheet describing the samples to analyze. The file must have a header row with the following required columns:</p>
+<ul>
+<li><code>sample</code>: a unique sample identifier containing no whitespace; used as the <code>meta.id</code> that names per-sample outputs.</li>
+<li><code>bam</code>: path to an existing BAM file for the sample (must end in <code>.bam</code>).</li>
+</ul>
+<p>See <code>schemas/input_schema.json</code> for the full validation rules.</p></div>
                
           </div>
            
         </section>
-
+         
         <!-- Config Section -->
-        
+         
 
         <!-- Workflows Section -->
         
         <section id="workflows" class="section hidden">
+          
           <h1 class="text-3xl font-bold mb-4 text-slate-800">Workflows</h1>
           <p class="mb-4 text-slate-600">This page documents all workflows in the pipeline.</p>
-
-          
+           
           <div
             id="workflow-entry"
             class="bg-white border border-slate-200 rounded-lg p-4 mb-4"
@@ -1550,7 +1584,7 @@ <h1 class="text-3xl font-bold mb-4 text-slate-800">Workflows</h1>
               </span>
                
               <a
-                href="https://github.com/fulcrumgenomics/nf-fgsv/blob/73e7adf5d96a2031f89519bbb378d8e19954aeb7/main.nf#L19-L42"
+                href="https://github.com/fg-labs/nf-fgsv/blob/f7298efb052edc211b63921113eaa18d78d85aa2/main.nf#L35-L51"
                 target="_blank"
                 rel="noopener noreferrer"
                 class="ml-2 text-slate-400 hover:text-primary no-underline"
@@ -1562,7 +1596,7 @@ <h1 class="text-3xl font-bold mb-4 text-slate-800">Workflows</h1>
             </div>
             
             <div class="text-xs text-slate-400 mb-2">
-              Defined in <code>main.nf:19</code>
+              Defined in <code>main.nf:35</code>
             </div>
             
 
@@ -1573,6 +1607,19 @@ <h1 class="text-3xl font-bold mb-4 text-slate-800">Workflows</h1>
             
 
             <!-- Code documentation (Groovydoc) - show if present and different from meta description -->
+             
+            <div class="prose mb-4 text-slate-600"><p>Detect structural-variant breakpoints from aligned reads using fgsv.
+The <code>--input</code> sample sheet provides one <code>sample</code> identifier and <code>bam</code> path per
+row (see the <code>--input</code> parameter for the full column specification). Every
+per-sample output — the sorted BAM, SvPileup BAM and text, aggregated
+breakpoints, and BEDPE — is published via the <code>sample_outputs</code> topic into a
+directory named after the sample's <code>meta.id</code>. For each sample the workflow runs:</p>
+<ol>
+<li><code>COORDINATE_SORT</code> — coordinate-sort the input BAM with samtools.</li>
+<li><code>SV_PILEUP</code> — gather read-level evidence for structural variants (fgsv SvPileup).</li>
+<li><code>AGGREGATE_SV_PILEUP</code> — merge pileups that likely support the same breakpoint.</li>
+<li><code>AGGREGATE_SV_PILEUP_TO_BEDPE</code> — convert the aggregated breakpoints to BEDPE.</li>
+</ol></div>
             
 
             <!-- Components section (from meta.yml - modules/subworkflows used) -->
@@ -1594,10 +1641,10 @@ <h1 class="text-3xl font-bold mb-4 text-slate-800">Workflows</h1>
         <!-- Processes Section -->
         
         <section id="processes" class="section hidden">
+          
           <h1 class="text-3xl font-bold mb-4 text-slate-800">Processes</h1>
           <p class="mb-4 text-slate-600">This page documents all processes in the pipeline.</p>
-
-          
+           
           <div
             id="process-AGGREGATE_SV_PILEUP"
             class="bg-white border border-slate-200 rounded-lg p-4 mb-4"
@@ -1610,7 +1657,7 @@ <h1 class="text-3xl font-bold mb-4 text-slate-800">Processes</h1>
               <span class="font-bold text-primary-dark">AGGREGATE_SV_PILEUP</span>
               
               <a
-                href="https://github.com/fulcrumgenomics/nf-fgsv/blob/73e7adf5d96a2031f89519bbb378d8e19954aeb7/modules/aggregate_sv_pileup.nf#L12-L33"
+                href="https://github.com/fg-labs/nf-fgsv/blob/f7298efb052edc211b63921113eaa18d78d85aa2/modules/aggregate_sv_pileup.nf#L12-L36"
                 target="_blank"
                 rel="noopener noreferrer"
                 class="ml-2 text-slate-400 hover:text-primary no-underline"
@@ -1664,70 +1711,53 @@ <h3 class="text-lg font-semibold mt-4 mb-2">Inputs</h3>
                   <tr class="hover:bg-slate-50">
                     <td class="p-3 border-b border-slate-200">
                       <code class="bg-slate-100 px-1.5 py-0.5 rounded font-mono text-sm"
-                        >val(meta)<wbr>,<wbr> <wbr>path(bam)<wbr>,<wbr> <wbr>path(txt)<wbr></code
+                        >meta</code
                       >
                     </td>
                     <td class="p-3 border-b border-slate-200">
                       <code class="bg-slate-100 px-1.5 py-0.5 rounded font-mono text-sm"
-                        >tuple</code
+                        >val</code
                       >
                     </td>
                     <td class="p-3 border-b border-slate-200">
                       
-                      <div class="prose prose-sm"><p><code>meta</code>: Map containing sample information (must include 'id'); <code>bam</code>: Input BAM file; <code>txt</code>: SvPileup breakpoint output file</p></div>
+                      <div class="prose prose-sm"><p>Map containing sample information (must include 'id')</p></div>
                       
                     </td>
                   </tr>
-                   
-                </tbody>
-              </table>
-            </div>
-            
-
-            <!-- Outputs section - combine LSP outputs with meta.yml descriptions -->
-            
-            <h3 class="text-lg font-semibold mt-4 mb-2">Outputs</h3>
-            <div class="overflow-x-auto">
-              <table class="w-full border-collapse mb-4">
-                <thead>
-                  <tr>
-                    <th class="text-left p-3 border-b border-slate-200 bg-slate-100 font-semibold">
-                      Name
-                    </th>
-                    <th class="text-left p-3 border-b border-slate-200 bg-slate-100 font-semibold">
-                      Type
-                    </th>
-                    <th class="text-left p-3 border-b border-slate-200 bg-slate-100 font-semibold">
-                      Emit
-                    </th>
-                    <th class="text-left p-3 border-b border-slate-200 bg-slate-100 font-semibold">
-                      Description
-                    </th>
-                  </tr>
-                </thead>
-                <tbody>
-                    
+                  
                   <tr class="hover:bg-slate-50">
                     <td class="p-3 border-b border-slate-200">
                       <code class="bg-slate-100 px-1.5 py-0.5 rounded font-mono text-sm"
-                        >val(meta)<wbr>,<wbr> <wbr>file("*_svpileup.aggregate.txt")<wbr></code
+                        >bam</code
                       >
                     </td>
                     <td class="p-3 border-b border-slate-200">
                       <code class="bg-slate-100 px-1.5 py-0.5 rounded font-mono text-sm"
-                        >tuple</code
+                        >path</code
                       >
                     </td>
                     <td class="p-3 border-b border-slate-200">
                       
+                      <div class="prose prose-sm"><p>Input BAM file</p></div>
+                      
+                    </td>
+                  </tr>
+                  
+                  <tr class="hover:bg-slate-50">
+                    <td class="p-3 border-b border-slate-200">
                       <code class="bg-slate-100 px-1.5 py-0.5 rounded font-mono text-sm"
                         >txt</code
                       >
-                      
+                    </td>
+                    <td class="p-3 border-b border-slate-200">
+                      <code class="bg-slate-100 px-1.5 py-0.5 rounded font-mono text-sm"
+                        >path</code
+                      >
                     </td>
                     <td class="p-3 border-b border-slate-200">
                       
-                      <div class="prose prose-sm"><p>Tuple of meta and aggregated SvPileup output file</p></div>
+                      <div class="prose prose-sm"><p>SvPileup breakpoint output file</p></div>
                       
                     </td>
                   </tr>
@@ -1735,6 +1765,9 @@ <h3 class="text-lg font-semibold mt-4 mb-2">Outputs</h3>
                 </tbody>
               </table>
             </div>
+            
+
+            <!-- Outputs section - combine LSP outputs with meta.yml descriptions -->
              
 
             <!-- Authors/Maintainers (from meta.yml) -->
@@ -1753,7 +1786,7 @@ <h3 class="text-lg font-semibold mt-4 mb-2">Outputs</h3>
               <span class="font-bold text-primary-dark">AGGREGATE_SV_PILEUP_TO_BEDPE</span>
               
               <a
-                href="https://github.com/fulcrumgenomics/nf-fgsv/blob/73e7adf5d96a2031f89519bbb378d8e19954aeb7/modules/aggregate_sv_pileup_to_bedpe.nf#L11-L31"
+                href="https://github.com/fg-labs/nf-fgsv/blob/f7298efb052edc211b63921113eaa18d78d85aa2/modules/aggregate_sv_pileup_to_bedpe.nf#L11-L34"
                 target="_blank"
                 rel="noopener noreferrer"
                 class="ml-2 text-slate-400 hover:text-primary no-underline"
@@ -1807,70 +1840,35 @@ <h3 class="text-lg font-semibold mt-4 mb-2">Inputs</h3>
                   <tr class="hover:bg-slate-50">
                     <td class="p-3 border-b border-slate-200">
                       <code class="bg-slate-100 px-1.5 py-0.5 rounded font-mono text-sm"
-                        >val(meta)<wbr>,<wbr> <wbr>path(txt)<wbr></code
+                        >meta</code
                       >
                     </td>
                     <td class="p-3 border-b border-slate-200">
                       <code class="bg-slate-100 px-1.5 py-0.5 rounded font-mono text-sm"
-                        >tuple</code
+                        >val</code
                       >
                     </td>
                     <td class="p-3 border-b border-slate-200">
                       
-                      <div class="prose prose-sm"><p><code>meta</code>: Map containing sample information (must include 'id'); <code>txt</code>: Aggregated SvPileup output file</p></div>
+                      <div class="prose prose-sm"><p>Map containing sample information (must include 'id')</p></div>
                       
                     </td>
                   </tr>
-                   
-                </tbody>
-              </table>
-            </div>
-            
-
-            <!-- Outputs section - combine LSP outputs with meta.yml descriptions -->
-            
-            <h3 class="text-lg font-semibold mt-4 mb-2">Outputs</h3>
-            <div class="overflow-x-auto">
-              <table class="w-full border-collapse mb-4">
-                <thead>
-                  <tr>
-                    <th class="text-left p-3 border-b border-slate-200 bg-slate-100 font-semibold">
-                      Name
-                    </th>
-                    <th class="text-left p-3 border-b border-slate-200 bg-slate-100 font-semibold">
-                      Type
-                    </th>
-                    <th class="text-left p-3 border-b border-slate-200 bg-slate-100 font-semibold">
-                      Emit
-                    </th>
-                    <th class="text-left p-3 border-b border-slate-200 bg-slate-100 font-semibold">
-                      Description
-                    </th>
-                  </tr>
-                </thead>
-                <tbody>
-                    
+                  
                   <tr class="hover:bg-slate-50">
                     <td class="p-3 border-b border-slate-200">
                       <code class="bg-slate-100 px-1.5 py-0.5 rounded font-mono text-sm"
-                        >val(meta)<wbr>,<wbr> <wbr>file("*_svpileup.aggregate.bedpe")<wbr></code
-                      >
-                    </td>
-                    <td class="p-3 border-b border-slate-200">
-                      <code class="bg-slate-100 px-1.5 py-0.5 rounded font-mono text-sm"
-                        >tuple</code
+                        >txt</code
                       >
                     </td>
                     <td class="p-3 border-b border-slate-200">
-                      
                       <code class="bg-slate-100 px-1.5 py-0.5 rounded font-mono text-sm"
-                        >bedpe</code
+                        >path</code
                       >
-                      
                     </td>
                     <td class="p-3 border-b border-slate-200">
                       
-                      <div class="prose prose-sm"><p>Tuple of meta and BEDPE format output file</p></div>
+                      <div class="prose prose-sm"><p>Aggregated SvPileup output file</p></div>
                       
                     </td>
                   </tr>
@@ -1878,6 +1876,9 @@ <h3 class="text-lg font-semibold mt-4 mb-2">Outputs</h3>
                 </tbody>
               </table>
             </div>
+            
+
+            <!-- Outputs section - combine LSP outputs with meta.yml descriptions -->
              
 
             <!-- Authors/Maintainers (from meta.yml) -->
@@ -1896,7 +1897,7 @@ <h3 class="text-lg font-semibold mt-4 mb-2">Outputs</h3>
               <span class="font-bold text-primary-dark">COORDINATE_SORT</span>
               
               <a
-                href="https://github.com/fulcrumgenomics/nf-fgsv/blob/73e7adf5d96a2031f89519bbb378d8e19954aeb7/modules/coordinate_sort.nf#L10-L31"
+                href="https://github.com/fg-labs/nf-fgsv/blob/f7298efb052edc211b63921113eaa18d78d85aa2/modules/coordinate_sort.nf#L10-L31"
                 target="_blank"
                 rel="noopener noreferrer"
                 class="ml-2 text-slate-400 hover:text-primary no-underline"
@@ -1949,70 +1950,35 @@ <h3 class="text-lg font-semibold mt-4 mb-2">Inputs</h3>
                   <tr class="hover:bg-slate-50">
                     <td class="p-3 border-b border-slate-200">
                       <code class="bg-slate-100 px-1.5 py-0.5 rounded font-mono text-sm"
-                        >val(meta)<wbr>,<wbr> <wbr>path(bam)<wbr></code
+                        >meta</code
                       >
                     </td>
                     <td class="p-3 border-b border-slate-200">
                       <code class="bg-slate-100 px-1.5 py-0.5 rounded font-mono text-sm"
-                        >tuple</code
+                        >val</code
                       >
                     </td>
                     <td class="p-3 border-b border-slate-200">
                       
-                      <div class="prose prose-sm"><p><code>meta</code>: Map containing sample information (must include 'id'); <code>bam</code>: Input BAM file to be sorted</p></div>
+                      <div class="prose prose-sm"><p>Map containing sample information (must include 'id')</p></div>
                       
                     </td>
                   </tr>
-                   
-                </tbody>
-              </table>
-            </div>
-            
-
-            <!-- Outputs section - combine LSP outputs with meta.yml descriptions -->
-            
-            <h3 class="text-lg font-semibold mt-4 mb-2">Outputs</h3>
-            <div class="overflow-x-auto">
-              <table class="w-full border-collapse mb-4">
-                <thead>
-                  <tr>
-                    <th class="text-left p-3 border-b border-slate-200 bg-slate-100 font-semibold">
-                      Name
-                    </th>
-                    <th class="text-left p-3 border-b border-slate-200 bg-slate-100 font-semibold">
-                      Type
-                    </th>
-                    <th class="text-left p-3 border-b border-slate-200 bg-slate-100 font-semibold">
-                      Emit
-                    </th>
-                    <th class="text-left p-3 border-b border-slate-200 bg-slate-100 font-semibold">
-                      Description
-                    </th>
-                  </tr>
-                </thead>
-                <tbody>
-                    
+                  
                   <tr class="hover:bg-slate-50">
                     <td class="p-3 border-b border-slate-200">
                       <code class="bg-slate-100 px-1.5 py-0.5 rounded font-mono text-sm"
-                        >val(meta)<wbr>,<wbr> <wbr>file("*_sorted.bam")<wbr></code
-                      >
-                    </td>
-                    <td class="p-3 border-b border-slate-200">
-                      <code class="bg-slate-100 px-1.5 py-0.5 rounded font-mono text-sm"
-                        >tuple</code
+                        >bam</code
                       >
                     </td>
                     <td class="p-3 border-b border-slate-200">
-                      
                       <code class="bg-slate-100 px-1.5 py-0.5 rounded font-mono text-sm"
-                        >bam</code
+                        >path</code
                       >
-                      
                     </td>
                     <td class="p-3 border-b border-slate-200">
                       
-                      <div class="prose prose-sm"><p>Tuple of meta and coordinate-sorted BAM file</p></div>
+                      <div class="prose prose-sm"><p>Input BAM file to be sorted</p></div>
                       
                     </td>
                   </tr>
@@ -2020,6 +1986,9 @@ <h3 class="text-lg font-semibold mt-4 mb-2">Outputs</h3>
                 </tbody>
               </table>
             </div>
+            
+
+            <!-- Outputs section - combine LSP outputs with meta.yml descriptions -->
              
 
             <!-- Authors/Maintainers (from meta.yml) -->
@@ -2038,7 +2007,7 @@ <h3 class="text-lg font-semibold mt-4 mb-2">Outputs</h3>
               <span class="font-bold text-primary-dark">SV_PILEUP</span>
               
               <a
-                href="https://github.com/fulcrumgenomics/nf-fgsv/blob/73e7adf5d96a2031f89519bbb378d8e19954aeb7/modules/sv_pileup.nf#L11-L33"
+                href="https://github.com/fg-labs/nf-fgsv/blob/f7298efb052edc211b63921113eaa18d78d85aa2/modules/sv_pileup.nf#L10-L35"
                 target="_blank"
                 rel="noopener noreferrer"
                 class="ml-2 text-slate-400 hover:text-primary no-underline"
@@ -2050,7 +2019,7 @@ <h3 class="text-lg font-semibold mt-4 mb-2">Outputs</h3>
             </div>
             
             <div class="text-xs text-slate-400 mb-2">
-              Defined in <code>modules/sv_pileup.nf:11</code>
+              Defined in <code>modules/sv_pileup.nf:10</code>
             </div>
             
 
@@ -2091,70 +2060,17 @@ <h3 class="text-lg font-semibold mt-4 mb-2">Inputs</h3>
                   <tr class="hover:bg-slate-50">
                     <td class="p-3 border-b border-slate-200">
                       <code class="bg-slate-100 px-1.5 py-0.5 rounded font-mono text-sm"
-                        >val(meta)<wbr>,<wbr> <wbr>path(bam)<wbr></code
-                      >
-                    </td>
-                    <td class="p-3 border-b border-slate-200">
-                      <code class="bg-slate-100 px-1.5 py-0.5 rounded font-mono text-sm"
-                        >tuple</code
-                      >
-                    </td>
-                    <td class="p-3 border-b border-slate-200">
-                      
-                      <div class="prose prose-sm"><p><code>meta</code>: Map containing sample information (must include 'id'); <code>bam</code>: Input BAM file</p></div>
-                      
-                    </td>
-                  </tr>
-                   
-                </tbody>
-              </table>
-            </div>
-            
-
-            <!-- Outputs section - combine LSP outputs with meta.yml descriptions -->
-            
-            <h3 class="text-lg font-semibold mt-4 mb-2">Outputs</h3>
-            <div class="overflow-x-auto">
-              <table class="w-full border-collapse mb-4">
-                <thead>
-                  <tr>
-                    <th class="text-left p-3 border-b border-slate-200 bg-slate-100 font-semibold">
-                      Name
-                    </th>
-                    <th class="text-left p-3 border-b border-slate-200 bg-slate-100 font-semibold">
-                      Type
-                    </th>
-                    <th class="text-left p-3 border-b border-slate-200 bg-slate-100 font-semibold">
-                      Emit
-                    </th>
-                    <th class="text-left p-3 border-b border-slate-200 bg-slate-100 font-semibold">
-                      Description
-                    </th>
-                  </tr>
-                </thead>
-                <tbody>
-                    
-                  <tr class="hover:bg-slate-50">
-                    <td class="p-3 border-b border-slate-200">
-                      <code class="bg-slate-100 px-1.5 py-0.5 rounded font-mono text-sm"
-                        >val(meta)<wbr>,<wbr> <wbr>file("*_svpileup.txt")<wbr></code
+                        >meta</code
                       >
                     </td>
                     <td class="p-3 border-b border-slate-200">
                       <code class="bg-slate-100 px-1.5 py-0.5 rounded font-mono text-sm"
-                        >tuple</code
+                        >val</code
                       >
                     </td>
                     <td class="p-3 border-b border-slate-200">
                       
-                      <code class="bg-slate-100 px-1.5 py-0.5 rounded font-mono text-sm"
-                        >txt</code
-                      >
-                      
-                    </td>
-                    <td class="p-3 border-b border-slate-200">
-                      
-                      <div class="prose prose-sm"><p>Tuple of meta and SvPileup breakpoint output file</p></div>
+                      <div class="prose prose-sm"><p>Map containing sample information (must include 'id')</p></div>
                       
                     </td>
                   </tr>
@@ -2162,24 +2078,17 @@ <h3 class="text-lg font-semibold mt-4 mb-2">Outputs</h3>
                   <tr class="hover:bg-slate-50">
                     <td class="p-3 border-b border-slate-200">
                       <code class="bg-slate-100 px-1.5 py-0.5 rounded font-mono text-sm"
-                        >val(meta)<wbr>,<wbr> <wbr>file("*_svpileup.bam")<wbr></code
-                      >
-                    </td>
-                    <td class="p-3 border-b border-slate-200">
-                      <code class="bg-slate-100 px-1.5 py-0.5 rounded font-mono text-sm"
-                        >tuple</code
+                        >bam</code
                       >
                     </td>
                     <td class="p-3 border-b border-slate-200">
-                      
                       <code class="bg-slate-100 px-1.5 py-0.5 rounded font-mono text-sm"
-                        >bam</code
+                        >path</code
                       >
-                      
                     </td>
                     <td class="p-3 border-b border-slate-200">
                       
-                      <div class="prose prose-sm"><p>Tuple of meta and SvPileup BAM file</p></div>
+                      <div class="prose prose-sm"><p>Input BAM file</p></div>
                       
                     </td>
                   </tr>
@@ -2187,6 +2096,9 @@ <h3 class="text-lg font-semibold mt-4 mb-2">Outputs</h3>
                 </tbody>
               </table>
             </div>
+            
+
+            <!-- Outputs section - combine LSP outputs with meta.yml descriptions -->
              
 
             <!-- Authors/Maintainers (from meta.yml) -->
@@ -2270,13 +2182,14 @@ <h3 class="text-lg font-semibold mt-4 mb-2">Outputs</h3>
               <a href="https://github.com/ewels/nf-docs" target="_blank" rel="noopener noreferrer"
                 >nf-docs</a
               >
-              <span class="nf-docs-version">v0.2.0</span>
-              <span>on 2026-03-03 19:13:28 UTC</span>
+              <span class="nf-docs-version">v0.3.0</span>
+              <span>on 2026-05-27 21:22:19 UTC</span>
             </div>
           </div>
         </footer>
       </main>
 
+      
       <!-- Right Sidebar - Page Table of Contents -->
       <aside
         id="right-nav"
@@ -2395,9 +2308,11 @@ <h3 class="text-lg font-semibold mt-4 mb-2">Outputs</h3>
         <!-- Functions TOC -->
         
       </aside>
+      
     </div>
 
     <script>
+      
       // Track current section
       let currentSection = 'overview';
 
@@ -2652,7 +2567,7 @@ <h3 class="text-lg font-semibold mt-4 mb-2">Outputs</h3>
           
           {
             name: "(entry)",
-            docstring: "",
+            docstring: "Detect structural-variant breakpoints from aligned reads using fgsv.\nThe `--input` sample sheet provides one `sample` identifier and `bam` path per\nrow (see the `--input` parameter for the full column specification). Every\nper-sample output \u2014 the sorted BAM, SvPileup BAM and text, aggregated\nbreakpoints, and BEDPE \u2014 is published via the `sample_outputs` topic into a\ndirectory named after the sample\u0027s `meta.id`. For each sample the workflow runs:\n1. `COORDINATE_SORT` \u2014 coordinate-sort the input BAM with samtools.\n2. `SV_PILEUP` \u2014 gather read-level evidence for structural variants (fgsv SvPileup).\n3. `AGGREGATE_SV_PILEUP` \u2014 merge pileups that likely support the same breakpoint.\n4. `AGGREGATE_SV_PILEUP_TO_BEDPE` \u2014 convert the aggregated breakpoints to BEDPE.",
             file: "main.nf",
             id: "workflow-entry",
             section: "workflows"
@@ -2701,7 +2616,7 @@ <h3 class="text-lg font-semibold mt-4 mb-2">Outputs</h3>
           
           {
             name: "input",
-            description: "Path to tab-separated file containing information about the samples in the experiment.",
+            description: "Path to a tab-separated values (TSV) sample sheet describing the samples to analyze. The file must have a header row with the following required columns:\n\n- `sample`: a unique sample identifier containing no whitespace; used as the `meta.id` that names per-sample outputs.\n- `bam`: path to an existing BAM file for the sample (must end in `.bam`).\n\nSee `schemas/input_schema.json` for the full validation rules.",
             group: "Main workflow parameters",
             id: "param-input",
             section: "inputs"
@@ -3156,6 +3071,7 @@ <h2 class="text-xl font-semibold mb-4 pb-2 border-b border-slate-200">
 
       mobileTocLink.addEventListener('click', showMobileToc);
       mobileTocBack.addEventListener('click', showMobileMainNav);
+      
 
       // ==================== Dark Mode Toggle ====================
 
diff --git a/docs/examples/nf-fgsv/json/pipeline-api.json b/docs/examples/nf-fgsv/json/pipeline-api.json
index ed90cb0..8a9aa3b 100644
--- a/docs/examples/nf-fgsv/json/pipeline-api.json
+++ b/docs/examples/nf-fgsv/json/pipeline-api.json
@@ -3,17 +3,17 @@
     "name": "nf-fgsv workflow parameters",
     "description": "Nextflow workflow for running fgsv.",
     "version": "0.1.0",
-    "repository": "https://github.com/fulcrumgenomics/nf-fgsv",
+    "repository": "https://github.com/fg-labs/nf-fgsv",
     "authors": [
       "Fulcrum Genomics"
     ],
-    "readme_content": "> [!NOTE]  \n> This repository is primarily for testing the latest Nextflow features and the workflow is relatively simple.\n\nThis is a Nextflow workflow for running [fgsv](https://github.com/fulcrumgenomics/fgsv) on a BAM file to gather evidence for structural variation via breakpoint detection.\n\n## Set up Environment\n\nMake sure [Pixi](https://pixi.sh/latest/#installation) and [Docker](https://docs.docker.com/engine/install/) are installed.\n\nThe environment for this analysis is in [pixi.toml](pixi.toml) and is named `nf-fgsv`.\n\nTo install:\n\n```console\npixi install\n```\n\n## Run the Workflow\n\nTo save on typing, a pixi task is available which aliases `nextflow run main.nf`.\n\n```console\npixi run \\\n    nf-workflow \\\n        -profile \"local,docker\" \\\n        --input tests/data/basic_input.tsv\n```\n\n## Available Execution Profiles\n\nSeveral default profiles are available:\n\n* `local` limits the resources used by the workflow to (hopefully) reasonable levels\n* `docker` specifies docker containers should be used for process execution\n* `linux` adds `--user root` to docker `runOptions`\n\n## Inputs\n\nA full description of input parameters is available using the workflow `--help` parameter, `pixi run nf-workflow --help`.\n\nThe required columns in the `--input` samplesheet are:\n\n| Field | Type | Description |\n|-------|------|-------------|\n| `sample` | String, no whitespace | Sample identifier |\n| `bam` | Absolute path | Path to the BAM file for this sample (may be an AWS S3 path) |\n\n### Parameter files\n\nIf using more than a few parameters, consider saving them in a YAML format file (e.g. [tests/integration/params.yml](tests/integration/params.yml)).\n\n```console\npixi run \\\n    nf-workflow \\\n        -profile \"local,docker\" \\\n        -params-file my_params.yml\n```\n\n## Outputs\n\nThe output directory can be specified using the `-output-dir` Nextflow parameter.\nThe default output directory is `results/`.\n`-output-dir` cannot be specified in a `params.yml` file, because it is a Nextflow parameter rather than a workflow parameter.\nIt must be specified on the command line or in a `nextflow.config` file.\n\n```console\npixi run \\\n    nf-workflow \\\n        -profile \"local,docker\" \\\n        --input tests/data/basic_input.tsv \\\n        -output-dir results\n```\n\n<details>\n<summary>Click to toggle output directory structure</summary>\n\n\n```console\nresults\n└── {sample_name}\n    ├── {sample_name}_sorted.bam                # Coordinate-sorted BAM file\n    ├── {sample_name}_svpileup.txt              # SvPileup breakpoint candidates\n    ├── {sample_name}_svpileup.bam              # BAM with SV tags from SvPileup\n    ├── {sample_name}_svpileup.aggregate.txt    # Aggregated/merged breakpoint pileups\n    └── {sample_name}_svpileup.aggregate.bedpe  # Aggregated pileups in BEDPE format\n```\n\n</details>\n\n### Output File Descriptions\n\n| File | Description |\n|------|-------------|\n| `*_sorted.bam` | Input BAM sorted by genomic coordinates using samtools sort |\n| `*_svpileup.txt` | Candidate structural variant breakpoints identified by [fgsv SvPileup](https://github.com/fulcrumgenomics/fgsv) |\n| `*_svpileup.bam` | BAM file with SV-related tags added by SvPileup |\n| `*_svpileup.aggregate.txt` | Merged breakpoint pileups from [fgsv AggregateSvPileup](https://github.com/fulcrumgenomics/fgsv) |\n| `*_svpileup.aggregate.bedpe` | Aggregated pileups converted to [BEDPE format](https://bedtools.readthedocs.io/en/latest/content/general-usage.html#bedpe-format) |\n\n## Contributing\n\nSee our [Contributing Guide](docs/CONTRIBUTING.md) for development and testing guidelines.\n\n\n"
+    "readme_content": "> [!NOTE]  \n> This repository is primarily for testing the latest Nextflow features and the workflow is relatively simple.\n\nThis is a Nextflow workflow for running [fgsv](https://github.com/fulcrumgenomics/fgsv) on a BAM file to gather evidence for structural variation via breakpoint detection.\n\n<p>\n<a href=\"https://fulcrumgenomics.com\">\n<picture>\n  <source media=\"(prefers-color-scheme: dark)\" srcset=\"https://raw.githubusercontent.com/fg-labs/nf-fgsv/main/.github/logos/fulcrumgenomics-dark.svg\">\n  <source media=\"(prefers-color-scheme: light)\" srcset=\"https://raw.githubusercontent.com/fg-labs/nf-fgsv/main/.github/logos/fulcrumgenomics-light.svg\">\n  <img alt=\"Fulcrum Genomics\" src=\"https://raw.githubusercontent.com/fg-labs/nf-fgsv/main/.github/logos/fulcrumgenomics-light.svg\" height=\"100\" width=\"25%\">\n</picture>\n</a>\n</p>\n\n[Visit us at Fulcrum Genomics](https://www.fulcrumgenomics.com) to learn more about how we can power your Bioinformatics with nf-fgsv and beyond.\n\n<a href=\"mailto:contact@fulcrumgenomics.com?subject=[GitHub inquiry]\"><img src=\"https://img.shields.io/badge/Email_us-%2338b44a.svg?&style=for-the-badge&logo=gmail&logoColor=white\"/></a>\n<a href=\"https://www.fulcrumgenomics.com\"><img src=\"https://img.shields.io/badge/Visit_Us-%2326a8e0.svg?&style=for-the-badge&logo=wordpress&logoColor=white\"/></a>\n\n## Set up Environment\n\nMake sure [Pixi](https://pixi.sh/latest/#installation) and [Docker](https://docs.docker.com/engine/install/) are installed.\n\nThe environment for this analysis is in [pixi.toml](pixi.toml) and is named `nf-fgsv`.\n\nTo install:\n\n```console\npixi install\n```\n\n## Run the Workflow\n\nTo save on typing, a pixi task is available which aliases `nextflow run main.nf`.\n\n```console\npixi run \\\n    nf-workflow \\\n        -profile \"local,docker\" \\\n        --input tests/data/basic_input.tsv\n```\n\n## Available Execution Profiles\n\nSeveral default profiles are available:\n\n* `local` limits the resources used by the workflow to (hopefully) reasonable levels\n* `docker` specifies docker containers should be used for process execution\n* `linux` adds `--user root` to docker `runOptions`\n\n## Inputs\n\nA full description of input parameters is available using the workflow `--help` parameter, `pixi run nf-workflow --help`.\n\nThe required columns in the `--input` samplesheet are:\n\n| Field | Type | Description |\n|-------|------|-------------|\n| `sample` | String, no whitespace | Sample identifier |\n| `bam` | Absolute path | Path to the BAM file for this sample (may be an AWS S3 path) |\n\n### Parameter files\n\nIf using more than a few parameters, consider saving them in a YAML format file (e.g. [tests/integration/params.yml](tests/integration/params.yml)).\n\n```console\npixi run \\\n    nf-workflow \\\n        -profile \"local,docker\" \\\n        -params-file my_params.yml\n```\n\n## Outputs\n\nThe output directory can be specified using the `-output-dir` Nextflow parameter.\nThe default output directory is `results/`.\n`-output-dir` cannot be specified in a `params.yml` file, because it is a Nextflow parameter rather than a workflow parameter.\nIt must be specified on the command line or in a `nextflow.config` file.\n\n```console\npixi run \\\n    nf-workflow \\\n        -profile \"local,docker\" \\\n        --input tests/data/basic_input.tsv \\\n        -output-dir results\n```\n\n<details>\n<summary>Click to toggle output directory structure</summary>\n\n\n```console\nresults\n└── {sample_name}\n    ├── {sample_name}_sorted.bam                # Coordinate-sorted BAM file\n    ├── {sample_name}_svpileup.txt              # SvPileup breakpoint candidates\n    ├── {sample_name}_svpileup.bam              # BAM with SV tags from SvPileup\n    ├── {sample_name}_svpileup.aggregate.txt    # Aggregated/merged breakpoint pileups\n    └── {sample_name}_svpileup.aggregate.bedpe  # Aggregated pileups in BEDPE format\n```\n\n</details>\n\n### Output File Descriptions\n\n| File | Description |\n|------|-------------|\n| `*_sorted.bam` | Input BAM sorted by genomic coordinates using samtools sort |\n| `*_svpileup.txt` | Candidate structural variant breakpoints identified by [fgsv SvPileup](https://github.com/fulcrumgenomics/fgsv) |\n| `*_svpileup.bam` | BAM file with SV-related tags added by SvPileup |\n| `*_svpileup.aggregate.txt` | Merged breakpoint pileups from [fgsv AggregateSvPileup](https://github.com/fulcrumgenomics/fgsv) |\n| `*_svpileup.aggregate.bedpe` | Aggregated pileups converted to [BEDPE format](https://bedtools.readthedocs.io/en/latest/content/general-usage.html#bedpe-format) |\n\n## Contributing\n\nSee our [Contributing Guide](docs/CONTRIBUTING.md) for development and testing guidelines.\n\n\n"
   },
   "inputs": [
     {
       "name": "input",
       "type": "string",
-      "description": "Path to tab-separated file containing information about the samples in the experiment.",
+      "description": "Path to a tab-separated values (TSV) sample sheet describing the samples to analyze. The file must have a header row with the following required columns:\n\n- `sample`: a unique sample identifier containing no whitespace; used as the `meta.id` that names per-sample outputs.\n- `bam`: path to an existing BAM file for the sample (must end in `.bam`).\n\nSee `schemas/input_schema.json` for the full validation rules.",
       "required": true,
       "format": "file-path",
       "pattern": ".*.tsv$",
@@ -24,15 +24,15 @@
   "workflows": [
     {
       "name": "",
-      "docstring": "",
+      "docstring": "Detect structural-variant breakpoints from aligned reads using fgsv.\nThe `--input` sample sheet provides one `sample` identifier and `bam` path per\nrow (see the `--input` parameter for the full column specification). Every\nper-sample output — the sorted BAM, SvPileup BAM and text, aggregated\nbreakpoints, and BEDPE — is published via the `sample_outputs` topic into a\ndirectory named after the sample's `meta.id`. For each sample the workflow runs:\n1. `COORDINATE_SORT` — coordinate-sort the input BAM with samtools.\n2. `SV_PILEUP` — gather read-level evidence for structural variants (fgsv SvPileup).\n3. `AGGREGATE_SV_PILEUP` — merge pileups that likely support the same breakpoint.\n4. `AGGREGATE_SV_PILEUP_TO_BEDPE` — convert the aggregated breakpoints to BEDPE.",
       "file": "main.nf",
-      "line": 19,
-      "end_line": 42,
+      "line": 35,
+      "end_line": 51,
       "inputs": [],
       "outputs": [],
       "calls": [],
       "is_entry": true,
-      "source_url": "https://github.com/fulcrumgenomics/nf-fgsv/blob/73e7adf5d96a2031f89519bbb378d8e19954aeb7/main.nf#L19-L42"
+      "source_url": "https://github.com/fg-labs/nf-fgsv/blob/f7298efb052edc211b63921113eaa18d78d85aa2/main.nf#L35-L51"
     }
   ],
   "processes": [
@@ -41,50 +41,54 @@
       "docstring": "Convert aggregated SvPileup output to BEDPE format using fgsv\nAggregateSvPileupToBedPE.",
       "file": "modules/aggregate_sv_pileup_to_bedpe.nf",
       "line": 11,
-      "end_line": 31,
+      "end_line": 34,
       "inputs": [
         {
-          "name": "val(meta), path(txt)",
-          "type": "tuple",
-          "description": "`meta`: Map containing sample information (must include 'id'); `txt`: Aggregated SvPileup output file",
-          "qualifier": "Tuple<Map, Path>"
-        }
-      ],
-      "outputs": [
+          "name": "meta",
+          "type": "val",
+          "description": "Map containing sample information (must include 'id')",
+          "qualifier": "Map"
+        },
         {
-          "name": "val(meta), file(\"*_svpileup.aggregate.bedpe\")",
-          "type": "tuple",
-          "description": "Tuple of meta and BEDPE format output file",
-          "emit": "bedpe"
+          "name": "txt",
+          "type": "path",
+          "description": "Aggregated SvPileup output file",
+          "qualifier": "Path"
         }
       ],
+      "outputs": [],
       "directives": {},
-      "source_url": "https://github.com/fulcrumgenomics/nf-fgsv/blob/73e7adf5d96a2031f89519bbb378d8e19954aeb7/modules/aggregate_sv_pileup_to_bedpe.nf#L11-L31"
+      "source_url": "https://github.com/fg-labs/nf-fgsv/blob/f7298efb052edc211b63921113eaa18d78d85aa2/modules/aggregate_sv_pileup_to_bedpe.nf#L11-L34"
     },
     {
       "name": "AGGREGATE_SV_PILEUP",
       "docstring": "Aggregate and merge pileups that are likely to support the same breakpoint\nusing fgsv AggregateSvPileup.",
       "file": "modules/aggregate_sv_pileup.nf",
       "line": 12,
-      "end_line": 33,
+      "end_line": 36,
       "inputs": [
         {
-          "name": "val(meta), path(bam), path(txt)",
-          "type": "tuple",
-          "description": "`meta`: Map containing sample information (must include 'id'); `bam`: Input BAM file; `txt`: SvPileup breakpoint output file",
-          "qualifier": "Tuple<Map, Path, Path>"
-        }
-      ],
-      "outputs": [
+          "name": "meta",
+          "type": "val",
+          "description": "Map containing sample information (must include 'id')",
+          "qualifier": "Map"
+        },
         {
-          "name": "val(meta), file(\"*_svpileup.aggregate.txt\")",
-          "type": "tuple",
-          "description": "Tuple of meta and aggregated SvPileup output file",
-          "emit": "txt"
+          "name": "bam",
+          "type": "path",
+          "description": "Input BAM file",
+          "qualifier": "Path"
+        },
+        {
+          "name": "txt",
+          "type": "path",
+          "description": "SvPileup breakpoint output file",
+          "qualifier": "Path"
         }
       ],
+      "outputs": [],
       "directives": {},
-      "source_url": "https://github.com/fulcrumgenomics/nf-fgsv/blob/73e7adf5d96a2031f89519bbb378d8e19954aeb7/modules/aggregate_sv_pileup.nf#L12-L33"
+      "source_url": "https://github.com/fg-labs/nf-fgsv/blob/f7298efb052edc211b63921113eaa18d78d85aa2/modules/aggregate_sv_pileup.nf#L12-L36"
     },
     {
       "name": "COORDINATE_SORT",
@@ -94,59 +98,51 @@
       "end_line": 31,
       "inputs": [
         {
-          "name": "val(meta), path(bam)",
-          "type": "tuple",
-          "description": "`meta`: Map containing sample information (must include 'id'); `bam`: Input BAM file to be sorted",
-          "qualifier": "Tuple<Map, Path>"
-        }
-      ],
-      "outputs": [
+          "name": "meta",
+          "type": "val",
+          "description": "Map containing sample information (must include 'id')",
+          "qualifier": "Map"
+        },
         {
-          "name": "val(meta), file(\"*_sorted.bam\")",
-          "type": "tuple",
-          "description": "Tuple of meta and coordinate-sorted BAM file",
-          "emit": "bam"
+          "name": "bam",
+          "type": "path",
+          "description": "Input BAM file to be sorted",
+          "qualifier": "Path"
         }
       ],
+      "outputs": [],
       "directives": {},
-      "source_url": "https://github.com/fulcrumgenomics/nf-fgsv/blob/73e7adf5d96a2031f89519bbb378d8e19954aeb7/modules/coordinate_sort.nf#L10-L31"
+      "source_url": "https://github.com/fg-labs/nf-fgsv/blob/f7298efb052edc211b63921113eaa18d78d85aa2/modules/coordinate_sort.nf#L10-L31"
     },
     {
       "name": "SV_PILEUP",
       "docstring": "Detect structural variant evidence from a BAM file using fgsv SvPileup.",
       "file": "modules/sv_pileup.nf",
-      "line": 11,
-      "end_line": 33,
+      "line": 10,
+      "end_line": 35,
       "inputs": [
         {
-          "name": "val(meta), path(bam)",
-          "type": "tuple",
-          "description": "`meta`: Map containing sample information (must include 'id'); `bam`: Input BAM file",
-          "qualifier": "Tuple<Map, Path>"
-        }
-      ],
-      "outputs": [
-        {
-          "name": "val(meta), file(\"*_svpileup.txt\")",
-          "type": "tuple",
-          "description": "Tuple of meta and SvPileup breakpoint output file",
-          "emit": "txt"
+          "name": "meta",
+          "type": "val",
+          "description": "Map containing sample information (must include 'id')",
+          "qualifier": "Map"
         },
         {
-          "name": "val(meta), file(\"*_svpileup.bam\")",
-          "type": "tuple",
-          "description": "Tuple of meta and SvPileup BAM file",
-          "emit": "bam"
+          "name": "bam",
+          "type": "path",
+          "description": "Input BAM file",
+          "qualifier": "Path"
         }
       ],
+      "outputs": [],
       "directives": {},
-      "source_url": "https://github.com/fulcrumgenomics/nf-fgsv/blob/73e7adf5d96a2031f89519bbb378d8e19954aeb7/modules/sv_pileup.nf#L11-L33"
+      "source_url": "https://github.com/fg-labs/nf-fgsv/blob/f7298efb052edc211b63921113eaa18d78d85aa2/modules/sv_pileup.nf#L10-L35"
     }
   ],
   "functions": [],
   "generated_by": {
-    "nf_docs_version": "0.2.0",
-    "generated_at": "2026-03-03T19:13:49.416189+00:00",
+    "nf_docs_version": "0.3.0",
+    "generated_at": "2026-05-27T21:23:03.433683+00:00",
     "nextflow_url": "https://nextflow.io",
     "nf_docs_url": "https://github.com/ewels/nf-docs"
   }
diff --git a/docs/examples/nf-fgsv/markdown/index.md b/docs/examples/nf-fgsv/markdown/index.md
index 88cd9cf..6ce3d60 100644
--- a/docs/examples/nf-fgsv/markdown/index.md
+++ b/docs/examples/nf-fgsv/markdown/index.md
@@ -22,9 +22,9 @@ Nextflow workflow for running fgsv.
 
 ## Links
 
-- [Repository](https://github.com/fulcrumgenomics/nf-fgsv)
+- [Repository](https://github.com/fg-labs/nf-fgsv)
 
 ---
 
 *This pipeline was built with [Nextflow](https://nextflow.io).
-Documentation generated by [nf-docs](https://github.com/ewels/nf-docs) v0.2.0 on 2026-03-03 19:14:06 UTC.*
+Documentation generated by [nf-docs](https://github.com/ewels/nf-docs) v0.3.0 on 2026-05-27 21:22:33 UTC.*
diff --git a/docs/examples/nf-fgsv/markdown/inputs.md b/docs/examples/nf-fgsv/markdown/inputs.md
index c3bb522..7de20c3 100644
--- a/docs/examples/nf-fgsv/markdown/inputs.md
+++ b/docs/examples/nf-fgsv/markdown/inputs.md
@@ -8,7 +8,12 @@ This page documents all input parameters for the pipeline.
 
 **Type:** `string` | **Required** | **Format:** `file-path`
 
-Path to tab-separated file containing information about the samples in the experiment.
+Path to a tab-separated values (TSV) sample sheet describing the samples to analyze. The file must have a header row with the following required columns:
+
+- `sample`: a unique sample identifier containing no whitespace; used as the `meta.id` that names per-sample outputs.
+- `bam`: path to an existing BAM file for the sample (must end in `.bam`).
+
+See `schemas/input_schema.json` for the full validation rules.
 
 **Pattern:** `.*.tsv$`
 
@@ -17,4 +22,4 @@ Path to tab-separated file containing information about the samples in the exper
 ---
 
 *This pipeline was built with [Nextflow](https://nextflow.io).
-Documentation generated by [nf-docs](https://github.com/ewels/nf-docs) v0.2.0 on 2026-03-03 19:14:06 UTC.*
+Documentation generated by [nf-docs](https://github.com/ewels/nf-docs) v0.3.0 on 2026-05-27 21:22:33 UTC.*
diff --git a/docs/examples/nf-fgsv/markdown/processes.md b/docs/examples/nf-fgsv/markdown/processes.md
index 693201f..6329aa6 100644
--- a/docs/examples/nf-fgsv/markdown/processes.md
+++ b/docs/examples/nf-fgsv/markdown/processes.md
@@ -20,13 +20,8 @@ AggregateSvPileupToBedPE.
 
 | Name | Type | Description |
 |------|------|-------------|
-| `val(meta), path(txt)` | `tuple` | `meta`: Map containing sample information (must include 'id'); `txt`: Aggregated SvPileup output file |
-
-### Outputs
-
-| Name | Type | Emit | Description |
-|------|------|------|-------------|
-| `val(meta), file("*_svpileup.aggregate.bedpe")` | `tuple` | `bedpe` | Tuple of meta and BEDPE format output file |
+| `meta` | `val` | Map containing sample information (must include 'id') |
+| `txt` | `path` | Aggregated SvPileup output file |
 
 
 ## AGGREGATE_SV_PILEUP {#aggregate-sv-pileup}
@@ -40,13 +35,9 @@ using fgsv AggregateSvPileup.
 
 | Name | Type | Description |
 |------|------|-------------|
-| `val(meta), path(bam), path(txt)` | `tuple` | `meta`: Map containing sample information (must include 'id'); `bam`: Input BAM file; `txt`: SvPileup breakpoint output file |
-
-### Outputs
-
-| Name | Type | Emit | Description |
-|------|------|------|-------------|
-| `val(meta), file("*_svpileup.aggregate.txt")` | `tuple` | `txt` | Tuple of meta and aggregated SvPileup output file |
+| `meta` | `val` | Map containing sample information (must include 'id') |
+| `bam` | `path` | Input BAM file |
+| `txt` | `path` | SvPileup breakpoint output file |
 
 
 ## COORDINATE_SORT {#coordinate-sort}
@@ -59,18 +50,13 @@ Sort a BAM file by genomic coordinates using samtools sort.
 
 | Name | Type | Description |
 |------|------|-------------|
-| `val(meta), path(bam)` | `tuple` | `meta`: Map containing sample information (must include 'id'); `bam`: Input BAM file to be sorted |
-
-### Outputs
-
-| Name | Type | Emit | Description |
-|------|------|------|-------------|
-| `val(meta), file("*_sorted.bam")` | `tuple` | `bam` | Tuple of meta and coordinate-sorted BAM file |
+| `meta` | `val` | Map containing sample information (must include 'id') |
+| `bam` | `path` | Input BAM file to be sorted |
 
 
 ## SV_PILEUP {#sv-pileup}
 
-*Defined in `modules/sv_pileup.nf:11`*
+*Defined in `modules/sv_pileup.nf:10`*
 
 Detect structural variant evidence from a BAM file using fgsv SvPileup.
 
@@ -78,17 +64,11 @@ Detect structural variant evidence from a BAM file using fgsv SvPileup.
 
 | Name | Type | Description |
 |------|------|-------------|
-| `val(meta), path(bam)` | `tuple` | `meta`: Map containing sample information (must include 'id'); `bam`: Input BAM file |
-
-### Outputs
-
-| Name | Type | Emit | Description |
-|------|------|------|-------------|
-| `val(meta), file("*_svpileup.txt")` | `tuple` | `txt` | Tuple of meta and SvPileup breakpoint output file |
-| `val(meta), file("*_svpileup.bam")` | `tuple` | `bam` | Tuple of meta and SvPileup BAM file |
+| `meta` | `val` | Map containing sample information (must include 'id') |
+| `bam` | `path` | Input BAM file |
 
 
 ---
 
 *This pipeline was built with [Nextflow](https://nextflow.io).
-Documentation generated by [nf-docs](https://github.com/ewels/nf-docs) v0.2.0 on 2026-03-03 19:14:06 UTC.*
+Documentation generated by [nf-docs](https://github.com/ewels/nf-docs) v0.3.0 on 2026-05-27 21:22:33 UTC.*
diff --git a/docs/examples/nf-fgsv/markdown/workflows.md b/docs/examples/nf-fgsv/markdown/workflows.md
index a14b179..45ca219 100644
--- a/docs/examples/nf-fgsv/markdown/workflows.md
+++ b/docs/examples/nf-fgsv/markdown/workflows.md
@@ -10,10 +10,21 @@ This page documents all workflows in the pipeline.
 
 **Entry workflow**
 
-*Defined in `main.nf:19`*
+*Defined in `main.nf:35`*
+
+Detect structural-variant breakpoints from aligned reads using fgsv.
+The `--input` sample sheet provides one `sample` identifier and `bam` path per
+row (see the `--input` parameter for the full column specification). Every
+per-sample output — the sorted BAM, SvPileup BAM and text, aggregated
+breakpoints, and BEDPE — is published via the `sample_outputs` topic into a
+directory named after the sample's `meta.id`. For each sample the workflow runs:
+1. `COORDINATE_SORT` — coordinate-sort the input BAM with samtools.
+2. `SV_PILEUP` — gather read-level evidence for structural variants (fgsv SvPileup).
+3. `AGGREGATE_SV_PILEUP` — merge pileups that likely support the same breakpoint.
+4. `AGGREGATE_SV_PILEUP_TO_BEDPE` — convert the aggregated breakpoints to BEDPE.
 
 
 ---
 
 *This pipeline was built with [Nextflow](https://nextflow.io).
-Documentation generated by [nf-docs](https://github.com/ewels/nf-docs) v0.2.0 on 2026-03-03 19:14:06 UTC.*
+Documentation generated by [nf-docs](https://github.com/ewels/nf-docs) v0.3.0 on 2026-05-27 21:22:33 UTC.*
diff --git a/docs/examples/nf-fgsv/table/README.md b/docs/examples/nf-fgsv/table/README.md
index ab74682..ebfc0cd 100644
--- a/docs/examples/nf-fgsv/table/README.md
+++ b/docs/examples/nf-fgsv/table/README.md
@@ -9,13 +9,13 @@
 
 | Name | Description | Type | Default | Required |
 |------|-------------|------|---------|:--------:|
-| `--input` | Path to tab-separated file containing information about the samples in the experiment. | `string` | n/a | yes |
+| `--input` | Path to a tab-separated values (TSV) sample sheet describing the samples to analyze. The file must have a header row with the following required columns:  - `sample`: a unique sample identifier containing no whitespace; used as the `meta.id` that names per-sample outputs. - `bam`: path to an existing BAM file for the sample (must end in `.bam`).  See `schemas/input_schema.json` for the full validation rules. | `string` | n/a | yes |
 
 ## Workflows
 
 | Name | Description | Entry |
 |------|-------------|:-----:|
-| *(entry)* | n/a | yes |
+| *(entry)* | Detect structural-variant breakpoints from aligned reads using fgsv. The `--input` sample sheet provides one `sample` identifier and `bam` path per row (see the `--input` parameter for the full column specification). Every per-sample output — the sorted BAM, SvPileup BAM and text, aggregated breakpoints, and BEDPE — is published via the `sample_outputs` topic into a directory named after the sample's `meta.id`. For each sample the workflow runs: 1. `COORDINATE_SORT` — coordinate-sort the input BAM with samtools. 2. `SV_PILEUP` — gather read-level evidence for structural variants (fgsv SvPileup). 3. `AGGREGATE_SV_PILEUP` — merge pileups that likely support the same breakpoint. 4. `AGGREGATE_SV_PILEUP_TO_BEDPE` — convert the aggregated breakpoints to BEDPE. | yes |
 
 ## Processes
 
@@ -30,54 +30,34 @@
 
 | Name | Type | Description |
 |------|------|-------------|
-| `val(meta), path(txt)` | `tuple` | `meta`: Map containing sample information (must include 'id'); `txt`: Aggregated SvPileup output file |
-
-### `AGGREGATE_SV_PILEUP_TO_BEDPE` Outputs
-
-| Name | Type | Emit | Description |
-|------|------|------|-------------|
-| `val(meta), file("*_svpileup.aggregate.bedpe")` | `tuple` | `bedpe` | Tuple of meta and BEDPE format output file |
+| `meta` | `val` | Map containing sample information (must include 'id') |
+| `txt` | `path` | Aggregated SvPileup output file |
 
 ### `AGGREGATE_SV_PILEUP` Inputs
 
 | Name | Type | Description |
 |------|------|-------------|
-| `val(meta), path(bam), path(txt)` | `tuple` | `meta`: Map containing sample information (must include 'id'); `bam`: Input BAM file; `txt`: SvPileup breakpoint output file |
-
-### `AGGREGATE_SV_PILEUP` Outputs
-
-| Name | Type | Emit | Description |
-|------|------|------|-------------|
-| `val(meta), file("*_svpileup.aggregate.txt")` | `tuple` | `txt` | Tuple of meta and aggregated SvPileup output file |
+| `meta` | `val` | Map containing sample information (must include 'id') |
+| `bam` | `path` | Input BAM file |
+| `txt` | `path` | SvPileup breakpoint output file |
 
 ### `COORDINATE_SORT` Inputs
 
 | Name | Type | Description |
 |------|------|-------------|
-| `val(meta), path(bam)` | `tuple` | `meta`: Map containing sample information (must include 'id'); `bam`: Input BAM file to be sorted |
-
-### `COORDINATE_SORT` Outputs
-
-| Name | Type | Emit | Description |
-|------|------|------|-------------|
-| `val(meta), file("*_sorted.bam")` | `tuple` | `bam` | Tuple of meta and coordinate-sorted BAM file |
+| `meta` | `val` | Map containing sample information (must include 'id') |
+| `bam` | `path` | Input BAM file to be sorted |
 
 ### `SV_PILEUP` Inputs
 
 | Name | Type | Description |
 |------|------|-------------|
-| `val(meta), path(bam)` | `tuple` | `meta`: Map containing sample information (must include 'id'); `bam`: Input BAM file |
-
-### `SV_PILEUP` Outputs
-
-| Name | Type | Emit | Description |
-|------|------|------|-------------|
-| `val(meta), file("*_svpileup.txt")` | `tuple` | `txt` | Tuple of meta and SvPileup breakpoint output file |
-| `val(meta), file("*_svpileup.bam")` | `tuple` | `bam` | Tuple of meta and SvPileup BAM file |
+| `meta` | `val` | Map containing sample information (must include 'id') |
+| `bam` | `path` | Input BAM file |
 
 ---
 
 *This pipeline was built with [Nextflow](https://nextflow.io).
-Documentation generated by [nf-docs](https://github.com/ewels/nf-docs) v0.2.0 on 2026-03-03 22:49:08 UTC.*
+Documentation generated by [nf-docs](https://github.com/ewels/nf-docs) v0.3.0 on 2026-05-27 21:22:48 UTC.*
 
 <!-- END_NF_DOCS -->
diff --git a/docs/examples/nf-fgsv/yaml/pipeline-api.yaml b/docs/examples/nf-fgsv/yaml/pipeline-api.yaml
index b7a24db..6c357ed 100644
--- a/docs/examples/nf-fgsv/yaml/pipeline-api.yaml
+++ b/docs/examples/nf-fgsv/yaml/pipeline-api.yaml
@@ -2,13 +2,21 @@ pipeline:
   name: nf-fgsv workflow parameters
   description: Nextflow workflow for running fgsv.
   version: 0.1.0
-  repository: https://github.com/fulcrumgenomics/nf-fgsv
+  repository: https://github.com/fg-labs/nf-fgsv
   authors:
   - Fulcrum Genomics
   readme_content: "> [!NOTE]  \n> This repository is primarily for testing the latest Nextflow features\
     \ and the workflow is relatively simple.\n\nThis is a Nextflow workflow for running [fgsv](https://github.com/fulcrumgenomics/fgsv)\
-    \ on a BAM file to gather evidence for structural variation via breakpoint detection.\n\n## Set up\
-    \ Environment\n\nMake sure [Pixi](https://pixi.sh/latest/#installation) and [Docker](https://docs.docker.com/engine/install/)\
+    \ on a BAM file to gather evidence for structural variation via breakpoint detection.\n\n<p>\n<a href=\"\
+    https://fulcrumgenomics.com\">\n<picture>\n  <source media=\"(prefers-color-scheme: dark)\" srcset=\"\
+    https://raw.githubusercontent.com/fg-labs/nf-fgsv/main/.github/logos/fulcrumgenomics-dark.svg\">\n\
+    \  <source media=\"(prefers-color-scheme: light)\" srcset=\"https://raw.githubusercontent.com/fg-labs/nf-fgsv/main/.github/logos/fulcrumgenomics-light.svg\"\
+    >\n  <img alt=\"Fulcrum Genomics\" src=\"https://raw.githubusercontent.com/fg-labs/nf-fgsv/main/.github/logos/fulcrumgenomics-light.svg\"\
+    \ height=\"100\" width=\"25%\">\n</picture>\n</a>\n</p>\n\n[Visit us at Fulcrum Genomics](https://www.fulcrumgenomics.com)\
+    \ to learn more about how we can power your Bioinformatics with nf-fgsv and beyond.\n\n<a href=\"\
+    mailto:contact@fulcrumgenomics.com?subject=[GitHub inquiry]\"><img src=\"https://img.shields.io/badge/Email_us-%2338b44a.svg?&style=for-the-badge&logo=gmail&logoColor=white\"\
+    /></a>\n<a href=\"https://www.fulcrumgenomics.com\"><img src=\"https://img.shields.io/badge/Visit_Us-%2326a8e0.svg?&style=for-the-badge&logo=wordpress&logoColor=white\"\
+    /></a>\n\n## Set up Environment\n\nMake sure [Pixi](https://pixi.sh/latest/#installation) and [Docker](https://docs.docker.com/engine/install/)\
     \ are installed.\n\nThe environment for this analysis is in [pixi.toml](pixi.toml) and is named `nf-fgsv`.\n\
     \nTo install:\n\n```console\npixi install\n```\n\n## Run the Workflow\n\nTo save on typing, a pixi\
     \ task is available which aliases `nextflow run main.nf`.\n\n```console\npixi run \\\n    nf-workflow\
@@ -44,7 +52,17 @@ pipeline:
 inputs:
 - name: input
   type: string
-  description: Path to tab-separated file containing information about the samples in the experiment.
+  description: 'Path to a tab-separated values (TSV) sample sheet describing the samples to analyze. The
+    file must have a header row with the following required columns:
+
+
+    - `sample`: a unique sample identifier containing no whitespace; used as the `meta.id` that names
+    per-sample outputs.
+
+    - `bam`: path to an existing BAM file for the sample (must end in `.bam`).
+
+
+    See `schemas/input_schema.json` for the full validation rules.'
   required: true
   format: file-path
   pattern: .*.tsv$
@@ -52,15 +70,33 @@ inputs:
 config_params: []
 workflows:
 - name: ''
-  docstring: ''
+  docstring: 'Detect structural-variant breakpoints from aligned reads using fgsv.
+
+    The `--input` sample sheet provides one `sample` identifier and `bam` path per
+
+    row (see the `--input` parameter for the full column specification). Every
+
+    per-sample output — the sorted BAM, SvPileup BAM and text, aggregated
+
+    breakpoints, and BEDPE — is published via the `sample_outputs` topic into a
+
+    directory named after the sample''s `meta.id`. For each sample the workflow runs:
+
+    1. `COORDINATE_SORT` — coordinate-sort the input BAM with samtools.
+
+    2. `SV_PILEUP` — gather read-level evidence for structural variants (fgsv SvPileup).
+
+    3. `AGGREGATE_SV_PILEUP` — merge pileups that likely support the same breakpoint.
+
+    4. `AGGREGATE_SV_PILEUP_TO_BEDPE` — convert the aggregated breakpoints to BEDPE.'
   file: main.nf
-  line: 19
-  end_line: 42
+  line: 35
+  end_line: 51
   inputs: []
   outputs: []
   calls: []
   is_entry: true
-  source_url: https://github.com/fulcrumgenomics/nf-fgsv/blob/73e7adf5d96a2031f89519bbb378d8e19954aeb7/main.nf#L19-L42
+  source_url: https://github.com/fg-labs/nf-fgsv/blob/f7298efb052edc211b63921113eaa18d78d85aa2/main.nf#L35-L51
 processes:
 - name: AGGREGATE_SV_PILEUP_TO_BEDPE
   docstring: 'Convert aggregated SvPileup output to BEDPE format using fgsv
@@ -68,77 +104,74 @@ processes:
     AggregateSvPileupToBedPE.'
   file: modules/aggregate_sv_pileup_to_bedpe.nf
   line: 11
-  end_line: 31
+  end_line: 34
   inputs:
-  - name: val(meta), path(txt)
-    type: tuple
-    description: '`meta`: Map containing sample information (must include ''id''); `txt`: Aggregated SvPileup
-      output file'
-    qualifier: Tuple<Map, Path>
-  outputs:
-  - name: val(meta), file("*_svpileup.aggregate.bedpe")
-    type: tuple
-    description: Tuple of meta and BEDPE format output file
-    emit: bedpe
+  - name: meta
+    type: val
+    description: Map containing sample information (must include 'id')
+    qualifier: Map
+  - name: txt
+    type: path
+    description: Aggregated SvPileup output file
+    qualifier: Path
+  outputs: []
   directives: {}
-  source_url: https://github.com/fulcrumgenomics/nf-fgsv/blob/73e7adf5d96a2031f89519bbb378d8e19954aeb7/modules/aggregate_sv_pileup_to_bedpe.nf#L11-L31
+  source_url: https://github.com/fg-labs/nf-fgsv/blob/f7298efb052edc211b63921113eaa18d78d85aa2/modules/aggregate_sv_pileup_to_bedpe.nf#L11-L34
 - name: AGGREGATE_SV_PILEUP
   docstring: 'Aggregate and merge pileups that are likely to support the same breakpoint
 
     using fgsv AggregateSvPileup.'
   file: modules/aggregate_sv_pileup.nf
   line: 12
-  end_line: 33
+  end_line: 36
   inputs:
-  - name: val(meta), path(bam), path(txt)
-    type: tuple
-    description: '`meta`: Map containing sample information (must include ''id''); `bam`: Input BAM file;
-      `txt`: SvPileup breakpoint output file'
-    qualifier: Tuple<Map, Path, Path>
-  outputs:
-  - name: val(meta), file("*_svpileup.aggregate.txt")
-    type: tuple
-    description: Tuple of meta and aggregated SvPileup output file
-    emit: txt
+  - name: meta
+    type: val
+    description: Map containing sample information (must include 'id')
+    qualifier: Map
+  - name: bam
+    type: path
+    description: Input BAM file
+    qualifier: Path
+  - name: txt
+    type: path
+    description: SvPileup breakpoint output file
+    qualifier: Path
+  outputs: []
   directives: {}
-  source_url: https://github.com/fulcrumgenomics/nf-fgsv/blob/73e7adf5d96a2031f89519bbb378d8e19954aeb7/modules/aggregate_sv_pileup.nf#L12-L33
+  source_url: https://github.com/fg-labs/nf-fgsv/blob/f7298efb052edc211b63921113eaa18d78d85aa2/modules/aggregate_sv_pileup.nf#L12-L36
 - name: COORDINATE_SORT
   docstring: Sort a BAM file by genomic coordinates using samtools sort.
   file: modules/coordinate_sort.nf
   line: 10
   end_line: 31
   inputs:
-  - name: val(meta), path(bam)
-    type: tuple
-    description: '`meta`: Map containing sample information (must include ''id''); `bam`: Input BAM file
-      to be sorted'
-    qualifier: Tuple<Map, Path>
-  outputs:
-  - name: val(meta), file("*_sorted.bam")
-    type: tuple
-    description: Tuple of meta and coordinate-sorted BAM file
-    emit: bam
+  - name: meta
+    type: val
+    description: Map containing sample information (must include 'id')
+    qualifier: Map
+  - name: bam
+    type: path
+    description: Input BAM file to be sorted
+    qualifier: Path
+  outputs: []
   directives: {}
-  source_url: https://github.com/fulcrumgenomics/nf-fgsv/blob/73e7adf5d96a2031f89519bbb378d8e19954aeb7/modules/coordinate_sort.nf#L10-L31
+  source_url: https://github.com/fg-labs/nf-fgsv/blob/f7298efb052edc211b63921113eaa18d78d85aa2/modules/coordinate_sort.nf#L10-L31
 - name: SV_PILEUP
   docstring: Detect structural variant evidence from a BAM file using fgsv SvPileup.
   file: modules/sv_pileup.nf
-  line: 11
-  end_line: 33
+  line: 10
+  end_line: 35
   inputs:
-  - name: val(meta), path(bam)
-    type: tuple
-    description: '`meta`: Map containing sample information (must include ''id''); `bam`: Input BAM file'
-    qualifier: Tuple<Map, Path>
-  outputs:
-  - name: val(meta), file("*_svpileup.txt")
-    type: tuple
-    description: Tuple of meta and SvPileup breakpoint output file
-    emit: txt
-  - name: val(meta), file("*_svpileup.bam")
-    type: tuple
-    description: Tuple of meta and SvPileup BAM file
-    emit: bam
+  - name: meta
+    type: val
+    description: Map containing sample information (must include 'id')
+    qualifier: Map
+  - name: bam
+    type: path
+    description: Input BAM file
+    qualifier: Path
+  outputs: []
   directives: {}
-  source_url: https://github.com/fulcrumgenomics/nf-fgsv/blob/73e7adf5d96a2031f89519bbb378d8e19954aeb7/modules/sv_pileup.nf#L11-L33
+  source_url: https://github.com/fg-labs/nf-fgsv/blob/f7298efb052edc211b63921113eaa18d78d85aa2/modules/sv_pileup.nf#L10-L35
 functions: []