Fix workflow list formatting

Author: Loyale

docs/probe-design-workflow.md

@@ -7,42 +7,54 @@ them.
 
 ## Pipeline overview (ordered)
 1. **Read FASTA record(s).**
-   - `designProbes` uses only the first FASTA record.
-   - `designProbesBatch` processes every record.
-   - A FASTA header can override the channel using `channel=...`.
-   - Genome masking is enabled by default and requires a registered species
-     (use `fetchMouseIndex` or `buildGenomeIndex`) or an explicit `--index`.
+
+    - `designProbes` uses only the first FASTA record.
+    - `designProbesBatch` processes every record.
+    - A FASTA header can override the channel using `channel=...`.
+    - Genome masking is enabled by default and requires a registered species
+      (use `fetchMouseIndex` or `buildGenomeIndex`) or an explicit `--index`.
 2. **Optional repeat masking (disabled by default).**
-   - If enabled, the input sequence is masked using RepeatMasker and masked bases
-     are converted to `N`. Tiles containing masked bases are discarded later.
+
+    - If enabled, the input sequence is masked using RepeatMasker and masked bases
+      are converted to `N`. Tiles containing masked bases are discarded later.
 3. **Tile the target sequence (reverse-complemented).**
-   - The sequence is scanned with a step size of 1 to generate 52-nt tiles by
-     default.
-   - Each tile is **reverse-complemented** so probes are antisense to the target.
-   - Any tile containing `N` is discarded immediately.
+
+    - The sequence is scanned with a step size of 1 to generate 52-nt tiles by
+      default.
+    - Each tile is **reverse-complemented** so probes are antisense to the target.
+    - Any tile containing `N` is discarded immediately.
 4. **Filter homopolymer runs (C and G).**
-   - Tiles are removed if they contain long runs of C's or G's beyond the allowed
-     thresholds.
+
+    - Tiles are removed if they contain long runs of C's or G's beyond the allowed
+      thresholds.
 5. **Filter hairpins.**
-   - Each tile is screened with `primer3` for self-hairpin structures.
-   - Tiles with a predicted hairpin melting temperature >= 45 C are removed.
+
+    - Each tile is screened with `primer3` for self-hairpin structures.
+    - Tiles with a predicted hairpin melting temperature >= 45 C are removed.
 6. **Genome uniqueness filtering (Bowtie2).**
-   - Remaining tiles are aligned to the reference genome index.
-   - Tiles with more than the allowed number of hits are removed.
+
+    - Remaining tiles are aligned to the reference genome index.
+    - Tiles with more than the allowed number of hits are removed.
 7. **GC-content filtering.**
-   - Tiles must fall within the allowed GC% range.
+
+    - Tiles must fall within the allowed GC% range.
 8. **Gibbs free energy filtering.**
-   - Tiles with binding free energies outside the allowed range are removed.
+
+    - Tiles with binding free energies outside the allowed range are removed.
 9. **Split tiles into probe halves.**
-   - Each tile is split into two 25-mers (for a 52-mer tile), dropping the two
-     middle bases to create a short gap.
+
+    - Each tile is split into two 25-mers (for a 52-mer tile), dropping the two
+      middle bases to create a short gap.
 10. **Optional dTm filtering.**
+
     - If enabled, tiles are removed when the temperature difference between
       the two halves is too large.
 11. **Select top N non-overlapping tiles.**
+
     - Tiles are ranked by how close their Gibbs free energy is to the target.
     - Overlapping tiles are skipped to keep probes spread out.
 12. **Add HCR initiators and spacers.**
+
     - Channel-specific initiator sequences are appended to the probe halves.
 
 ## Default parameters