diff --git a/nextflow/README.md b/nextflow/README.md
index c1e663b..a4bdabe 100644
--- a/nextflow/README.md
+++ b/nextflow/README.md
@@ -10,6 +10,7 @@ It is recommended that each workflow in `main.nf` is run sequentially to allow f
- The first workflow runs [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) on the raw fastq files and then [`MultiQC`](http://multiqc.info/) on those results
- To run this workflow alone use: `nextflow run main.nf -params-file params.json -profile iris -entry FASTQC_FASTQ`
+```mermaid
@@ -54,11 +55,13 @@ flowchart TB
+```
2. **Trimming and QC**
- The second workflow runs [`fastp`](https://github.com/OpenGene/fastp) to trim adapters and/or poly-X or poly-A tails, followed by [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and [`MultiQC`](http://multiqc.info/)
- To run this workflow alone use: `nextflow run main.nf -params-file params.json -profile iris -entry FASTP_FASTQ`
+```mermaid
@@ -103,11 +106,13 @@ flowchart TB
+```
3. **Alignment and indexing**
- The third workflow runs [`STAR`](https://github.com/alexdobin/STAR) on the adapter-trimmed fastq files followed by [`SAMtools`](https://sourceforge.net/projects/samtools/files/samtools/) indexing
- To run this workflow alone use: `nextflow run main.nf -params-file params.json -profile iris -entry STAR_FASTQ`
+```mermaid
@@ -152,11 +157,13 @@ flowchart TB
+```
4. **Post-alignment QC**
- The fourth workflow runs QC on the resulting BAM files ([`SAMtools`](https://sourceforge.net/projects/samtools/files/samtools/) `flagstat` and various [`RSeQC`](http://rseqc.sourceforge.net/) modules), followed by [`MultiQC`](http://multiqc.info/) on those results
- To run this workflow alone use: `nextflow run main.nf -params-file params.json -profile iris -entry QC_BAM`
+```mermaid
@@ -221,6 +228,7 @@ flowchart TB
+```
## Environment