Split out funcprofiler + rnaseq_auto fixture changes

These need engine-side follow-up work:
- funcprofiler.mmd: profiling->reporting trunk-Y kink, qc-crosses-merge
- funcprofiler_upstream.mmd: humann3 junction nearly horizontal
- rnaseq_auto.mmd (expanded): hisat2/bowtie2 stacking under y_spacing
  threshold, ascend-vs-descend z-order mismatch around
  bbsplit/sortmerna/ribodetector fan

Moved to PR #337.  Restored examples/rnaseq_auto.mmd to main's version
so this PR (docs gallery + hlatyping logo path + gallery script
infrastructure) lands without an engine block.

Author: pinin4fjords

docs/pipelines/index.md

@@ -708,181 +708,3 @@ Genome assembly from long reads and Hi-C data through purging, polishing, scaffo
         yahs -->|assemblies| asmstats
     ```
 
-## [nf-core/funcprofiler (upstream)](https://github.com/nf-core/funcprofiler)
-
-Upstream .mmd with a separate line per profiling tool (11 lines). Exposes routing issues with large bundles exiting a single port.
-
-![nf-core/funcprofiler (upstream)](../assets/renders/pipeline_funcprofiler_upstream.svg)
-
-??? note "Mermaid source"
-
-    ```text
-    %%metro title: nf-core/funcprofiler (upstream)
-    %%metro style: dark
-    %%metro line: qc | Preprocessing & QC | #4CAF50
-    %%metro line: concat | Merge & Concat | #2196F3
-    %%metro line: humann3 | HUMAnN v3 | #FF9800
-    %%metro line: humann4 | HUMAnN v4 | #FF5722
-    %%metro line: fmhfunprofiler | FMH FunProfiler | #E91E63
-    %%metro line: rgi | RGI | #CDDC39
-    %%metro line: mifaser | mifaser | #00BCD4
-    %%metro line: diamond | DIAMOND | #9C27B0
-    %%metro line: eggnog | eggNOG-mapper | #3F51B5
-    %%metro line: multiqc | Reporting | #795548
-    %%metro line: db | Database Prep | #607D8B
-    
-    graph LR
-        subgraph input[Input]
-            input_short([Short Read\nFASTQ])
-            input_dbs([Input Databases])
-            sr_qc(Preprocess)
-            merge(MERGE_RUNS)
-        end
-    
-        subgraph profiling[Functional Profiling]
-            humann3(HUMAnN v3)
-            humann4(HUMAnN v4)
-            fmhfunprofiler(FMH FunProfiler)
-            RGI(RGI)
-            mifaser(mifaser)
-            diamond(DIAMOND)
-            eggnog_mapper(eggNOG-mapper)
-        end
-    
-        subgraph QC[Quality Check]
-            multiqc(MultiQC)
-        end
-    
-        subgraph Output[Output]
-            output([Results Directory])
-        end
-    
-        %% DB Prep
-        input_dbs -->|db| humann3
-        input_dbs -->|db| humann4
-        input_dbs -->|db| fmhfunprofiler
-        input_dbs -->|db| RGI
-        input_dbs -->|db| mifaser
-        input_dbs -->|db| diamond
-        input_dbs -->|db| eggnog_mapper
-    
-        %% Preprocessing
-        input_short -->|qc| sr_qc
-        sr_qc -->|concat| merge
-    
-        %% Profiling split
-        merge -->|humann3| humann3
-        merge -->|humann4| humann4
-        merge -->|fmhfunprofiler| fmhfunprofiler
-        merge -->|rgi| RGI
-        merge -->|mifaser| mifaser
-        merge -->|diamond| diamond
-        merge -->|eggnog| eggnog_mapper
-    
-        %% Reporting
-        sr_qc -->|multiqc| multiqc
-        humann3 -->|multiqc| multiqc
-        humann4 -->|multiqc| multiqc
-        fmhfunprofiler -->|multiqc| multiqc
-        RGI -->|multiqc| multiqc
-        mifaser -->|multiqc| multiqc
-        diamond -->|multiqc| multiqc
-        eggnog_mapper -->|multiqc| multiqc
-    
-        %% Output
-        multiqc -->|multiqc| output
-        humann3 -->|humann3| output
-        humann4 -->|humann4| output
-        fmhfunprofiler -->|fmhfunprofiler| output
-        RGI -->|rgi| output
-        mifaser -->|mifaser| output
-        diamond -->|diamond| output
-        eggnog_mapper -->|eggnog| output
-    ```
-
-## [nf-core/funcprofiler (simplified)](https://github.com/nf-core/funcprofiler)
-
-Simplified to 3 lines: profiling, QC, and database prep. Same topology, cleaner routing.
-
-![nf-core/funcprofiler (simplified)](../assets/renders/pipeline_funcprofiler.svg)
-
-??? note "Mermaid source"
-
-    ```text
-    %%metro title: nf-core/funcprofiler
-    %%metro style: dark
-    %%metro line: profiling | Functional Profiling | #FF9800
-    %%metro line: qc | Preprocessing & QC | #4CAF50
-    %%metro line: db | Database Prep | #607D8B
-    %%metro legend: bl
-    %%metro compact_offsets: true
-    
-    graph LR
-        subgraph input [Input & Preprocessing]
-            %%metro exit: right | profiling, qc, db
-            input_short([Short Read\nFASTQ])
-            input_dbs([Input\nDatabases])
-            sr_qc[Preprocess]
-            merge[Merge Runs]
-    
-            input_short -->|qc| sr_qc
-            sr_qc -->|profiling| merge
-        end
-    
-        subgraph profiling [Functional Profiling]
-            %%metro entry: left | profiling, db
-            %%metro exit: right | profiling, qc
-            humann3[HUMAnN v3]
-            humann4[HUMAnN v4]
-            fmhfunprofiler[FMH FunProfiler]
-            RGI[RGI]
-            mifaser[mifaser]
-            diamond[DIAMOND]
-            eggnog_mapper[eggNOG-mapper]
-        end
-    
-        subgraph reporting [Reporting]
-            %%metro entry: left | profiling, qc
-            multiqc[MultiQC]
-            output([Results\nDirectory])
-    
-            multiqc -->|qc| output
-        end
-    
-        %% DB Prep: databases feed all profiling tools
-        input_dbs -->|db| humann3
-        input_dbs -->|db| humann4
-        input_dbs -->|db| fmhfunprofiler
-        input_dbs -->|db| RGI
-        input_dbs -->|db| mifaser
-        input_dbs -->|db| diamond
-        input_dbs -->|db| eggnog_mapper
-    
-        %% Profiling fan-out from merge
-        merge -->|profiling| humann3
-        merge -->|profiling| humann4
-        merge -->|profiling| fmhfunprofiler
-        merge -->|profiling| RGI
-        merge -->|profiling| mifaser
-        merge -->|profiling| diamond
-        merge -->|profiling| eggnog_mapper
-    
-        %% QC reporting
-        sr_qc -->|qc| multiqc
-        humann3 -->|qc| multiqc
-        humann4 -->|qc| multiqc
-        fmhfunprofiler -->|qc| multiqc
-        RGI -->|qc| multiqc
-        mifaser -->|qc| multiqc
-        diamond -->|qc| multiqc
-        eggnog_mapper -->|qc| multiqc
-    
-        %% Profiling results to output
-        humann3 -->|profiling| output
-        humann4 -->|profiling| output
-        fmhfunprofiler -->|profiling| output
-        RGI -->|profiling| output
-        mifaser -->|profiling| output
-        diamond -->|profiling| output
-        eggnog_mapper -->|profiling| output
-    ```