Add TODO for generating large Qualimap reference output

Author: ewels

TODO-run-qualimap.md

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+# TODO: Generate large Qualimap reference output
+
+## Problem
+
+The large Qualimap reference output (`benchmark/qualimap/large/`) is missing.
+Qualimap's RNA-seq mode name-sorts the entire BAM file, which requires ~50GB of
+temporary disk space for the 10GB GM12878 BAM (185M reads). This filled the disk
+during the first attempt.
+
+## Prerequisites
+
+- ~60GB free disk space
+- Docker installed
+- The Qualimap container: `quay.io/biocontainers/qualimap:2.3--hdfd78af_0`
+
+## Steps
+
+1. **Decompress the GTF** (Qualimap can't read gzipped GTF):
+
+   ```bash
+   gunzip -k benchmark/input/large/genes.gtf.gz
+   ```
+
+2. **Run Qualimap**:
+
+   ```bash
+   mkdir -p benchmark/qualimap/large
+   docker run --rm \
+     -v "$(pwd)/benchmark:/data" \
+     quay.io/biocontainers/qualimap:2.3--hdfd78af_0 \
+     qualimap rnaseq \
+       -bam /data/input/large/GM12878_REP1.markdup.sorted.bam \
+       -gtf /data/input/large/genes.gtf \
+       -outdir /data/qualimap_tmp_large \
+       --java-mem-size=8G \
+       -pe
+   ```
+
+   This will take a long time (1-2 hours). The name-sort phase is the bottleneck.
+
+3. **Copy the key output files**:
+
+   ```bash
+   cp benchmark/qualimap_tmp_large/rnaseq_qc_results.txt benchmark/qualimap/large/
+   cp "benchmark/qualimap_tmp_large/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt" benchmark/qualimap/large/
+   ```
+
+4. **Clean up**:
+
+   ```bash
+   rm -rf benchmark/qualimap_tmp_large
+   rm -f benchmark/input/large/genes.gtf
+   ```
+
+5. **Verify** — compare with RustQC output:
+
+   ```bash
+   diff benchmark/qualimap/large/rnaseq_qc_results.txt \
+        benchmark/RustQC/large/qualimap/rnaseq_qc_results.txt
+   diff benchmark/qualimap/large/coverage_profile_along_genes_\(total\).txt \
+        benchmark/RustQC/large/qualimap/coverage_profile_along_genes_\(total\).txt
+   ```
+
+6. **Commit**:
+
+   ```bash
+   git add benchmark/qualimap/large/
+   git commit -m "Add large Qualimap reference output"
+   git push
+   ```
+
+7. **Delete this file** once done.
+
+## Small dataset reference
+
+Already generated and committed at `benchmark/qualimap/small/`.