Add pipeline metro map

.github/workflows/metro-map.yml

@@ -0,0 +1,48 @@
+name: Render metro map
+
+on:
+  push:
+    branches: [dev, master]
+    paths:
+      - "assets/metro_map.mmd"
+  pull_request:
+    paths:
+      - "assets/metro_map.mmd"
+
+jobs:
+  render:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: astral-sh/setup-uv@v6
+
+      - name: Install nf-metro@1.1.0
+        run: uv tool install nf-metro
+
+      - name: Render metro map
+        run: |
+          nf-metro render assets/metro_map.mmd \
+            -o assets/metro_map.svg \
+            --theme nfcore \
+            --embed-font \
+            --fold-threshold 15
+
+      - name: Check for changes
+        id: diff
+        run: |
+          git diff --exit-code assets/metro_map.svg || echo "changed=true" >> "$GITHUB_OUTPUT"
+
+      - name: Commit updated SVG
+        if: steps.diff.outputs.changed == 'true' && github.event_name == 'push'
+        run: |
+          git config user.name "github-actions[bot]"
+          git config user.email "github-actions[bot]@users.noreply.github.com"
+          git add assets/metro_map.svg
+          git commit -m "chore: re-render metro map [skip ci]"
+          git push
+
+      - name: Warn on PR if SVG is stale
+        if: steps.diff.outputs.changed == 'true' && github.event_name == 'pull_request'
+        run: |
+          echo "::warning::assets/metro_map.svg is out of date with assets/metro_map.mmd — it will be re-rendered on merge."

README.md

@@ -78,8 +78,7 @@ BaseRecalibrator` and `GATK ApplyBQSR`)
   `--tools` adding `rna_filtering`)
 
 <p align="center">
-    <img title="RNADNAVAR Workflow"
-src="docs/images/rnadnavar_schemav3.png">
+    <img title="RNADNAVAR Workflow" src="assets/metro_map.svg">
 </p>
 
 ## Usage

assets/metro_map.mmd

@@ -0,0 +1,119 @@
+%%metro title: nf-core/rnadnavar
+%%metro logo: docs/images/nf-core-rnadnavar_logo_dark.png
+%%metro style: dark
+%%metro file: fastq_in | FASTQ
+%%metro file: report_out | HTML
+%%metro line: rna | RNA (Tumor + DNA Normal) | #e63946
+%%metro line: dna | DNA (Tumor + Normal) [OPTIONAL] | #4a90d9 | dashed
+%%metro line: realignment | Realignment (RNA) [OPTIONAL] | #f5c542 | dashed
+%%metro line_order: definition
+%%metro legend: bl
+
+graph LR
+    subgraph preprocessing [Pre-processing & Alignment]
+        fastq_in[ ]
+        fastqc[FastQC]
+        fastp[fastp]
+        bwa_mem[BWA-mem/BWA-mem2]
+        star[STAR]
+        samtools_merge[SAMtools Merge]
+
+        fastq_in -->|dna,rna| fastqc
+        fastqc -->|dna,rna| fastp
+        fastp -->|dna| bwa_mem
+        fastp -->|rna| star
+        bwa_mem -->|dna| samtools_merge
+        star -->|rna| samtools_merge
+    end
+
+    subgraph gatk_preproc [GATK Preprocessing]
+        markduplicates[MarkDuplicates]
+        splitncigar[SplitNCigarReads]
+        baserecalibrator[BaseRecalibrator]
+        applybqsr[ApplyBQSR]
+        samtools_stats[SAMtools Stats]
+        mosdepth[Mosdepth]
+
+        markduplicates -->|dna| baserecalibrator
+        markduplicates -->|rna| splitncigar
+        splitncigar -->|rna| baserecalibrator
+        baserecalibrator -->|dna,rna| applybqsr
+        applybqsr -->|dna,rna| samtools_stats
+        samtools_stats -->|dna,rna| mosdepth
+    end
+
+    subgraph variant_calling [Variant Calling (parallel)]
+        vc_fork[ ]
+        mutect2[Mutect2]
+        strelka[Strelka2]
+        sage[SAGE]
+        vc_join[ ]
+
+        vc_fork -->|dna,rna| mutect2
+        vc_fork -->|dna,rna| strelka
+        vc_fork -->|dna,rna| sage
+        mutect2 -->|dna,rna| vc_join
+        strelka -->|dna,rna| vc_join
+        sage -->|dna,rna| vc_join
+    end
+
+    subgraph normalization [Normalization & Annotation]
+        vt_decompose[VT Decompose]
+        vt_normalize[VT Normalize]
+        ensemblvep[Ensembl VEP]
+
+        vt_decompose -->|dna,rna| vt_normalize
+        vt_normalize -->|dna,rna| ensemblvep
+    end
+
+    subgraph consensus [Consensus & Filtering]
+        vcf2maf[vcf2MAF]
+        run_consensus[Consensus]
+        maf_filtering[MAF Filtering]
+
+        vcf2maf -->|dna,rna| run_consensus
+        run_consensus -->|dna,rna| maf_filtering
+    end
+
+    subgraph realign [Realignment (RNA) [OPTIONAL]]
+        maf2bed[MAF2BED]
+        extract_reads[Extract Reads]
+        hisat2[HISAT2]
+        markdup_re[MarkDuplicates]
+        splitncigar_re[SplitNCigarReads]
+        bqsr_re[BQSR]
+        varcall_re[Variant Calling]
+        norm_re[Normalization]
+        annotate_re[Annotation]
+        consensus_re[Consensus]
+        filter_re[MAF Filtering]
+
+        maf2bed -->|realignment| extract_reads
+        extract_reads -->|realignment| hisat2
+        hisat2 -->|realignment| markdup_re
+        markdup_re -->|realignment| splitncigar_re
+        splitncigar_re -->|realignment| bqsr_re
+        bqsr_re -->|realignment| varcall_re
+        varcall_re -->|realignment| norm_re
+        norm_re -->|realignment| annotate_re
+        annotate_re -->|realignment| consensus_re
+        consensus_re -->|realignment| filter_re
+    end
+
+    subgraph reporting [Reporting]
+        rna_filter[RNA MAF Filtering]
+        rna_filter -->|rna,realignment| multiqc
+        multiqc[MultiQC]
+        report_out[ ]
+
+        multiqc -->|rna,realignment| report_out
+    end
+
+    %% Inter-section edges
+    maf_filtering -->|realignment| maf2bed
+    samtools_merge -->|dna,rna| markduplicates
+    mosdepth -->|dna,rna| vc_fork
+    vc_join -->|dna,rna| vt_decompose
+    ensemblvep -->|dna,rna| vcf2maf
+    filter_re -->|realignment| rna_filter
+    maf_filtering -->|rna| rna_filter