changed README bulleting

nextflow/README.md

@@ -6,17 +6,21 @@ To run the pipeline on Iris use: `nextflow run main.nf -params-file params.json
 
 It is recommended that each workflow in `main.nf` is run sequentially to allow for users to inspect intermediate QC results and select optimal parameters for downstream tasks:
 
-1. **Initial QC**: 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`
+1. **Initial QC**
+    - 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`
 
-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`
+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`
 
-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`
+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`
 
-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`
+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`
 
 ## Environment