Format README

README.md

@@ -16,44 +16,45 @@
 
 # ![NanopathPipeline](docs/images/16S_Pipeline.png#gh-light-mode-only) ![NanopathPipeline](docs/images/16S_Pipeline_darkmode.png#gh-dark-mode-only)
 
-1. Initialize the data:
-      If a fastq directory is provided:
-         Concatenate fastq files using CAT_FASTQS.
-
-2. Validate input:
-      Use the INPUT_CHECK subworkflow to read samplesheet, validate, and stage input files.
-      Branch reads based on their status (discontinued or samples).
-
-3. Perform Quality Control:
-      Run ([`FASTP`](https://github.com/OpenGene/fastp)) for quality control, filtering, and preprocessing.
-      Filter out samples with no reads left after FASTP.
-      Run ([`FASTQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)) on the processed reads.
-
-4. Classfy and Cluster:
-      If specified, remove unclassified reads using ([`KRAKEN2`](https://github.com/DerrickWood/kraken2)).
-      Subset reads based on specified parameters (default 100k reads to keep memory requirements reasonable).
-      Perform k-mer frequency analysis with KMER_FREQS.
-      Perform read clustering with READ_CLUSTERING using ([`HDBSCAN`](https://github.com/scikit-learn-contrib/hdbscan)) and ([`UMAP`](https://umap-learn.readthedocs.io/en/latest/)).
-
-5. Split Clusters and Correct Errors:
-      Split clusters.
-      Perform error correction using ([`CANU`](https://github.com/marbl/canu)).
-
-6. Select and Polish Draft:
-      Select draft reads using ([`FASTANI`](https://github.com/ParBLiSS/FastANI)).
-      Polish drafts using ([`RACON`](https://github.com/isovic/racon)).
-      Generate final consensus using ([`MEDAKA`](https://github.com/nanoporetech/medaka)).
-
-7. Classify Taxonomically:
-      Based on chosen tool, classify consensus sequences with ([`BLAST`](https://www.ncbi.nlm.nih.gov/books/NBK279690/)), ([`SEQMATCH`](https://github.com/rdpstaff/SequenceMatch)), ([`KRAKEN`](https://github.com/DerrickWood/kraken2)) or all of them. 
-      Join classification results using JOIN_RESULTS.
-
-8. Estimate Abundace:
-      Estimate abundance per sample per detected species. 
-
-9. Generate Reports:
-      If report generation is chosen:
-         Generate HTML reports.
+1. **Initialize the data:**
+      - If a fastq directory is provided:
+         - Concatenate fastq files using CAT_FASTQS.
+
+2. **Validate input:**
+      - Use the INPUT_CHECK subworkflow to read samplesheet, validate, and stage input files.
+      - Branch reads based on their status (discontinued or samples).
+
+3. **Perform Quality Control:**
+      - Run ([`FASTP`](https://github.com/OpenGene/fastp)) for quality control, filtering, and preprocessing.
+      - Filter out samples with no reads left after FASTP.
+      - Run ([`FASTQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)) on the processed reads.
+
+4. **Classfy and Cluster:**
+      - If specified, remove unclassified reads using ([`KRAKEN2`](https://github.com/DerrickWood/kraken2)).
+      - Subset reads based on specified parameters (default 100k reads to keep memory requirements reasonable).
+      - Perform k-mer frequency analysis with KMER_FREQS.
+      - Perform read clustering with READ_CLUSTERING using ([`HDBSCAN`](https://github.com/scikit-learn-contrib/hdbscan)) and ([`UMAP`](https://umap-learn.readthedocs.io/en/latest/)).
+
+5. **Split Clusters and Correct Errors:**
+      - Split clusters.
+      - Perform error correction using ([`CANU`](https://github.com/marbl/canu)).
+
+6. **Select and Polish Draft:**
+      - Select draft reads using ([`FASTANI`](https://github.com/ParBLiSS/FastANI)).
+      - Polish drafts using ([`RACON`](https://github.com/isovic/racon)).
+      - Generate final consensus using ([`MEDAKA`](https://github.com/nanoporetech/medaka)).
+
+7. **Classify Taxonomically:**
+      - Based on chosen tool, classify consensus sequences with ([`BLAST`](https://www.ncbi.nlm.nih.gov/books/NBK279690/)), ([`SEQMATCH`](https://github.com/rdpstaff/SequenceMatch)), ([`KRAKEN`](https://github.com/DerrickWood/kraken2)) or all of them. 
+      - Join classification results using JOIN_RESULTS.
+
+8. **Estimate Abundace:**
+      - Estimate abundance per sample per detected species. 
+
+9. **Generate Reports:**
+      - If report generation is chosen:
+         - Generate HTML reports.
+
 ## Usage
 
 > **Note**